@text
References: "THE KINEMAGE: A TOOL FOR SCIENTIFIC COMMUNICATION"
D.C. Richardson and J.S. Richardson (1992) Protein Science vol.1, pp. 3-9
  Also Trends in Biochem. Sci. (1994) 19: 135-8

                  Contents of file  DEMO5_3A.KIN:
    READER'S TUTORIAL (scroll this window to read text):
*{Kin 1}* CPase A active site motions (basic operations, pointIDs, animation)
*{Kin 2}* Carbonic anhydrase, Calphas & active site (zoom, center, stereo, views, find, kaleidoscope) 
*{Kin 3}* Streptavidin/biotin complex (ball&sticks, viewIDs)
*{Kin 4}* Geodesic dome, constructed from a cube (animated sequence, wordlist fontsize)
*{Kin 5}* Leucine zipper structure (slab, ztrans, options, write Postscript)
*{Kin 6}* Alpha helix (measures, drawline, construction, prune, dragline, and labels)

	[Demo5_3b.kin is an author's tutorial:  palette, format, on-screen editing, etc]

     A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display.  Operations on the displayed kinemage respond within a fraction of a second:  the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be animated.  The image can be recentered, zoomed, put in stereo, or the front and back clipped away;  distances, angles, and dihedrals can be measured.   The kinemage can be edited on-screen:  colors changed, multiple viewpoints saved, button names edited, lines pruned away or new ones drawn, etc.
     A kinemage is prepared and specified by an author, teacher, researcher, or anyone else in order to better communicate ideas that depend on 3-dimensional information.  The kinemages are distributed as plain text files of commented display lists and accompanying explanations.  They are viewed and explored in an openended way by the reader using the simple graphics program called MAGE, which runs on Macintosh, PC, or Unix computers.  A utility (called PREKIN) helps authors prepare the kinemages.  Kinemages were originally implemented under the auspices of the Innovative Technology Fund and the Protein Society, and the programming and maintenance are done by David C. Richardson. 

         *{KINEMAGE 1}* - Motion in the active site of Carboxypeptidase A

     To see kinemage 1, click on the graphics window showing behind (or click in a hypertext field delimited with * and {} symbols, like the one above).  This kinemage is an animation of the change between the conformations of carboxypeptidase A with and without bound substrate (Gly-Tyr); it includes the active site region of files 3CPA and 5CPA from the Brookhaven Protein Data Bank, or "PDB".  Many features of the kinemage display are self-explanatory, and can be worked out by exploring the possibilities yourself.  Detailed suggestions are given below, and should eventually be read to make sure you do not miss any of the major functionalities.  
     You can move forward either the present text window, the graphics window, or the caption window by clicking in them.  To avoid switching windows to read this tutorial, the first few pages of the Demo.kin file can be printed out using a word-processor.  The windows can be moved around by dragging their top bars, or resized by dragging in the lower right corner.  The text and caption windows are scrollable; the graphics image is rescaled when its window is resized.  If you fill the screen with it, you can bring the text back by choosing 'show text' under the 'Help' pulldown menu.  Later, you can select another kinemage by pulling down the 'Kinemage' menu and either releasing on 'Next' or choosing a different number (refer to the list at the beginning of the text window).
     Use the mouse to ROTATE the image: dragging across the top of the graphics window will rotate around Z (in the plane of the screen) and dragging anywhere else will rotate around the Y or the X axis or a combination.  Fairly slow movements work best.  Smoothness of rotation depends on the number of vectors in the display and the speed and size of the computer.  Depth-cuing is done primarily by color intensity; there is also a simple sort of hidden-line removal.  To reset the image to the start-up view, pull down the 'Views' menu and release on View1.  As many as 60 preset views may be included in a kinemage (the active ones are in black, with identifying labels); a checkmark shows the last one you picked.  As a reader, you can select a favorite view of your own, save it with 'Set Reader's View', and return to it later.  Try this out, and also try all the preset views.
     To ANIMATE the carboxypeptidase image, click repeatedly on the 'animate' button at the bottom of the button panel in the graphics window, at whatever speed suits you (alternatively, animate by pressing the 'a' character on the keyboard).  The big changes here are the appearance of the Gly-Tyr (red) and the motion of Tyr 248 (cyan), but many other parts of the structure move slightly.  Turn to a different orientation and try the animation again.  This particular animation has only two states, but the program can cycle through many states (in a multi-state animation, you can cycle between 2 successive states by alternating 'a' and 'A').  Also, some kinemages may have a second animation, called '2animate'.
     Now TURN ON and OFF the various display groups and sets, by clicking in the appropriate button box.  Try turning on both '3cpa-GY' and '5cpa-apo' at the same time, by clicking to get an X in both their button boxes.  Now turn off the 'Tyr 248' button;  this one is a "master" button which controls vectorlists inside more than one group, so the Tyr 248 vectors disappear for both conformations.  Turn off 'GlyTyr' as well, and animate again, to see motions of the other sidechains.  Then animate with just mainchain and Zn turned on, to see subtle shifts in the backbone.  The 'static' group contains things that don't change in the animation:  the yellow ball for the Zn, and a set of labels which are originally turned off.  Turn on and off the 'static' group and the display objects underneath it, to see how the button logic works: an individual object can be turned off either by its own button or by a subgroup or group above it in the heirarchy.
     Now try out some INFORMATIONal features.  Turn on the markers, pick an atom, and one of the two markers will move there.  A 'pointID' for that atom is printed at the bottom left of the graphics window; this would usually contain residue name and number and atom name, but can be freely specified in the kinemage file to be any character string.  Pick a second atom - the markers follow along, the pointID for the second atom is shown, and the distance between the two atoms is given.  (PointID and distance functions work fine without the markers on, once you are familiar with them.)  You can measure the distance between two atoms, or between the same atom in two different conformations.
     The 'Edit' and 'Display' pulldown menus, the file-writing features, and most of the 'Tools' menu are explained in later kinemages, either below or in file Demo3_1b.kin.  For each menu a 'Help' entry, such as 'Edit Help', gives brief explanations of the menu items.    'MAGE key shortcuts', under 'Help', tells you about keyboard shortcuts (like 's' for stereo).
     The 'Tools' menu contains some commonly-used features such as 'Find' and 'measures', but also features of more specialized use.  One that you may want to use is 'count', to find out the total number of vectors, dots, and labels turned on at present and the total number of coordinate triples in the file for the kinemage.  To return from a message box such as that one, just click in it.  'XYZ point' turns on a display of the currently picked x,y,z values at the top of the screen, and 'gnomon' turns on a green marker at the current center of rotation, with lines parallel to the x,y,z axes of the molecular coordinates.
	  
        *{KINEMAGE 2}* - carbonic anhydrase Calphas, active site, & mutants

     The second kinemage (pull down the kinemage menu and release on 'next') shows the C alpha BACKBONE of human carbonic anhydrase II, highlighting the active-site Zinc and its ligands (blue) and a loop (white) whose sidechain roles were studied using saturation mutagenesis, by Joseph Krebs and Carol Fierke at Duke University.  Rotate this figure to appreciate the big, curving beta sheet, the active site cavity, and the position of the loop.  
     On the "Tools" pulldown menu is a function called "FIND", which searches for character strings in the pointID's.  Suppose, for instance, you remember that Pro 30 and Pro 202 in carbonic anhydrase are cis prolines and you want to see where they are in the structure.  In the "Find" dialog box, ask it to look for the two strings "pro" and "202" ("find" is not sensitive to upper vs lower case).  It will put a marker on the point, or center it if you turn on pickcenter.  "Find" acts just like a mouse-click, so you can also use it to do things like add a label or draw a line, if those functions are enabled.  It will not find a point that is not currently displayed.  If you now "find" Pro 30 (as a "search from beginning"), the information line will tell you how far apart the two prolines are.  Turn the markers back off afterward.
     Try out the ZOOM function, starting from View1.  The sliders at the right side of the graphics window work just like ordinary scroll bars: you can move them slowly by clicking on the arrows, or make larger jumps by clicking in the open scrollbar, or you can drag the slider.  Try clicking once or twice in the lower part of the zoom scrollbar to enlarge the image by large steps, then on the upper arrow to reduce it slowly.  Then zoom in further; the maximum zoom factor is 10.
     With the zoom factor at about 3.0, choose "STEREO on" under the "Display" pulldown menu, or more conveniently type the 's' key on the keyboard.  MAGE stereo divides the graphics window in half vertically, with left and right images differing by a 6 degree rotation.  Such side-by-side stereo can be used with a suitable viewer*, or else just by relaxing your eyes to focus toward infinity, letting the two images drift together until they overlap, and then focussing on the fused image to see 3-D.  Each half-window is clipped at the centerline as well as the edges, so that the stereo can be used with large, or even zoomed, images.  However, you may often want either a smaller zoom factor than in mono, or a different window shape.  You can toggle between wall-eye and cross-eye stereo by typing 'c'; such a setting will last until you toggle it off or the program is quit and restarted.
     Things like zoom factor can also be preset by the author:  choose View4 and turn on "mutant sc".  Turn off the gold Calphas for a clear view of the loop, and turn them back on to judge what is buried.  Experiment with changing the thickness of the "zslab" to control how much depth is shown.  If the "zclip" button is turned off, the slab will only control the amount of depth-cuing.  Multiple mutants were isolated for each site in this loop, and the role of each amino acid was deduced from the pattern of effects observed for its mutants.  Five such categories are COLOR-KEYED and labelled.  Magenta residues are found important for folding of the molecule; they are mainly aromatics on the beta sheet.  Green residues affect the rate of CO2 hydration and yellow residues affect the pKa; both sets are close to the active site (except for Glu 205).  The red residue is important for thermostability;  it is a cis proline at the end of the loop (the same Pro 202 we "found" earlier).  Changes in the gray amino acids did not have significant effects.
     To concentrate on one mutant, or on the Zn and its tetrahedral N ligands, turn on the "PICKCENTER" button, click on an atom to center it, and then turn pickcenter back off.  (It is best to leave pickcenter off when you are not actively using it, since it is disorienting to have the image jump every time you pick a point.)  Then zoom in close, or try View3 for the Zn.  The Zn atom and the His ligand N atoms are marked with balls.  The ends of the brown bond vectors are UNPICKABLE POINTS (try it!), which avoids the likelihood of errors when measuring distances between atoms.
     In View4 with the mutants on, invoke the "KALEIDOSCOPE" function by pressing the 'k' key.  Then rotate slowly, optimizing the aesthetic effects.  The 'f' key (for "flatland") will let you scroll in the plane of the screen.  Toggle 'k' and 'f' again to return to normal rotation.

		*{KINEMAGE 3}* - Streptavidin/biotin complex

     Kin. 3 uses a BALL-AND-STICK representation to highlight the tight binding of biotin to a site tucked in one end of the beta-barrel of a streptavidin subunit.  Stereo really enhances View1.  Color-coded balls show the non-C atoms of the biotin and the protein atoms to which they H-bond.  [The balls are specified by a "balllist" in the kinemage file;  Mage draws a colored circle, with a small highlight, at each of the balllist points and shortens the adjacent vectors appropriately.]  Note that the views here have brief labels called 'VIEWID's, specified by the author when saving the view.  View2 and View3 are overviews from the side and the end of the beta barrel;  turn off the sidechains to see the position of the biotin, and turn off the biotin to see the crevice waiting to bind it.

		*{KINEMAGE 4}* - Geodesic dome construction

     Kin. 4 shows how to construct a Buckminster Fuller-type geodesic dome house starting from a cube, to emphasize the fact that kinemages need not be about molecules.  Each step is explained on the kinemage, so there is less dependence on this text window - just step through the whole sequence, using the 'animate' button or the 'a' key.
     First an icosahedron is constructed inside the cube; then pentagons are placed around its vertices and hexagons in its faces to form a soccer ball; then triangles are constructed on each of the soccer-ball faces to make a 180-triangle "Bucky ball".  (Note that not all edges are equal - measure some.)  The parts not needed for a dome house are deleted, then lower walls and a cupola are added, to produce the final dome house.  View4 shows the dome from the top.
     Because of the regular geometry, this kinemage is in PERSPECTIVE.  Try turning off perspective (under the "Display" pulldown); the effect is especially noticeable with the initial cube and the final dome.
     Each text explanation is specified by a 'WORDLIST' in the kinemage file, which acts like a multi-line label.  The FONTSIZE has also been changed.  Since the fonts do not come out the same on all monitors, it is usually better for the user to change fontsize when desired (the most important use is for visibility of the information line when using kinemages in an interactive lecture).  Try this yourself, using the 'Font sizes' dialog box under the 'Display' menu.

		*{KINEMAGE 5}* - Interface contact in a Leucine Zipper structure

     Kin. 5 shows the GCN4 leucine zipper dimer, viewed from the end.  The two chains have identical sequences and are oriented parallel, with the N-termini toward you.  Just the Calphas and the interface sidechains are shown.  Toggle off the 'zclip' button to see the full depth.  Supercoiling allows the two helices to stay the same distance apart along their entire length;  in contrast, most paired helices in globular proteins are straighter and diverge toward the ends.  Here, the interhelical contacts are made by sets of residues that look like wide rungs on a ladder (choose View2 to see a side view of the "ladder").  Every other rung contains a pair of orange leucines; alternate rungs contain pairs of gold valines (except for Met 2, and the hotpink Asn 16 near the middle).
     Choose View6 and turn off all but the Leu sidechains, to try out some of the 'Display' options and the WRITE POSTSCRIPT feature.  This view looks directly down one helix, with the other one coiling around it.  On the 'Display' menu, turn on 'Black&White' to get a black-on white image, and then turn off 'OneWidth' to get line-width depth-cuing.  [The third linewidth option, 'ThinLine', gives lines only one pixel wide;  it speeds up rotation on some PC's, and is good for superpositions of multiple structures.]  Now choose 'Write PostScript' on the 'File' menu:  Mage will write a PostScript file of the contents of the graphics window, with smooth lines.  The file can be read and sent to a printer by many utility programs, for instance the Adobe "Downloader" utility that comes with the Mac operating system, or with Freedom of Press for a non-postscript printer.  (If you have a color Postscript printer, then you can do this in color.)
     For a detailed tour of the Leu zipper helix-helix contacts, choose View3 and move the slider to the top of the ZTRANS scrollbar;  you should see just a little backbone and the sidechains of Met 2 at the beginning of each helix.  [Turn off Black&White and MultiWidth.] Now hold down the mouse near the bottom of the ztrans scrollbar (just above the arrow) to move the structure through the visible slab.  A little more than one "rung", or layer, will be in view at a time.  Notice how similar the geometry is for each rung of Leu sidechains (orange).  Val rungs (gold or hotpink) are also similar to one another, but different in detail from Leu rungs.  Hold at the top of the scrollbar to go back the other way.
     To see a grouping of contact residues that looks more like a zipper, choose View4, turn off "heptad sc" and turn on "zipper sc".  Although the major contacts are made side-to-side within one rung or layer, there are also two vertical zippers of sidechains (green in front, and pink in back) for which a stripe of leucines from one helix interdigitate with a stripe of valines from the other helix.  Look just at the green ones ("front zip") and then just at the pink ones ("rear zip").  View5 looks at the two zipper layers from the side.

		*{KINEMAGE 6}* - Alpha-helix:  measures and the "draw new" tools
 
     Kinemage 6 shows an asparagine as the "N-cap" (the first residue, half in and half out) of an alpha-helix (from thermolysin).  That Asn sidechain mimics the conformation and interactions of another residue's-worth of main chain at the beginning of the helix.  Click on the Od1 of Asn 280 (red atom, on gold sidechain), then click on the mainchain N just below it (blue atom) - the information line should say "n gln 283", with a distance of about 2.7 A.  Move around, try all views (especially the closeup), and/or use stereo to see the geometry.
    Choose "MEASURES" on the "Tools" menu.  Starting at the Asn, pick successively the Calpha, carbonyl C, N, etc. along the main chain, and watch the information line display.  In the dihedral angle position you will get 0.0 until you have picked 4 atoms, and then omega (close to 180), phi (near -60 for helix), psi (near -40 in helix), omega, phi, psi etc.  Turn the "measure" button off and on again, to restart it, and click on the Asn N, Calpha, Cbeta, and Cgamma to measure its Chi1 angle (near +60).
     On the "Edit" menu is "DRAW NEW", which enables a set of tools for adding lines or labels to the kinemage and lets you set some parameters for those tools.  First choose "Drawnew setup", edit the "shorten line" value in the dialog box to 0.7, and Accept;  then choose "Draw New".  There will now be 6 new buttons: "Labels", "drawline", "construct4", "construct5", "dragline", and "eraselast", with the drawline one checked.  Click on each of 2 atoms that form an H-bond, and a green line will be drawn between them, shortened for clarity.  [This is not quite the same geometry as the backbone H-bonds produced by PREKIN, which use calculated H positions, but it is a reasonable approximation.]
     Click "LABELS", and then pick some points in the image to show their pointID's as labels.  Try "eraselast" to get rid of the last one or two of them.  The new lines or labels you make (they can be intermixed) are under control of a new button called "new group".  They can be edited and written out along with other modifications (see Demo5_3b.kin), or alternatively just the newly-drawn things can be written out and pasted into the kinemage file.  If you write out a set of labels, you will probably want to edit what they say; for instance, putting just " G" at a glycine Calpha works well as a stand-in for a sidechain.
     Click "DRAGLINE", then pick a point in the image and slowly drag the mouse away from it.  When you let go, the line will stay there.  If you pick the end of the most recent dragline you can reposition it rather than starting a new one.  The ends of such dragged lines can be picked and used for other functions, for example recentering the image or making labels.
     Now try a more elaborate combination of measures and drawline, to draw an axis for the helix.  Choose "Drawnew setup" again, change the shorten-line value to -2.5 (so the axis will be lengthened out to the ends of the helix), click "draw line in 2 parts", and accept.  Then with the "drawline" button on, pick the 1st and 2nd Calpha atoms starting with Asn 280 (turn on the Cbetas if you find them helpful), then the 3rd and 4th; then pick the midpoint of each of your 2 new lines, to get a line whose midpoint is the center of the first 4 Calphas.  Repeat the equivalent process with 4 Calphas at the other end of the helix.  Now draw a line between the center-points at each helix end, to get a helix-axis line.  To neaten up the image, choose "PRUNE" on the Edit menu, turn on the new "prune" button that appears, and pick the ends of your construction lines so that the drawn helix axis is all that remains.  Look down the helix in View2 to see that the axis is really well placed.
     The "CONSTRUCT4" tool is an inverse version of "measures" - you pick 3 points, and it gives you a dialog box to specify the length, angle, and dihedral for adding a new line to a 4th point.  For example, you could construct a Cbeta at one of the Calphas that doesn't have one now.  The easiest way is to use "measures" to get the correct angle values from another example, so turn on "measures" and click successively on the N, C, Calpha, and Cbeta within the Asn residue.  [Go to the "Drawnew setup" dialog and set the shorten-line value back to zero.]  Turn measures off and construct4 on, and click on the N, C, and Calpha of the residue you want to provide with a Cbeta.  In the dialog box, choose "last measures" and OK, and the Calpha-Cbeta vector should appear; turn on the "Cbetas" button to see whether you got it right. 
     "CONSTRUCT5" is a set of more elaborate tools that let you, for instance, construct the perpendicular between two helix axes.  Turn on "new helix", choose View4, and then make sure the shorten-line value is set to zero in the Drawnew setup dialog.  Turn on the "Construct5" button, and pick the ends of your helix axis and then those of the new axis.  In the resulting dialog box, choose "Perpendicular between lines 1-2 & 3-4".  Pick ends of the new green line to find the distance between these two helices.
     When you leave a changed kinemage like this one without writing it out, the program puts up a reminder message.

FOOTNOTE
*  One example of a stereo viewer suitable for use with a computer display (with mirrors rather than lenses) is made by the German firm of GBH ??, and is available in the US from Aldrich or from ??, (Fla, phone).

REFERENCES
   Bernstein et al. (1977) J. Mol. Biol. 112: 535 - describes the original Protein Data Bank; files are available at http://www.pdb.bnl.gov
   Christianson and Lipscomb (1986) PNAS 83: 7568 - crystal structure of substrate binding to carboxypeptidase A at low temperature (PDB file 3CPA)
   Erickson, Jones, and Liljas (1988) Proteins 4: 274 - crystal structure of human carbonic anhydrase II (PDB file 1CA2)
   O'Shea et al. (1991) Science 254: 539 - crystal Structure of GCN4 Leucine Zipper (PDB file 2ZTA)
   Rees, Lewis, and Lipscomb (1983) J. Mol. Biol. 168: 387 - crystal structure of carboxypeptidase A (PDB file 5CPA)
   Weber et al. (1989) Science 243: 85 - crystal structure of streptavidin/biotin complex (PDB file 1STP)



@kinemage 1
@caption
Motion at the active site of carboxypeptidase A, in the presence and absence of substrate (click the 'animate' button).  The portions shown are the Zn (yellow), the GlyTyr peptide (red), and the mainchain (white) and most sidechains (cyan) for residues 144-5, 164, 240-253, 256, 268, and 270.  
(From Brookhaven PDB files 3CPA and 5CPA)
@onewidth
@viewid {front}
@zoom 1.31
@zslab 170
@center -1.484 33.317 -12.127
@matrix
0.731163 0.575927 0.365662 -0.570013 0.810239 -0.136374 -0.374813 -0.108721 0.920703
@2viewid {side}
@2zoom 1.25
@2zslab 180
@2center -3.410 33.453 -11.363
@2matrix
-0.100335 0.532741 -0.840309 -0.636759 0.614573 0.465659 0.764508 0.581795 0.277564
@3viewid {closer}
@3zoom 1.31
@3zslab 160
@3center -1.850 33.453 -13.048
@3matrix
0.731163 0.575927 0.365662 -0.570013 0.810239 -0.136374 -0.374813 -0.108721 0.920703
@master {main ch}
@master {Tyr 248}
@master {other sc}
@master {GlyTyr}
@group {3cpa - GY} dominant animate
@vectorlist {mc} color= white master= {main ch}
{asn 144 n}P 2.428 23.666 -9.773
{asn 144 ca}1.787 24.574 -10.737
{asn 144 c}2.730 25.677 -11.297
{asn 144 o}2.222 26.628 -11.944
{P}P 2.730 25.677 -11.297
{arg 145 n}4.000 25.483 -11.166
{arg 145 ca}5.002 26.260 -11.873
{arg 145 c}5.977 25.409 -12.655
{arg 145 o}6.994 25.949 -13.139
{tyr 240 n}P -13.143 37.506 -12.207
{tyr 240 ca}-12.665 36.697 -13.350
{tyr 240 c}-11.810 37.529 -14.279
{tyr 240 o}-11.956 38.787 -14.278
{P}P -11.810 37.529 -14.279
{gly 241 n}-10.960 36.862 -14.983
{gly 241 ca}-10.012 37.473 -15.886
{gly 241 c}-8.823 36.580 -16.158
{gly 241 o}-8.850 35.409 -15.775
{P}P -8.823 36.580 -16.158
{ser 242 n}-7.946 37.134 -17.002
{ser 242 ca}-6.626 36.383 -17.266
{ser 242 c}-5.845 36.353 -15.969
{ser 242 o}-5.964 37.285 -15.177
{P}P -5.845 36.353 -15.969
{ile 243 n}-4.985 35.353 -15.787
{ile 243 ca}-4.157 35.284 -14.574
{ile 243 c}-3.339 36.545 -14.303
{ile 243 o}-3.320 37.063 -13.173
{P}P -3.339 36.545 -14.303
{ile 244 n}-2.573 36.929 -15.300
{ile 244 ca}-1.565 38.006 -15.188
{ile 244 c}-2.269 39.278 -14.853
{ile 244 o}-1.729 40.077 -14.115
{P}P -2.269 39.278 -14.853
{thr 245 n}-3.444 39.553 -15.416
{thr 245 ca}-4.222 40.820 -15.134
{thr 245 c}-4.842 40.777 -13.765
{thr 245 o}-4.980 41.848 -13.123
{P}P -4.842 40.777 -13.765
{thr 246 n}-5.274 39.589 -13.280
{thr 246 ca}-6.126 39.594 -12.106
{thr 246 c}-5.280 39.427 -11.035
{thr 246 o}-5.668 39.916 -9.965
{P}P -5.280 39.427 -11.035
{ile 247 n}-4.277 38.560 -11.220
{ile 247 ca}-3.516 38.099 -10.013
{ile 247 c}-2.132 38.708 -10.160
{ile 247 o}-1.915 39.836 -9.710
{P}P -2.132 38.708 -10.160
{tyr 248 n}-1.292 37.979 -10.848
{tyr 248 ca}0.148 38.297 -10.940
{tyr 248 c}0.752 37.409 -11.987
{tyr 248 o}0.752 36.423 -12.388
{P}P 0.752 37.409 -11.987
{gln 249 n}1.908 37.852 -12.490
{gln 249 ca}2.722 37.019 -13.362
{gln 249 c}2.979 35.695 -12.678
{gln 249 o}3.442 35.637 -11.537
{P}P 2.979 35.695 -12.678
{ala 250 n}2.786 34.628 -13.478
{ala 250 ca}3.046 33.478 -12.902
{ala 250 c}3.403 32.610 -14.130
{ala 250 o}2.579 32.420 -15.014
{P}P 3.403 32.610 -14.130
{ser 251 n}4.512 31.950 -14.026
{ser 251 ca}5.076 31.113 -15.110
{ser 251 c}4.928 29.625 -14.683
{ser 251 o}4.698 29.333 -13.505
{P}P 4.928 29.625 -14.683
{gly 252 n}4.779 28.819 -15.736
{gly 252 ca}4.777 27.326 -15.553
{gly 252 c}3.400 26.785 -15.073
{gly 252 o}3.390 25.638 -14.503
{P}P 3.400 26.785 -15.073
{gly 253 n}2.325 27.445 -15.420
{gly 253 ca}1.052 26.987 -14.943
{gly 253 c}0.376 26.028 -15.952
{gly 253 o}0.700 25.985 -17.114
{asp 256 n}P -1.897 27.545 -18.933
{asp 256 ca}-1.078 28.182 -20.019
{asp 256 c}-0.637 27.080 -20.960
{asp 256 o}-0.814 27.020 -22.184
{thr 268 n}P -8.800 28.065 -14.580
{thr 268 ca}-8.472 27.683 -13.200
{thr 268 c}-9.465 28.275 -12.216
{thr 268 o}-9.745 29.515 -12.353
{glu 270 n}P -10.147 29.289 -8.270
{glu 270 ca}-9.599 29.432 -6.885
{glu 270 c}-10.846 29.535 -6.013
{glu 270 o}-11.580 30.523 -6.100
@vectorlist {sc - Y 248} color= cyan master= {Tyr 248}
P 0.148 38.297 -10.940
{tyr 248 cb}0.860 38.127 -9.528
{tyr 248 cg}0.516 36.822 -8.850
{tyr 248 cd1}-0.782 36.648 -8.279
{tyr 248 ce1}-1.159 35.425 -7.638
{tyr 248 cz}-0.217 34.367 -7.640
{tyr 248 ce2}1.047 34.527 -8.175
{tyr 248 cd2}1.385 35.735 -8.830
{tyr 248 cg}0.516 36.822 -8.850
P -0.217 34.367 -7.640
{tyr 248 oh}-0.520 33.159 -7.009
@vectorlist {sc - other} color= cyan master= {other sc}
P 1.787 24.574 -10.737
{asn 144 cb}0.513 25.160 -10.107
{asn 144 cg}-0.452 25.550 -11.283
{asn 144 od1}-0.386 24.919 -12.276
P -0.452 25.550 -11.283
{asn 144 nd2}-1.100 26.673 -11.140
{Arg 145}P 5.002 26.260 -11.873
{arg 145 cb}5.743 27.129 -10.808
{arg 145 cg}5.176 28.546 -10.852
{arg 145 cd}5.256 29.159 -9.470
{arg 145 ne}4.362 30.316 -9.476
{arg 145 cz}3.037 30.108 -9.407
{arg 145 nh1}2.400 29.194 -10.155
P 3.037 30.108 -9.407
{arg 145 nh2}2.379 30.869 -8.554
P -4.157 35.284 -14.574
{ile 243 cb}-3.205 34.014 -14.734
{ile 243 cg1}-4.102 32.746 -14.997
{ile 243 cd1}-3.248 31.549 -15.629
P -3.205 34.014 -14.734
{ile 243 cg2}-2.136 33.863 -13.652
P -3.520 38.000 -10.000
{ile 247 cb}-3.485 36.546 -9.920
{ile 247 cg1}-4.888 35.950 -10.039
{ile 247 cd1}-4.786 34.488 -10.650
P -3.485 36.546 -9.920
{ile 247 cg2}-2.852 36.127 -8.540
P 3.046 33.478 -12.902
{ala 250 cb}1.822 32.942 -12.217
{P}P -1.078 28.182 -20.019
{asp 256 cb}-1.078 29.023 -19.424
{asp 256 cg}-0.433 30.269 -18.648
{asp 256 od1}-1.664 30.496 -18.566
P -0.433 30.269 -18.648
{asp 256 od2}0.409 30.989 -18.093
P -8.472 27.683 -13.200
{thr 268 cb}-7.070 28.198 -12.658
{thr 268 og1}-6.150 28.262 -13.758
P -7.070 28.198 -12.658
{thr 268 cg2}-6.635 27.372 -11.437
{Glu 270}P -9.599 29.432 -6.885
{glu 270 cb}-8.773 30.719 -6.848
{glu 270 cd}-6.533 31.679 -7.483
{glu 270 oe1}-5.474 31.715 -8.076
P -6.533 31.679 -7.483
{glu 270 oe2}-6.577 32.215 -6.353
@vectorlist {GlyTyr} color= red master= {GlyTyr}
{gly 1 n}P -3.506 29.042 -4.526
{gly 1 ca}-3.806 29.803 -5.749
{gly 1 c}-2.850 29.382 -6.862
{gly 1 o}-1.984 28.516 -6.662
P -2.850 29.382 -6.862
{tyr 2 n}-3.020 29.999 -8.017
{tyr 2 ca}-2.133 29.729 -9.153
{tyr 2 c}-0.755 30.002 -8.540
{tyr 2 o}0.084 29.095 -8.427
P -0.755 30.002 -8.540
{tyr 2 oxt}-0.540 31.247 -8.157
P -2.133 29.729 -9.153
{tyr 2 cb}-2.536 30.638 -10.330
{tyr 2 cg}-2.016 30.130 -11.682
{tyr 2 cd1}-0.712 30.494 -12.060
{tyr 2 ce1}-0.212 30.028 -13.345
{tyr 2 cz}-1.033 29.327 -14.160
{tyr 2 ce2}-2.333 28.952 -13.800
{tyr 2 cd2}-2.812 29.412 -12.538
{tyr 2 cg}-2.016 30.130 -11.682
P -1.033 29.327 -14.160
{tyr 2 oh}-0.570 28.906 -15.388
@group {5cpa - apo} dominant animate
@vectorlist {mc} color= white master= {main ch}
P 2.428 23.666 -9.773
{asn 144 ca}1.787 24.574 -10.737
{asn 144 c}2.730 25.677 -11.297
{asn 144 o}2.222 26.628 -11.944
P 2.730 25.677 -11.297
{arg 145 n}3.975 25.500 -11.153
{arg 145 ca}4.973 26.306 -11.833
{arg 145 c}5.940 25.430 -12.610
{arg 145 o}6.947 25.967 -13.119
P -13.190 37.484 -12.237
{tyr 240 ca}-12.677 36.653 -13.354
{tyr 240 c}-11.843 37.526 -14.280
{tyr 240 o}-11.970 38.794 -14.293
P -11.843 37.526 -14.280
{gly 241 n}-10.966 36.859 -14.987
{gly 241 ca}-9.952 37.498 -15.783
{gly 241 c}-8.803 36.562 -16.115
{gly 241 o}-8.835 35.372 -15.807
P -8.803 36.562 -16.115
{ser 242 n}-7.907 37.120 -16.923
{ser 242 ca}-6.624 36.400 -17.268
{ser 242 c}-5.854 36.379 -15.938
{ser 242 o}-5.987 37.288 -15.113
P -5.854 36.379 -15.938
{ile 243 n}-5.034 35.370 -15.809
{ile 243 ca}-4.176 35.270 -14.590
{ile 243 c}-3.367 36.546 -14.348
{ile 243 o}-3.309 37.006 -13.202
P -3.367 36.546 -14.348
{ile 244 n}-2.594 36.889 -15.346
{ile 244 ca}-1.596 37.990 -15.224
{ile 244 c}-2.313 39.268 -14.889
{ile 244 o}-1.718 39.988 -14.127
P -2.313 39.268 -14.889
{thr 245 n}-3.496 39.588 -15.400
{thr 245 ca}-4.199 40.936 -15.155
{thr 245 c}-4.848 40.884 -13.812
{thr 245 o}-5.057 41.887 -13.118
P -4.848 40.884 -13.812
{thr 246 n}-5.257 39.638 -13.340
{thr 246 ca}-6.112 39.594 -12.165
{thr 246 c}-5.316 39.444 -10.860
{thr 246 o}-5.653 40.042 -9.827
P -5.316 39.444 -10.860
{ile 247 n}-4.320 38.572 -10.974
{ile 247 ca}-3.334 38.436 -9.848
{ile 247 c}-2.095 39.173 -10.320
{ile 247 o}-1.960 40.377 -10.154
P -2.095 39.173 -10.320
{tyr 248 n}-1.260 38.407 -11.003
{tyr 248 ca}0.182 38.759 -11.145
{tyr 248 c}0.762 37.707 -12.034
{tyr 248 o}0.126 36.624 -12.290
P 0.762 37.707 -12.034
{gln 249 n}1.816 38.142 -12.707
{gln 249 ca}2.682 37.250 -13.486
{gln 249 c}2.938 35.974 -12.704
{gln 249 o}3.373 35.980 -11.578
P 2.938 35.974 -12.704
{ala 250 n}2.728 34.858 -13.390
{ala 250 ca}2.973 33.496 -12.868
{ala 250 c}3.383 32.637 -14.106
{ala 250 o}2.608 32.464 -15.038
P 3.383 32.637 -14.106
{ser 251 n}4.459 31.907 -13.965
{ser 251 ca}5.022 31.078 -15.036
{ser 251 c}4.877 29.584 -14.690
{ser 251 o}4.612 29.263 -13.536
P 4.877 29.584 -14.690
{gly 252 n}4.846 28.780 -15.740
{gly 252 ca}4.782 27.298 -15.656
{gly 252 c}3.409 26.767 -15.168
{gly 252 o}3.397 25.658 -14.524
P 3.409 26.767 -15.168
{gly 253 n}2.340 27.502 -15.438
{gly 253 ca}1.064 27.098 -14.993
{gly 253 c}0.393 26.086 -15.968
{gly 253 o}0.694 26.054 -17.130
P -1.883 27.490 -18.869
{asp 256 ca}-1.123 28.159 -20.000
{asp 256 c}-0.694 27.060 -20.967
{asp 256 o}-0.780 27.039 -22.194
P -8.832 28.062 -14.572
{thr 268 ca}-8.469 27.707 -13.209
{thr 268 c}-9.480 28.302 -12.235
{thr 268 o}-9.736 29.544 -12.410
P -10.073 29.355 -8.243
{glu 270 ca}-9.585 29.457 -6.853
{glu 270 c}-10.827 29.539 -6.006
{glu 270 o}-11.573 30.500 -6.154
@vectorlist {sc - Y 248} color= cyan master= {Tyr 248}
P 0.182 38.759 -11.145
{tyr 248 cb}0.892 38.892 -9.743
{tyr 248 cg}2.184 39.699 -9.838
{tyr 248 cd1}3.480 39.082 -9.773
{tyr 248 ce1}4.676 39.868 -9.860
{tyr 248 cz}4.545 41.250 -10.100
{tyr 248 ce2}3.295 41.870 -10.102
{tyr 248 cd2}2.135 41.076 -10.043
{tyr 248 cg}2.184 39.699 -9.838
P 4.545 41.250 -10.100
{tyr 248 oh}5.647 42.116 -10.164
@vectorlist {sc - other} color= cyan master= {other sc}
P 1.787 24.574 -10.737
{asn 144 cb}0.490 25.188 -10.119
{asn 144 cg}-0.490 25.549 -11.272
{asn 144 od1}-0.443 24.952 -12.266
P -0.490 25.549 -11.272
{asn 144 nd2}-1.137 26.698 -11.143
P 4.973 26.306 -11.833
{arg 145 cb}5.736 27.136 -10.752
{arg 145 cg}4.818 28.303 -10.327
{arg 145 cd}5.286 28.930 -9.012
{arg 145 ne}4.915 30.375 -9.175
{arg 145 cz}3.724 30.692 -8.654
{arg 145 nh1}3.025 29.704 -8.076
P 3.720 30.690 -8.650
{arg 145 nh2}3.300 31.940 -8.770
P -4.176 35.270 -14.590
{ile 243 cb}-3.237 34.014 -14.764
{ile 243 cg1}-4.098 32.719 -14.968
{ile 243 cd1}-3.149 31.528 -15.485
P -3.237 34.014 -14.764
{ile 243 cg2}-2.172 33.868 -13.636
P -3.334 38.436 -9.848
{ile 247 cb}-3.123 36.919 -9.538
{ile 247 cg1}-4.468 36.229 -9.241
{ile 247 cd1}-4.315 34.669 -9.293
P -3.123 36.919 -9.538
{ile 247 cg2}-2.159 36.778 -8.316
P 2.973 33.496 -12.868
{ala 251 cb}1.788 32.873 -12.207
P -1.123 28.159 -20.000
{asp 256 cb}-0.023 29.036 -19.523
{asp 256 cg}-0.415 30.256 -18.717
{asp 256 od1}-1.630 30.457 -18.547
P -0.415 30.256 -18.717
{asp 256 od2}0.423 30.932 -18.132
P -8.469 27.707 -13.209
{thr 268 cb}-7.074 28.247 -12.710
{thr 268 og1}-6.099 28.157 -13.752
P -7.074 28.247 -12.710
{thr 268 cg2}-6.692 27.437 -11.427
P -9.585 29.457 -6.853
{glu 270 cb}-8.714 30.693 -6.798
{glu 270 cg}-7.407 30.687 -7.563
{glu 270 cd}-6.329 29.955 -6.732
{glu 270 oe1}-5.236 29.628 -7.154
P -6.329 29.955 -6.732
{glu 27 oe2}-6.678 29.598 -5.620
@group {static}
@labellist {labels} color= pink off
{Gly-Tyr}-2.133 29.729 -9.153
{Tyr 248}0.148 38.297 -10.940
{Glu 270}-9.599 29.432 -6.885
{Arg 145}5.002 26.260 -11.873
{Zn}-3.285 26.315 -5.571
@subgroup {metal}
@balllist {Zn} color= gray radius= 0.4
{Zn}-3.285 26.315 -5.57

@kinemage 2
@caption
Polypeptide backbone of human carbonic anhydrase II.  The active site is flanked at the left by a large, curved beta sheet and at right by a set of loops.  Highlighted in white is the active site loop (residues 191-211) whose mutants were studied.  The Zinc is marked in cyan and its 3 His ligands in skyblue.  Zoom in and recenter (see text for instructions) to see detail of the Zn ligands or of sidechains on the mutagenized loop (turn on "mutant sc").  (From PDB file 1CA2)
@onewidth
@viewid {overview}
@zoom 1.18
@zslab 160
@center -7.657 -1.437 16.207
@matrix
0.940290 0.185490 0.285390 -0.102170 -0.645960 0.756500 0.324680 -0.740490 -0.588440
@2viewid {active site}
@2zoom 2.19
@2zslab 110
@2center -5.779 -0.497 16.985
@2matrix
0.950141 -0.282975 -0.130988 0.011017 -0.389349 0.921024 -0.311628 -0.876545 -0.366819
@3viewid {Zn closeup}
@3zoom 4.52
@3zslab 140
@3center -7.314 -2.455 15.216
@3matrix
0.857796 -0.490305 -0.154228 0.513085 0.834627 0.200350 0.030491 -0.250991 0.967509
@4viewid {mutated loop}
@4zoom 1.42
@4zslab 170
@4center -9.025 -1.368 19.263
@4matrix
0.927164 -0.064291 0.369102 -0.374451 -0.191844 0.907184 0.012487 -0.979318 -0.201943
@group {1CA2 ca}
@vectorlist {Calpha} color= gold
{his 4}P 9.940 0.115 8.847
{trp 5}7.704 -1.477 11.480
{gly 6}5.440 -4.296 10.398
{tyr 7}4.456 -7.735 11.642
{gly 8}7.323 -9.910 10.382
{lys 9}10.070 -11.562 12.410
{his 10}12.454 -8.733 11.657
{asn 11}10.160 -5.720 12.170
{gly 12}7.465 -7.200 14.370
{pro 13}5.920 -6.095 17.650
{glu 14}8.927 -7.335 19.610
{his 15}10.993 -4.700 17.810
{trp 16}8.728 -1.632 17.960
{his 17}10.173 -0.340 21.236
{lys 18}13.457 0.670 19.495
{asp 19}11.676 3.264 17.337
{phe 20}8.756 3.866 19.815
{pro 21}9.932 3.498 23.432
{ile 22}6.364 4.120 24.640
{ala 23}5.896 0.498 23.520
{lys 24}7.015 -0.380 27.053
{gly 25}4.712 2.168 28.700
{glu 26}2.282 1.910 31.600
{arg 27}-0.960 1.888 29.568
{gln 28}-0.216 -0.194 26.480
{ser 29}-2.840 -2.135 24.580
{pro 30}-4.092 -4.763 23.856
{val 31}-4.555 -6.730 27.100
{asp 32}-6.100 -10.030 28.200
{ile 33}-9.530 -9.476 29.730
{asp 34}-9.640 -11.636 32.900
{thr 35}-13.364 -11.992 33.412
{his 36}-13.315 -12.970 37.080
{thr 37}-11.164 -9.998 37.960
{ala 38}-13.025 -7.336 35.925
{lys 39}-15.124 -5.165 38.262
{tyr 40}-18.847 -4.523 37.663
{asp 41}-19.250 -0.722 37.818
{pro 42}-22.865 0.347 38.300
{ser 43}-22.057 4.018 37.758
{leu 44}-21.200 3.205 34.145
{lys 45}-23.850 4.400 31.670
{pro 46}-25.077 2.602 28.575
{leu 47}-23.178 3.285 25.360
{ser 48}-24.790 5.683 22.965
{val 49}-24.030 4.770 19.343
{ser 50}-25.617 7.230 16.863
{tyr 51}-24.575 6.138 13.382
{asp 52}-27.730 6.814 11.370
{gln 53}-26.067 9.750 9.616
{ala 54}-22.670 8.209 8.970
{thr 55}-20.965 9.145 5.712
{ser 56}-18.324 6.660 4.518
{leu 57}-16.016 8.006 1.780
{arg 58}-13.356 5.424 0.978
{ile 59}-11.402 2.288 1.723
{leu 60}-7.616 2.180 1.596
{asn 61}-4.953 -0.491 2.000
{asn 62}-2.328 1.297 4.183
{gly 63}0.190 -1.480 4.193
{his 64}-0.863 -2.938 7.608
{ala 65}-4.632 -3.173 7.190
{phe 66}-7.480 -1.645 5.223
{asn 67}-9.365 1.410 6.708
{val 68}-12.910 2.443 5.806
{glu 69}-12.788 6.273 6.266
{phe 70}-15.676 8.530 7.186
{asp 71}-16.388 12.250 6.934
{asp 72}-15.730 13.583 10.480
{ser 73}-16.132 17.293 9.658
{gln 74}-19.488 17.303 11.477
{asp 75}-21.090 15.284 14.270
{lys 76}-22.717 12.836 11.796
{ala 77}-21.590 9.518 13.440
{val 78}-20.864 9.680 17.140
{leu 79}-20.326 7.686 20.300
{lys 80}-21.225 9.020 23.760
{gly 81}-22.144 7.610 27.160
{gly 82}-20.500 4.480 28.637
{pro 83}-17.403 5.758 30.472
{leu 84}-16.977 8.692 28.090
{asp 85}-17.368 12.380 28.617
{gly 86}-18.534 14.340 25.576
{thr 87}-18.788 13.484 21.947
{tyr 88}-16.463 11.285 19.953
{arg 89}-16.730 11.357 16.153
{leu 90}-16.172 8.263 14.020
{ile 91}-13.130 8.702 11.767
{gln 92}-12.400 5.152 10.463
{phe 93}-12.780 1.420 11.175
{his 94}-10.286 -1.397 10.390
{phe 95}-9.680 -5.020 11.473
{his 96}-6.846 -7.256 12.722
{trp 97}-6.970 -10.914 11.584
{gly 98}-4.982 -14.110 11.650
{ser 99}-3.534 -16.633 9.216
{leu 100}-5.737 -19.236 10.957
{asp 101}-9.183 -19.042 12.592
{gly 102}-7.556 -19.796 15.970
{gln 103}-5.945 -16.352 16.180
{gly 104}-6.314 -12.780 14.892
{ser 105}-7.863 -10.644 17.710
{glu 106}-5.643 -8.297 19.746
{his 107}-7.686 -8.360 22.937
{thr 108}-8.274 -11.820 24.410
{val 109}-10.982 -12.954 26.868
{asp 110}-9.737 -15.300 29.610
{lys 111}-6.892 -15.870 27.160
{lys 112}-9.254 -16.920 24.350
{lys 113}-8.247 -15.480 20.957
{tyr 114}-10.903 -14.736 18.270
{ala 115}-10.504 -14.930 14.462
{ala 116}-10.485 -11.164 14.065
{glu 117}-11.050 -7.928 15.892
{leu 118}-12.860 -4.816 14.503
{his 119}-11.835 -1.368 15.750
{leu 120}-14.180 1.640 15.310
{val 121}-11.953 4.732 15.958
{his 122}-13.417 7.890 17.406
{trp 123}-11.868 11.214 18.478
{asn 124}-12.970 13.670 21.195
{thr 125}-14.463 16.740 19.405
{lys 127}-13.315 19.110 22.208
{tyr 128}-9.824 18.764 20.680
{gly 129}-10.917 19.905 17.238
{asp 130}-9.003 17.478 15.000
{phe 131}-7.785 13.882 15.176
{gly 132}-4.155 15.057 15.255
{lys 133}-4.745 17.085 18.457
{ala 134}-6.832 14.316 20.052
{val 135}-4.005 11.711 19.842
{gln 136}-1.939 13.960 22.143
{gln 137}-4.450 13.786 25.004
{pro 138}-5.196 11.150 27.657
{asp 139}-8.935 11.124 26.788
{gly 140}-8.380 11.870 23.090
{leu 141}-9.760 8.728 21.455
{ala 142}-12.398 6.123 22.064
{val 143}-12.058 2.717 20.304
{leu 144}-15.016 0.327 20.103
{gly 145}-13.583 -3.208 19.905
{ile 146}-15.698 -6.038 18.426
{phe 147}-14.590 -9.676 18.226
{leu 148}-15.337 -11.820 15.123
{lys 149}-15.854 -15.612 15.422
{val 150}-16.256 -17.903 12.328
{gly 151}-19.776 -19.220 11.935
{ser 152}-22.590 -17.798 9.808
{ala 153}-22.082 -15.026 7.310
{lys 154}-22.495 -11.368 8.410
{pro 155}-24.637 -9.723 5.755
{gly 156}-23.518 -6.218 6.664
{leu 157}-19.894 -7.160 6.007
{gln 158}-20.163 -8.390 2.395
{lys 159}-19.914 -4.955 0.727
{val 160}-16.523 -4.578 2.414
{val 161}-15.570 -8.148 1.398
{asp 162}-16.430 -7.450 -2.259
{val 163}-14.220 -4.344 -2.702
{leu 164}-10.940 -5.853 -1.283
{asp 165}-10.078 -6.988 -4.790
{ser 166}-9.583 -3.363 -5.707
{ile 167}-7.212 -2.334 -2.912
{lys 168}-5.100 -5.480 -2.958
{thr 169}-1.683 -3.815 -2.440
{lys 170}-0.298 -1.030 -0.210
{gly 171}-1.300 2.505 -1.208
{lys 172}-4.435 1.557 -3.210
{ser 173}-7.774 3.226 -2.355
{ala 174}-11.340 2.958 -3.730
{asp 175}-14.490 5.053 -3.405
{phe 176}-16.565 3.506 -0.627
{thr 177}-19.750 5.536 -0.128
{asn 178}-23.013 4.810 1.593
{phe 179}-21.640 1.972 3.830
{asp 180}-23.670 1.823 7.130
{pro 181}-21.560 0.658 10.106
{arg 182}-24.710 -0.297 11.935
{gly 183}-24.613 -3.648 10.114
{leu 184}-21.416 -4.532 12.065
{leu 185}-22.797 -4.245 15.605
{pro 186}-23.807 -7.233 17.745
{glu 187}-27.254 -7.197 19.375
{ser 188}-25.950 -6.424 22.860
{leu 189}-23.935 -3.342 23.830
{asp 190}-22.580 -4.870 27.094
{tyr 191}-18.876 -3.965 27.388
{val 211}P -14.588 -3.820 24.140
{leu 212}-17.988 -5.445 23.440
{lys 213}-18.734 -8.738 25.260
{glu 214}-20.698 -10.200 22.304
{pro 215}-18.810 -11.295 19.190
{ile 216}-20.277 -10.997 15.720
{ser 217}-19.860 -14.134 13.575
{val 218}-18.640 -14.110 9.964
{ser 219}-18.230 -16.965 7.466
{ser 220}-15.070 -18.880 6.758
{glu 221}-15.222 -17.493 3.170
{gln 222}-15.604 -13.854 4.375
{val 223}-12.434 -14.147 6.546
{leu 224}-10.695 -15.905 3.660
{lys 225}-10.863 -12.760 1.494
{phe 226}-9.216 -10.617 4.202
{arg 227}-6.268 -13.020 3.954
{lys 228}-5.840 -12.375 0.212
{leu 229}-4.610 -8.800 0.833
{asn 230}-0.942 -7.810 0.588
{phe 231}1.352 -5.855 2.907
{asn 232}3.512 -5.054 -0.120
{gly 233}2.904 -2.443 -2.762
{glu 234}2.150 -3.330 -6.370
{gly 235}5.038 -4.840 -8.336
{glu 236}6.783 -6.000 -5.153
{pro 237}7.200 -9.565 -3.923
{glu 238}3.883 -10.680 -2.498
{glu 239}3.470 -10.957 1.244
{leu 240}0.008 -11.946 2.460
{met 241}-1.560 -9.467 4.910
{val 242}-2.092 -11.980 7.768
{asp 243}-1.458 -11.850 11.505
{asn 244}-1.473 -8.010 11.706
{trp 245}-2.166 -8.252 15.450
{arg 246}-0.119 -7.138 18.454
{pro 247}-0.032 -9.543 21.403
{ala 248}-1.383 -8.777 24.892
{gln 249}0.533 -6.255 26.984
{pro 250}0.938 -6.150 30.775
{leu 251}-2.104 -4.663 32.585
{lys 252}0.165 -3.096 35.206
{asn 253}-2.437 -2.359 37.892
{arg 254}-4.983 -0.762 35.548
{gln 255}-8.450 -1.930 36.403
{ile 256}-10.798 -3.364 33.803
{lys 257}-14.422 -2.370 34.523
{ala 258}-17.533 -4.130 33.266
{ser 259}-20.900 -2.633 32.432
{phe 260}-22.622 -5.940 33.344
@vectorlist {mut loop} color= white
{tyr 191}P -18.876 -3.965 27.388
{trp 192}-15.627 -3.936 29.294
{thr 193}-13.610 -0.703 29.466
{tyr 194}-10.064 0.306 30.446
{pro 195}-7.573 3.093 29.675
{gly 196 n}-6.172 2.720 27.752
{gly 196 ca}-5.056 2.058 26.993
{gly 196 c}-4.480 2.915 25.898
{ser 197}-3.320 3.008 23.736
{leu 198}-3.198 2.705 19.945
{thr 199}-2.114 -0.862 19.014
{thr 200}0.158 0.190 16.144
{pro 201 n}2.170 1.574 16.006
{pro 201 ca}2.947 2.797 16.200
{pro 202 n}2.084 5.063 16.255
{pro 202 ca}2.920 5.474 17.390
{leu 203}1.342 3.549 20.304
{leu 204}0.138 6.770 21.897
{glu 205}-1.625 6.314 25.240
{cys 206}-4.730 8.307 24.355
{val 207}-7.361 5.628 24.200
{thr 208}-10.396 4.762 26.204
{trp 209}-11.105 1.166 25.123
{ile 210}-14.682 -0.095 24.912
{val 211}-14.588 -3.820 24.140
@subgroup {His lig} dominant
@balllist {His N} color= blue radius= 0.150
{his 94 ne2}-7.528 -0.707 13.770
{his 96 ne2}-6.000 -3.468 14.754
{his 119 nd1}-8.127 -2.175 16.625
@vectorlist {sc His} color= sky
{his 94 ca}P -10.286 -1.397 10.390
{his 94 cb}-8.804 -0.880 10.320
{his 94 cg}-8.360 -0.482 11.734
{his 94 nd1}-8.477 0.648 12.357
{his 94 ce1}-7.986 0.567 13.610
{his 94 ne2}-7.528 -0.707 13.770
{his 94 cd2}-7.755 -1.329 12.614
{his 94 cg}-8.360 -0.482 11.734
{his 96 ca}P -6.846 -7.256 12.722
{his 96 cb}-6.188 -7.093 14.130
{his 96 cg}-5.970 -5.603 14.353
{his 96 nd1}-4.786 -5.048 14.100
{his 96 ce1}-4.844 -3.734 14.356
{his 96 ne2}-6.000 -3.468 14.754
{his 96 cd2}-6.823 -4.620 14.782
{his 96 cg}-5.970 -5.603 14.353
{his 119 ca}P -11.835 -1.368 15.750
{his 119 cb}-10.343 -1.014 15.977
{his 119 cg}-9.510 -1.987 16.740
{his 119 nd1}-8.127 -2.175 16.625
{his 119 ce1}-7.768 -3.117 17.430
{his 119 ne2}-8.867 -3.564 18.160
{his 119 cd2}-9.934 -2.873 17.700
{his 119 cg}-9.510 -1.987 16.740
@subgroup {Zn} dominant
@balllist {Zn} color= cyan radius= 0.400
{Zn}-6.788 -1.620 15.380
@subgroup {N-Zn} dominant
@vectorlist {Zn-N bonds} color= brown
{his 119 nd1}P U -7.777 -2.030 16.300
{Zn}U -7.138 -1.765 15.706
{"}P U -6.974 -1.390 14.976
{his 94 ne2}U -7.342 -0.936 14.174
{his 96 ne2}P U -6.187 -3.029 14.903
{Zn}U -6.600 -2.059 15.231
@group {mutant sc} off
@vectorlist {folding} color= magenta
{tyr 191 ca}P -18.876 -3.965 27.388
{tyr 191 cb}-18.682 -2.530 26.750
{tyr 191 cg}-19.143 -1.364 27.640
{tyr 191 cd1}-18.243 -0.712 28.475
{tyr 191 ce1}-18.593 0.377 29.245
{tyr 191 cz}-19.897 0.848 29.182
{tyr 191 ce2}-20.857 0.209 28.370
{tyr 191 cd2}-20.437 -0.882 27.566
{tyr 191 cg}-19.143 -1.364 27.640
{tyr 191 cz}P -19.897 0.848 29.182
{tyr 191 oh}-20.360 1.872 29.947
{trp 192 ca}P -15.627 -3.936 29.294
{trp 192 cb}-14.570 -5.083 29.257
{trp 192 cg}-15.074 -6.395 29.700
{trp 192 cd1}-15.352 -6.862 30.970
{trp 192 ne1}-15.727 -8.180 30.935
{trp 192 ce2}-15.777 -8.590 29.610
{trp 192 cz3}P -15.556 -8.880 26.860
{trp 192 ce3}-15.200 -7.674 27.443
{trp 192 cd2}-15.336 -7.522 28.820
{trp 192 ce2}P -15.777 -8.590 29.610
{trp 192 cz2}-16.100 -9.830 29.054
{trp 192 ch2}-15.990 -9.942 27.678
{trp 192 cz3}-15.556 -8.880 26.860
{trp 192 cg}P -15.074 -6.395 29.700
{trp 192 cd2}-15.336 -7.522 28.820
{trp 192 ce2}-15.777 -8.590 29.610
{tyr 194 ca}P -10.064 0.306 30.446
{tyr 194 cb}-9.183 -0.992 30.618
{tyr 194 cg}-8.520 -1.380 29.297
{tyr 194 cd1}-7.203 -1.056 29.040
{tyr 194 ce1}-6.607 -1.388 27.820
{tyr 194 cz}-7.277 -2.120 26.914
{tyr 194 ce2}-8.586 -2.506 27.123
{tyr 194 cd2}-9.257 -2.142 28.305
{tyr 194 cg}-8.520 -1.380 29.297
{tyr 194 cz}P -7.277 -2.120 26.914
{tyr 194 oh}-6.635 -2.486 25.702
{gly 196 n}P -6.172 2.720 27.752
{gly 196 ca}-5.056 2.058 26.993
{gly 196 c}-4.480 2.915 25.898
{trp 209 ca}P -11.105 1.166 25.123
{trp 209 cb}-10.063 0.017 25.248
{trp 209 cg}-8.926 0.173 24.315
{trp 209 cd1}-7.700 0.720 24.510
{trp 209 ne1}-7.002 0.696 23.332
{trp 209 ce2}-7.677 -0.010 22.390
{trp 209 cz2}-7.355 -0.279 21.072
{trp 209 ch2}-8.308 -0.957 20.316
{trp 209 cz3}-9.566 -1.309 20.850
{trp 209 ce3}-9.890 -0.963 22.156
{trp 209 cd2}-8.923 -0.330 22.928
{trp 209 cg}P -8.926 0.173 24.315
{trp 209 cd2}-8.923 -0.330 22.928
{trp 209 ce2}-7.677 -0.010 22.390
@vectorlist {thermostab} color= red
{pro 202 ca}P 2.920 5.474 17.390
{pro 202 cb}2.906 7.015 17.154
{pro 202 cg}1.458 7.220 16.847
{pro 202 cd}1.244 6.220 15.708
{pro 202 n}2.084 5.063 16.255
@vectorlist {pKa} color= yellow
{pro 201 ca}P 2.947 2.797 16.200
{pro 201 cb}4.168 2.558 15.348
{pro 201 cg}4.397 1.080 15.435
{pro 201 cd}2.906 0.532 15.307
{pro 201 n}2.170 1.574 16.006
{glu 205 ca}P -1.625 6.314 25.240
{glu 205 cb}-0.723 6.150 26.517
{glu 205 cg}0.320 5.006 26.378
{glu 205 cd}1.257 4.832 27.544
{glu 205 oe1}1.600 5.753 28.275
{glu 205 cd}P 1.257 4.832 27.544
{glu 205 oe2}1.637 3.660 27.752
@vectorlist {CO2 hydr} color= green
{leu 198 ca}P -3.198 2.705 19.945
{leu 198 cb}-2.458 3.640 18.963
{leu 198 cg}-2.974 5.100 18.926
{leu 198 cd1}-2.020 5.927 18.083
{leu 198 cg}P -2.974 5.100 18.926
{leu 198 cd2}-4.380 5.077 18.402
{thr 199 ca}P -2.114 -0.862 19.014
{thr 199 cb}-3.170 -2.058 19.066
{thr 199 og1}-3.865 -2.086 17.814
{thr 199 cb}P -3.170 -2.058 19.066
{thr 199 cg2}-4.033 -1.974 20.350
{leu 203 ca}P 1.342 3.550 20.304
{leu 203 cb}2.566 2.615 20.700
{leu 203 cg}2.766 1.515 19.617
{leu 203 cd}4.206 1.000 19.784
{leu 203 cg}P 2.766 1.515 19.617
{leu 203 cd2}1.706 0.457 19.860
{leu 204 ca}P 0.138 6.770 21.897
{leu 204 cb}-0.280 8.030 21.083
{leu 204 cg}0.867 8.582 20.200
{leu 204 cd1}0.262 9.755 19.383
{leu 204 cg}P 0.867 8.582 20.200
{leu 204 cd2}1.962 9.048 21.074
@vectorlist {no effects} color= gray
{thr 193 ca}P -13.610 -0.703 29.466
{thr 193 cb}-14.550 0.570 29.510
{thr 193 og1}-13.724 1.715 29.076
{thr 193 cb}P -14.550 0.570 29.510
{thr 193 cg2}-15.070 0.920 30.925
{pro 195 ca}P -7.573 3.093 29.675
{pro 195 cb}-7.089 4.015 30.760
{pro 195 cg}-7.236 3.246 32.052
{pro 195 cd}-8.096 2.008 31.768
{pro 195 n}-8.395 2.077 30.316
{ser 197 ca}P -3.320 3.008 23.736
{ser 197 cb}-1.824 2.677 23.987
{ser 197 og}-1.460 1.362 23.570
{thr 200 ca}P 0.158 0.189 16.144
{thr 200 cb}-0.380 0.236 14.685
{thr 200 og1}-1.213 1.466 14.636
{thr 200 cb}P -0.380 0.236 14.685
{thr 200 cg2}-1.250 -0.972 14.268
{cys 206 ca}P -4.730 8.307 24.355
{cys 206 cb}-4.445 9.207 23.060
{cys 206 sg}-4.343 8.200 21.510
{val 207 ca}P -7.360 5.628 24.200
{val 207 cb}-7.085 4.430 23.168
{val 207 cg1}-8.480 3.880 22.756
{val 207 cb}P -7.085 4.430 23.168
{val 207 cg2}-6.228 4.739 22.005
{thr 208 ca}P -10.396 4.762 26.204
{thr 208 cb}-11.625 5.543 26.680
{thr 208 og1}-11.090 6.682 27.470
{thr 208 cb}P -11.625 5.543 26.680
{thr 208 cg2}-12.660 4.797 27.553
{ile 210 ca}P -14.682 -0.095 24.912
{ile 210 cb}-15.827 0.900 24.568
{ile 210 cg1}-15.497 2.254 25.327
{ile 210 cd1}-16.423 3.394 24.856
{ile 210 cb}P -15.827 0.900 24.568
{ile 210 cg2}-17.180 0.322 24.956

@kinemage 3
@caption
Binding of biotin (pinktint) to streptavidin (white Calphas).  Balls are shown for non-C atoms in biotin and for the protein atoms to which they H-bond.  Aromatic sidechains are in seagreen, polar in cyan, and hydrophobics in gold.  View2 and 3 are overviews that show the complex from the side or the end of the streptavidin beta barrel.  
(From PDB file 1STP) 
@onewidth 
@viewid {biotin}
@zoom 2.84
@zslab 190
@center 12.757 1.842 -10.065
@matrix
-.58183 -.49984 -.64158 .36962 .54018 -.75603 .72447 -.67703 -.12954
@2viewid {side}
@2zoom 1.31
@2zslab 170
@2center 15.698 4.840 -1.611
@2matrix
-.828437 -.440747 -.345587 .382962 .004488 -.923754 .408695 -.89762 .165072
@3viewid {end}
@3zoom 1.49
@3zslab 200
@3center 15.698 4.840 -1.611
@3matrix
-.82289 .09343 -.56046 .33179 .87976 -.3405 .46126 -.46615 -.75495
@group {strp'avidin} 
@vectorlist {Calphas} color= white 
{ca ala 13}P 23.655 4.852 11.146 {ca ala 13}23.655 4.852 11.146
{ca glu 14}25.757 7.295 9.106
{ca ala 15}28.67 4.909 8.567
{ca gly 16}26.26 1.979 8.24
{ca thr 18}26.543 5.243 3.598
{ca gly 19}27.589 3.066 0.677
{ca thr 20}26.448 1.364 -2.504
{ca trp 21}23.46 -1.019 -2.257
{ca tyr 22}21.665 -3.337 -4.707
{ca asn 23}18.094 -4.622 -4.582
{ca gln 24}16.644 -7.892 -5.84
{ca leu 25}16.205 -6.397 -9.351
{ca gly 26}19.82 -5.25 -9.805
{ca ser 27}19.066 -1.569 -9.167
{ca thr 28}21.858 0.544 -7.672
{ca phe 29}21.351 2.921 -4.76
{ca ile 30}24.331 5.124 -3.867
{ca val 31}23.764 7.04 -0.618
{ca thr 32}25.48 9.272 1.883
{ca ala 33}23.84 9.711 5.293
{ca gly 34}24.472 13.215 6.66
{ca ala 35}25.01 13.822 10.383
{ca asp 36}21.8 15.85 10.408
{ca gly 37}19.573 12.989 9.186
{ca ala 38}19.845 13.896 5.492
{ca leu 39}20.141 11.349 2.674
{ca thr 40}21.515 12.36 -0.742
{ca gly 41}22.809 10.241 -3.619
{ca thr 42}21.958 8.561 -6.875
{ca tyr 43}19.562 5.875 -8.014
{ca glu 44}19.679 3.749 -11.155
{ca ser 45}16.9 1.311 -12.007
{ca ala 46}17.404 -1.996 -13.776
{ca val 47}13.779 -1.828 -14.973
{ca gly 48}11.032 0.5 -16.128
{c gly 48}11.504 1.583 -17.076
{o gly 48}12.52 1.485 -17.76
{c gly 48}P 11.504 1.583 -17.076 {n asn 49}10.714 2.649 -17.113
{ca asn 49}10.959 3.808 -17.958
{ca ala 50}14.448 4.747 -16.826
{ca glu 51}18.076 4.961 -17.884
{ca ser 52}21.277 6.059 -16.183
{ca arg 53}21.356 7.846 -12.823
{ca tyr 54}18.725 9.923 -11.065
{ca val 55}19.028 12.269 -8.104
{ca leu 56}17.532 11.137 -4.791
{ca thr 57}16.785 12.995 -1.571
{ca gly 58}15.611 11.533 1.754
{ca arg 59}15.712 11.605 5.559
{ca tyr 60}16.561 9.023 8.255
{ca asp 61}16.312 8.662 12.035
{ca ser 62}19.698 10.044 13.123
{ca ala 63}19.269 8.898 16.767
{ca pro 64}17.851 5.382 16.587
{ca ala 65}16.691 3.58 19.74
{ca thr 66}19.392 1.585 21.541
{ca asp 67}17.317 -1.607 21.933
{ca gly 68}18.569 -2.991 18.583
{ca ser 69}15.505 -1.941 16.49
{ca gly 70}16.062 -0.857 12.851
{ca thr 71}16.518 2.78 11.791
{ca ala 72}13.488 4.31 10.
{ca leu 73}14.277 6.062 6.705
{ca gly 74}12.801 7.136 3.367
{ca trp 75}13.811 8.648 0.02
{ca thr 76}12.293 9.887 -3.245
{ca val 77}13.345 9.878 -6.879
{ca ala 78}11.527 11.98 -9.524
{ca trp 79}12.09 9.978 -12.733
{ca lys 80}13.627 12.753 -14.77
{ca asn 81}17.289 13.196 -15.767
{ca asn 82}19.071 14.534 -18.878
{ca tyr 83}18.255 11.426 -20.913
{ca arg 84}14.559 11.133 -20.114
{ca asn 85}11.424 11.939 -18.209
{ca ala 86}8.96 9.23 -17.165
{ca his 87}6.696 11.798 -15.45
{ca ser 88}6.558 9.721 -12.259
{ca ala 89}8.013 9.587 -8.736
{ca thr 90}8.845 6.726 -6.375
{ca thr 91}9.047 6.864 -2.594
{ca trp 92}10.731 4.136 -0.556
{ca ser 93}9.809 3.787 3.113
{ca gly 94}11.686 1.224 5.216
{ca gln 95}14.243 0.581 7.925
{ca tyr 96}17.969 -0.09 8.024
{ca val 97}19.099 -3.245 9.852
{ca gly 98}22.762 -3.431 10.808
{ca gly 99}24.98 -6.419 11.461
{ca ala 100}26.839 -9.199 9.704
{ca glu 101}24.564 -8.952 6.689
{ca ala 102}23.224 -5.38 6.804
{ca arg 103}19.956 -4.85 4.941
{ca ile 104}17.494 -2.111 4.015
{ca asn 105}13.897 -3.426 3.913
{ca thr 106}11.451 -1.144 2.13
{ca gln 107}8.001 -0.722 0.641
{ca trp 108}7.536 1.79 -2.187
{ca leu 109}4.843 3.768 -3.948
{ca leu 110}5.289 4.743 -7.631
{ca thr 111}3.009 7.534 -8.802
{ca ser 112}2.522 8.551 -12.424
{ca gly 113}1.176 12.008 -13.36
{ca thr 114}-2.239 11.094 -14.831
{ca thr 115}-5.41 12.821 -16.057
{ca glu 116}-8.257 12.928 -13.505
{ca ala 117}-10.121 10.18 -15.335
{ca asn 118}-7.187 7.828 -14.72
{ca ala 119}-6.134 8.787 -11.179
{ca trp 120}-7.671 5.564 -9.84
{ca lys 121}-4.771 3.721 -11.464
{ca ser 122}-1.908 6.145 -10.907
{ca thr 123}0.003 4.256 -8.184
{ca leu 124}1.915 0.983 -7.96
{ca val 125}3.05 -0.698 -4.724
{ca gly 126}5.907 -3.151 -4.106
{ca his 127}8.853 -3.885 -1.804
{ca asp 128}12.621 -3.925 -2.37
{ca thr 129}15.402 -5.38 -0.202
{ca phe 130}18.876 -3.819 -0.463
{ca thr 131}22.169 -5.389 0.57
{ca lys 132}25.78 -4.312 0.127
{ca val 133}25.682 -7.551 -1.835
@balllist {mc N} color= sky radius= .2 
{n asn 49}10.714 2.649 -17.113
@group {side ch} 
@subgroup {aromatics} dominant 
@balllist {tyr O} color= red radius= .2 
{oh tyr 43}15.879 0.861 -6.317
@vectorlist {tyr} color= sea 
{ca tyr 43}P 19.562 5.875 -8.014 {cb tyr 43}18.119 5.957 -7.475
{cg tyr 43}17.509 4.591 -7.205
{cd1 tyr 43}16.91 3.828 -8.213
{ce1 tyr 43}16.372 2.579 -7.972
{cz tyr 43}16.399 2.086 -6.666
{oh tyr 43}15.879 0.861 -6.317
{cg tyr 43}P 17.509 4.591 -7.205 {cd2 tyr 43}17.545 4.068 -5.912
{ce2 tyr 43}16.996 2.82 -5.633
{cz tyr 43}16.399 2.086 -6.666
{ca tyr 54}P 18.725 9.923 -11.065 {cb tyr 54}17.271 9.365 -11.04
{cg tyr 54}16.817 8.909 -12.407
{cd1 tyr 54}17.21 7.658 -12.899
{ce1 tyr 54}16.824 7.231 -14.163
{cz tyr 54}16.036 8.07 -14.969
{oh tyr 54}15.67 7.673 -16.218
{cg tyr 54}P 16.817 8.909 -12.407 {cd2 tyr 54}16.048 9.723 -13.233
{ce2 tyr 54}15.652 9.315 -14.506
{cz tyr 54}16.036 8.07 -14.969
@vectorlist {trp} color= sea 
{ca trp 79}P 12.09 9.978 -12.733 {cb trp 79}11.396 8.658 -13.04
{cg trp 79}11.396 7.697 -11.898
{cd1 trp 79}10.366 7.465 -11.028
{ne1 trp 79}10.747 6.511 -10.106
{ce2 trp 79}12.027 6.115 -10.358
{ne1 trp 79}10.747 6.511 -10.106
{cg trp 79}P 11.396 7.697 -11.898 {cd2 trp 79}12.478 6.839 -11.487
{ce2 trp 79}12.027 6.115 -10.358
{cz2 trp 79}12.815 5.175 -9.707
{ch2 trp 79}14.085 4.97 -10.228
{cd2 trp 79}P 12.478 6.839 -11.487 {ce3 trp 79}13.763 6.62 -11.971
{cz3 trp 79}14.556 5.692 -11.32
{ch2 trp 79}14.085 4.97 -10.228
{ca trp 92}P 10.731 4.136 -0.556 {cb trp 92}12.117 3.616 -0.895
{cg trp 92}12.359 2.952 -2.197
{cd1 trp 92}12.351 1.587 -2.463
{ne1 trp 92}12.64 1.37 -3.782
{ce2 trp 92}12.827 2.576 -4.412
{ne1 trp 92}12.64 1.37 -3.782
{cg trp 92}P 12.359 2.952 -2.197 {cd2 trp 92}12.675 3.59 -3.451
{ce2 trp 92}12.827 2.576 -4.412
{cz2 trp 92}13.121 2.852 -5.733
{ch2 trp 92}13.239 4.181 -6.093
{cd2 trp 92}P 12.675 3.59 -3.451 {ce3 trp 92}12.779 4.92 -3.827
{cz3 trp 92}13.066 5.198 -5.158
{ch2 trp 92}13.239 4.181 -6.093
{ca trp 108}P 7.536 1.79 -2.187 {cb trp 108}8.705 1.719 -3.183
{cg trp 108}8.786 0.499 -4.029
{cd1 trp 108}9.642 -0.563 -3.89
{ne1 trp 108}9.418 -1.494 -4.866
{ce2 trp 108}8.413 -1.051 -5.682
{ne1 trp 108}9.418 -1.494 -4.866
{cg trp 108}P 8.786 0.499 -4.029 {cd2 trp 108}7.994 0.204 -5.202
{ce2 trp 108}8.413 -1.051 -5.682
{cz2 trp 108}7.829 -1.643 -6.802
{ch2 trp 108}6.808 -0.945 -7.436
{cd2 trp 108}P 7.994 0.204 -5.202 {ce3 trp 108}6.966 0.88 -5.859
{cz3 trp 108}6.387 0.292 -6.97
{ch2 trp 108}6.808 -0.945 -7.436
@subgroup {Hphobic} dominant 
@vectorlist {phe} color= gold 
{ca phe 130}P 18.876 -3.819 -0.463 {cb phe 130}19.105 -2.322 -0.528
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@caption
Click on "animate" button to see sequence of geodesic dome construction, starting with cube and icosahedron.
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{c} .332 .873 -.413
{c} P .668 .745 .205 {c} .589 .591 .59
{c} .332 .873 .413
{c} P .205 .668 .745 {c} .589 .591 .59
{c} .413 .332 .873
{c} P .745 .205 .668 {c} .589 .591 .59
{c} .873 .413 .332
{c} P -.332 .873 -.413 {c} -.365 .954 0.
{c} -.668 .745 -.205
{c} P -.668 .745 .205 {c} -.365 .954 0.
{c} -.332 .873 .413
{c} P 0. 1. .208 {c} -.365 .954 0.
{c} 0. 1. -.208
{c} P -.332 .873 .413 {c} -.59 .589 .589
{c} -.668 .745 .205
{c} P -.873 .413 .332 {c} -.59 .589 .589
{c} -.745 .205 .668
{c} P -.413 .332 .873 {c} -.59 .589 .589
{c} -.205 .668 .745
{c} P -1. .208 0. {c} -.955 -.001 .364
{c} -1. -.208 0.
{c} P -.873 -.413 .332 {c} -.955 -.001 .364
{c} -.745 -.205 .668
{c} P -.745 .205 .668 {c} -.955 -.001 .364
{c} -.873 .413 .332
{c} P -.745 -.205 .668 {c} -.591 -.59 .589
{c} -.873 -.413 .332
{c} P -.668 -.745 .205 {c} -.591 -.59 .589
{c} -.332 -.873 .413
{c} P -.205 -.668 .745 {c} -.591 -.59 .589
{c} -.413 -.332 .873
{c} P -.668 -.745 -.205 {c} -.364 -.954 -.001
{c} -.332 -.873 -.413
{c} P 0. -1. -.208 {c} -.364 -.954 -.001
{c} 0. -1. .208
{c} P -.332 -.873 .413 {c} -.364 -.954 -.001
{c} -.668 -.745 .205
{c} P -.873 -.413 -.332 {c} -.589 -.589 -.59
{c} -.745 -.205 -.668
{c} P -.413 -.332 -.873 {c} -.589 -.589 -.59
{c} -.205 -.668 -.745
{c} P -.332 -.873 -.413 {c} -.589 -.589 -.59
{c} -.668 -.745 -.205
{c} P -.208 0. -1. {c} .001 -.364 -.955
{c} .208 0. -1.
{c} P .413 -.332 -.873 {c} .001 -.364 -.955
{c} .205 -.668 -.745
{c} P -.205 -.668 -.745 {c} .001 -.364 -.955
{c} -.413 -.332 -.873
{c} P -.413 .332 -.873 {c} 0. .365 -.954
{c} -.205 .668 -.745
{c} P .205 .668 -.745 {c} 0. .365 -.954
{c} .413 .332 -.873
{c} P .208 0. -1. {c} 0. .365 -.954
{c} -.208 0. -1.
{c} P -.745 .205 -.668 {c} -.591 .59 -.589
{c} -.873 .413 -.332
{c} P -.668 .745 -.205 {c} -.591 .59 -.589
{c} -.332 .873 -.413
{c} P -.205 .668 -.745 {c} -.591 .59 -.589
{c} -.413 .332 -.873
{c} P -1. -.208 0. {c} -.955 .001 -.364
{c} -1. .208 0.
{c} P -.873 .413 -.332 {c} -.955 .001 -.364
{c} -.745 .205 -.668
{c} P -.745 -.205 -.668 {c} -.955 .001 -.364
{c} -.873 -.413 -.332
@vectorlist {pent ribs} color= green 
{c} P 1. .209 0. {1st point} .869 .537 0.
{c} .873 .413 -.332
{c} P .668 .745 -.205 {1st point} .869 .537 0.
{c} .668 .745 .205
{1st point} P .869 .537 0. {c} .873 .413 .332
{c} P .413 -.332 -.873 {c} .535 -.001 -.869
{c} .208 0. -1.
{c} P .413 .332 -.873 {c} .535 -.001 -.869
{c} .745 .205 -.668
{c} P .535 -.001 -.869 {c} .745 -.205 -.668
{c} P .205 .668 -.745 {c} 0. .867 -.538
{c} -.205 .668 -.745
{c} P -.332 .873 -.413 {c} 0. .867 -.538
{c} 0. 1. -.208
{c} P 0. .867 -.538 {c} .332 .873 -.413
{c} P .332 .873 .413 {c} .001 .869 .535
{c} 0. 1. .208
{c} P -.332 .873 .413 {c} .001 .869 .535
{c} -.205 .668 .745
{c} P .001 .869 .535 {c} .205 .668 .745
{c} P -.668 .745 -.205 {c} -.868 .537 -.001
{c} -.873 .413 -.332
{c} P -1. .208 0. {c} -.868 .537 -.001
{c} -.873 .413 .332
{c} P -.868 .537 -.001 {c} -.668 .745 .205
{c} P -.208 0. -1. {c} -.536 -.001 -.869
{c} -.413 -.332 -.873
{c} P -.745 -.205 -.668 {c} -.536 -.001 -.869
{c} -.745 .205 -.668
{c} P -.536 -.001 -.869 {c} -.413 .332 -.873
{c} P .205 -.668 -.745 {c} .001 -.868 -.537
{c} .332 -.873 -.413
{c} P 0. -1. -.208 {c} .001 -.868 -.537
{c} -.332 -.873 -.413
{c} P .001 -.868 -.537 {c} -.205 -.668 -.745
{c} P 1. -.208 0. {c} .869 -.536 .001
{c} .873 -.413 .332
{c} P .668 -.745 .205 {c} .869 -.536 .001
{c} .668 -.745 -.205
{c} P .869 -.536 .001 {c} .873 -.413 -.332
{c} P .745 .205 .668 {c} .537 .001 .868
{c} .413 .332 .873
{c} P .208 0. 1. {c} .537 .001 .868
{c} .413 -.332 .873
{c} P .537 .001 .868 {c} .745 -.205 .668
{c} P -.208 0. 1. {c} -.536 .001 .869
{c} -.413 .332 .873
{c} P -.745 .205 .668 {c} -.536 .001 .869
{c} -.745 -.205 .668
{c} P -.536 .001 .869 {c} -.413 -.332 .873
{c} P -.873 -.413 .332 {c} -.869 -.535 .001
{c} -1. -.208 0.
{c} P -.873 -.413 -.332 {c} -.869 -.535 .001
{c} -.668 -.745 -.205
{c} P -.869 -.535 .001 {c} -.668 -.745 .205
{c} P .205 -.668 .745 {c} 0. -.867 .538
{c} -.205 -.668 .745
{c} P -.332 -.873 .413 {c} 0. -.867 .538
{c} 0. -1. .208
{c} P 0. -.867 .538 {c} .332 -.873 .413
@group {geo-icoso} dominant animate moview= 2
@vectorlist {theicos} instance= {icosohedron}
@wordlist {next} master= {words}
<show inside
 icosahedron> -.812 -.667 -.434
@subgroup {ball} instance= {geo}
@group {dome-icso} dominant animate moview= 2
@vectorlist {theicos} instance= {icosohedron}
@wordlist {next} master= {words}
<delete parts
 not needed
 for dome> 0 0 0
@subgroup {dome tris}
@vectorlist {Dome pents} color= sea 
{c} P .873 .413 -.332 {c} 1. .209 0.
{c} .873 .413 .332
{c} .668 .745 .205
{c} .668 .745 -.205
{c} .873 .413 -.332
{c} P 1. -.208 0. {c} .873 -.413 .332
{c} .668 -.745 .205
{c} .668 -.745 -.205
{c} .873 -.413 -.332
{c} 1. -.208 0.
{c} P .745 .205 -.668 {c} .745 -.205 -.668
{c} .413 -.332 -.873
{c} .208 0. -1.
{c} .413 .332 -.873
{c} .745 .205 -.668
{c} P .745 .205 .668 {c} .745 -.205 .668
{c} .413 -.332 .873
{c} .208 0. 1.
{c} .413 .332 .873
{c} .745 .205 .668
{c} P .332 .873 .413 {c} .205 .668 .745
{c} -.205 .668 .745
{c} -.332 .873 .413
{c} 0. 1. .208
{c} .332 .873 .413
{c} P .332 .873 -.413 {c} .205 .668 -.745
{c} -.205 .668 -.745
{c} -.332 .873 -.413
{c} 0. 1. -.208
{c} .332 .873 -.413
@vectorlist {Dome hexs} color= sea 
{c} P .873 .413 .332 {c} .745 .205 .668
{c} P .745 -.205 .668 {c} .873 -.413 .332
{c} P 1. -.208 0. {c} 1. .209 0.
{c} P .873 .413 -.332 {c} .745 .205 -.668
{c} P .745 -.205 -.668 {c} .873 -.413 -.332
{c} P .413 .332 -.873 {c} .205 .668 -.745
{c} P .205 .668 .745 {c} .413 .332 .873
{c} P .332 .873 .413 {c} .668 .745 .205
{c} P 0. 1. .208 {c} 0. 1. -.208
{c} P .332 .873 -.413 {c} .668 .745 -.205
@vectorlist {Dome 6 ribs} color= sea 
{1st point} P .954 -.001 .364 {c} .873 -.413 .332
{1st point} P .954 -.001 .364 {c} 1. -.208 0.
{1st point} P .954 -.001 .364 {c} 1. .209 0.
{1st point} P .954 -.001 .364 {c} .873 .413 .332
{1st point} P .954 -.001 .364 {c} .745 .205 .668
{1st point} P .954 -.001 .364 {c} .745 -.205 .668
{c} P .745 .205 -.668 {c} .954 .001 -.364
{c} .873 .413 -.332
{c} P 1. .209 0. {c} .954 .001 -.364
{c} 1. -.208 0.
{c} P .873 -.413 -.332 {c} .954 .001 -.364
{c} .745 -.205 -.668
{c} P .413 .332 -.873 {c} .589 .59 -.589
{c} .205 .668 -.745
{c}P .332 .873 -.413 {c} .589 .59 -.589
{c} .668 .745 -.205
{c} P .873 .413 -.332 {c} .589 .59 -.589
{c} .745 .205 -.668
{c} P 0. 1. -.208 {c} .364 .955 .001
{c} 0. 1. .208
{c} P .332 .873 .413 {c} .364 .955 .001
{c} .668 .745 .205
{c} P .668 .745 -.205 {c} .364 .955 .001
{c} .332 .873 -.413
{c} P .668 .745 .205 {c} .589 .591 .59
{c} .332 .873 .413
{c} P .205 .668 .745 {c} .589 .591 .59
{c} .413 .332 .873
{c} P .745 .205 .668 {c} .589 .591 .59
{c} .873 .413 .332
@vectorlist {Dome 5 ribs} color= sea 
{c} P 1. .209 0. {1st point} .869 .537 0.
{c} .873 .413 -.332
{c} P .668 .745 -.205 {1st point} .869 .537 0.
{c} .668 .745 .205
{1st point} P .869 .537 0. {c} .873 .413 .332
{c} P .413 -.332 -.873 {c} .535 -.001 -.869
{c} .208 0. -1.
{c} P .413 .332 -.873 {c} .535 -.001 -.869
{c} .745 .205 -.668
{c} P .535 -.001 -.869 {c} .745 -.205 -.668
{c} P .205 .668 -.745 {c} 0. .867 -.538
{c} -.205 .668 -.745
{c} P -.332 .873 -.413 {c} 0. .867 -.538
{c} 0. 1. -.208
{c} P 0. .867 -.538 {c} .332 .873 -.413
{c} P .332 .873 .413 {c} .001 .869 .535
{c} 0. 1. .208
{c} P -.332 .873 .413 {c} .001 .869 .535
{c} -.205 .668 .745
{c} P .001 .869 .535 {c} .205 .668 .745
{c} P 1. -.208 0. {c} .869 -.536 .001
{c} .873 -.413 .332
{c} P .668 -.745 .205 {c} .869 -.536 .001
{c} .668 -.745 -.205
{c} P .869 -.536 .001 {c} .873 -.413 -.332
{c} P .745 .205 .668 {c} .537 .001 .868
{c} .413 .332 .873
{c} P .208 0. 1. {c} .537 .001 .868
{c} .413 -.332 .873
{c} P .537 .001 .868 {c} .745 -.205 .668
@group {dome-walls} dominant animate moview= 2
@vectorlist {walls} color= sea 
{c} P -.205 .668 -.745 {c} -.375 .563 -.745
{c} P -.332 .873 -.413 {c} -.502 .768 -.413
{c} P -.332 .873 .413 {c} -.502 .768 .413
{c} P -.205 .668 .745 {c} -.375 .563 .745
{c} P .413 -.332 -.873 {c} .243 -.437 -.873
{c} P .208 0. -1. {c} 0.038 -.105 -1.
{c} P .208 0. 1. {c} 0.038 -.105 1.
{c} P .413 -.332 .873 {c} .243 -.437 .873
{c} P .668 -.745 .205 {c} .498 -.85 .205
{c} P .668 -.745 -.205 {c} .498 -.85 -.205
{c} P .745 -.205 .668 {c} .277 -.494 .668
{c} P .873 -.413 .332 {c} .405 -.702 .332
{c} P 0. 1. -.208 {c} -.468 .711 -.209
{c} P 0. 1. .208 {c} -.468 .711 .207
{c} P .413 .332 -.873 {c} -0.055 0.043 -.873
{c} P .205 .668 -.745 {c} -.263 .379 -.745
{c} P .745 -.205 -.668 {c} .277 -.494 -.668
{c} P .873 -.413 -.332 {c} .405 -.702 -.332
{c} P .413 .332 .873 {c} -0.055 0.043 .873
{c} P .205 .668 .745 {c} -.263 .379 .745
{c} P 0.038 -.105 1. {c} .243 -.437 .873
{c} .277 -.494 .668
{c} .405 -.702 .332
{c} .498 -.85 .205
{c} .498 -.85 -.205
{c} .405 -.702 -.332
{c} .277 -.494 -.668
{c} .243 -.437 -.873
{c} 0.038 -.105 -1.
{c} -0.055 0.043 -.873
{c} -.263 .379 -.745
{c} -.375 .563 -.745
{c} -.502 .768 -.413
{c} -.468 .711 -.209
{c} -.468 .711 .207
{c} -.502 .768 .413
{c} -.375 .563 .745
{c} -.263 .379 .745
{c} -0.055 0.043 .873
{c} 0.038 -.105 1.
@wordlist {house} master= {words}
<build walls> -.177 -.14 -.468
@subgroup {dometri} instance= {dome tris}
@group {dome-all} dominant animate moview= 2
@vectorlist {domewalls} instance= {walls}
@vectorlist {cupola} color= sea 
{c} P .668 .745 .205 {c} .838 .85 .205
{c} P .873 .413 .332 {c} 1.043 .518 .332
{c} P 1. .209 0. {c} 1.17 .314 0.
{c} P .873 .413 -.332 {c} 1.043 .519 -.332
{c} P .668 .745 -.205 {c} .838 .85 -.205
{c} P .869 .537 0. {c} 1.039 .643 0.
{c} P 1.17 .314 0. {c} 1.207 .221 .001
{c} P 1.043 .519 -.332 {c} 1.044 .484 -.426
{c} P .838 .85 -.205 {c} .781 .909 -.263
{c} P .838 .85 .205 {c} .782 .909 .263
{c} P 1.043 .518 .332 {c} 1.044 .483 .426
{c} P .782 .909 .263 {c} 1.044 .483 .426
{c} 1.207 .221 .001
{c} 1.044 .484 -.426
{c} .781 .909 -.263
{c} .782 .909 .263
{c} P 1.039 .643 0. {c} .838 .85 -.205
{c} P 1.039 .643 0. {c} .838 .85 .205
{c} P 1.039 .643 0. {c} 1.043 .518 .332
{c} P 1.039 .643 0. {c} 1.043 .519 -.332
{c} P 1.039 .643 0. {c} 1.17 .314 0.
@wordlist {house} master= {words}
<add cupola> -.177 -.14 -.468
@subgroup {dometri} instance= {dome tris}
@group {The Dome} dominant animate moview= 3
@vectorlist {domewalls} instance= {walls}
@vectorlist {dometop} instance= {cupola}
@wordlist {house} master= {words}
<Now you can
 move in!> -.177 -.14 -.468
@subgroup {dometri} instance= {dome tris}
@kinemage 5
@caption 
Leucine zipper peptide dimer - view from the end.  Calphas of chain A are white, chain B yellowtint; sidechains are colored by their "heptad" position: Leu (d) in orange; Val (a) in gold, and others not shown.  Zoom in further and translate through the structure; see the text window for detailed instructions.  From Brookhaven Data Bank file 2ZTA and ProTour2.kin.
@onewidth
@zoom 2.1
@matrix 
-.409699 .413261 .813242 -.733 -.679811 -.023817 .543009 -.605864 .581438 
@2viewid {ladder}
@2zoom 1.38
@2zslab 120
@2matrix 
-.438874 .781392 -.443639 -.70434 .00741 .709825 .557939 .623996 .547113 
@3viewid {thin slab}
@3zoom 3.0
@3zslab 100
@3matrix 
-.409699 .413261 .813242 -.733 -.679811 -.023817 .543009 -.605864 .581438 
@4viewid {zippers}
@4zoom 2.1
@4zslab 160
@4center 18.254 18.524 6.574
@4matrix 
-.438874 .781392 -.443639 -.70434 .00741 .709825 .557939 .623996 .547113
@5viewid {side}
@5zoom 2.04
@5zslab 160
@5center 18.254 18.524 6.574
@5matrix 
-.360067 .803085 .474769 .781886 -0.017841 0.623167 0.508926 0.595597 -0.621497 
@6viewid {to write PS}
@6zoom 2.41
@6zslab 480
@6center 22.512 17.719 9.068
@6matrix
-.40962 .3459 .84413 -.81082 -.56211 -.16312 .41807 -.75125 .51072
@group {Calphas}
@vectorlist {A chain} color= white 
{ca arg 1} P 38.127 14.684 15.695 {ca met 2} 36.66 18.155 15.84
{ca lys 3} 37.33 19.06 12.267
{ca gln 4} 35.67 15.982 10.84
{ca leu 5} 32.643 16.6 13.126
{ca glu 6} 32.395 20.303 12.225
{ca asp 7} 32.448 19.407 8.572
{ca lys 8} 29.714 16.773 9.066
{ca val 9} 27.517 19.463 10.67
{ca glu 10} 28.153 21.876 7.674
{ca glu 11} 27.355 19.15 5.237
{ca leu 12} 24.14 18.084 6.963
{ca leu 13} 22.953 21.628 7.228
{ca ser 14} 23.635 22.12 3.513
{ca lys 15} 21.673 18.905 2.595
{ca asn 16} 18.92 20.03 4.916
{ca tyr 17} 18.583 23.458 3.27
{ca his 18} 18.464 21.654 -0.143
{ca leu 19} 15.562 19.515 1.148
{ca glu 20} 13.734 22.442 2.62
{ca asn 21} 14.082 24.25 -.792
{ca glu 22} 12.464 21.235 -2.495
{ca val 23} 9.567 21.098 .055
{ca ala 24} 8.696 24.74 -.647
{ca arg 25} 8.757 24.218 -4.31
{ca leu 26} 6.58 21.183 -3.91
{ca lys 27} 4.334 23.132 -1.617
{ca lys 28} 3.872 25.752 -4.34
{ca leu 29} 2.917 22.842 -6.655
{ca val 30} .184 21.71 -4.154
{ca gly 31} -1.672 24.948 -4.007
@vectorlist {B chain} color=paleyellow
{ca arg 1} P 32.954 20.476 22.253 {ca met 2} 33.142 16.905 20.93
{ca lys 3} 29.997 15.7 22.554
{ca gln 4} 27.846 18.716 21.617
{ca leu 5} 28.993 18.455 17.966
{ca glu 6} 28.047 14.698 17.988
{ca asp 7} 24.653 15.646 19.293
{ca lys 8} 24.16 18.326 16.627
{ca val 9} 25.022 15.78 13.85
{ca glu 10} 22.418 13.406 15.44
{ca glu 11} 19.857 16.105 15.505
{ca leu 12} 20.537 17.187 11.822
{ca leu 13} 20.506 13.546 10.735
{ca ser 14} 16.977 13.025 12.308
{ca lys 15} 15.768 16.242 10.722
{ca asn 16} 17.148 15.287 7.314
{ca tyr 17} 15.212 11.918 7.396
{ca his 18} 12.044 13.664 8.32
{ca leu 19} 12.542 16.087 5.334
{ca glu 20} 13.32 13.222 2.974
{ca asn 21} 10.096 11.435 4.006
{ca glu 22} 8.192 14.685 3.595
{ca val 23} 9.67 15.232 .157
{ca ala 24} 8.7 11.725 -.835
{ca arg 25} 5.052 12.23 .462
{ca leu 26} 4.613 15.62 -1.37
{ca lys 27} 6.086 14.333 -4.63
{ca lys 28} 3.73 11.297 -4.703
{ca leu 29} .8 13.434 -3.964
{ca val 30} 1.817 16.156 -6.362
{ca gly 31} 3.33 14.592 -9.406
@group {heptad sc}
@vectorlist {d: Leu} color=orange
{ca leu A5} P 32.643 16.6 13.126 {cb leu A5} 32.46 16.42 14.67
{cg leu A5} 32.495 15.02 15.313
{cd1 leu A5} 32.86 15.235 16.79
{cg leu A5} P 32.495 15.02 15.313 {cd2 Aleu 5} 31.102 14.392 15.26
{ca leu A12} P 24.14 18.084 6.963 {cb leu A12} 23.9 17.347 8.3
{cg leu A12} 24.408 15.918 8.203
{cd1 leu A12} 24.58 15.3 9.56
{cg leu A12} P 24.408 15.918 8.203 {cd2 leu A12} 23.332 15.098 7.556
{ca leu A19} P 15.562 19.515 1.148 {cb leu A19} 15.57 18.356 2.134
{cg leu A19} 16.384 17.163 1.675
{cd1 leu A19} 16.71 16.315 2.883
{cg leu A19} P 16.384 17.163 1.675 {cd2 leu A19} 15.594 16.277 .73
{ca leu 26} P 6.58 21.183 -3.91 {cb leu A26} 6.845 19.727 -3.578
{cg leu A26} 7.913 19.102 -4.402
{cd1 leu A26} 8.753 18.277 -3.443
{cg leu A26} P 7.913 19.102 -4.402 {cd2 Aleu 26} 7.178 18.174 -5.34
{ca leu B5} P 28.993 18.455 17.966 {cb Bleu 5} 30.46 18.668 17.427
{cg leu B5} 31.045 20.115 17.486
{cd1 leu B5} 32.538 20.142 17.182
{cg leu B5} P 31.045 20.115 17.486 {cd2 Bleu 5} 30.427 21.023 16.45
{ca leu B12} P 20.537 17.187 11.822 {cb Bleu 12} 21.825 17.848 11.224
{cg leu B12} 22. 19.29 11.694
{cd1 leu B12} 23.31 19.983 11.275
{cg leu B12} P 22. 19.29 11.694 {cd2 leu B12} 20.78 20.092 11.305
{ca leu B19} P 12.542 16.087 5.334 {cb Bleu 19} 13.622 17.152 5.14
{cg leu B19} 13.501 18.332 6.097
{cd1 leu B19} 14.723 19.256 5.994
{cg leu B19} P 13.5 18.332 6.097 {cd2 Bleu 19} 12.203 19.1 5.877
{ca leu B26} P 4.613 15.62 -1.37 {cb Bleu 26} 5.357 16.95 -1.034
{cg leu B26} 4.935 17.73 .23
{cd1 leu B26} 5.716 19.032 .37
{cg leu B26} P 4.935 17.73 .23 {cd2 leu B26} 3.495 18.16 .132
@vectorlist {Asn 16} color=hotpink
{ca asn B16} P 17.148 15.287 7.314 {cb asn 16} 18.628 14.868 7.155
{cg asn B16} 19.12 14.552 5.75
{od1 asn B16} 19.236 13.376 5.377
{cg asn B16} P 19.12 14.552 5.75 {nd2 asn 16} 19.58 15.576 5.036
{ca asn A16} P 18.92 20.03 4.916 {cb asn 16} 18.758 20.06 6.426
{cg asn A16} 18.773 18.704 7.105
{od1 asn A16} 18.912 17.604 6.512
{cg asn A16} P 18.773 18.704 7.105 {nd2 asn 16} 18.717 18.82 8.413
@vectorlist {a: Val} color=gold
{ca met A2} P 36.66 18.155 15.84 {cb met A2} 37.212 19.245 16.74
{cg met A2} 36.06 19.824 17.54
{sd met A2} 36.542 20.556 19.116
{ce met A2} 38.18 21.188 18.664
{ca val A9} P 27.517 19.463 10.67 {cb val A9} 27.758 20.28 12.002
{cg1 val A9} 26.726 21.386 12.216
{cb val A9} P 27.758 20.28 12.002 {cg2 val A9} 27.75 19.406 13.26
{ca val A23} P 9.567 21.098 0.055 {cb val A23} 9.673 20.85 1.6
{cg1 val A23} 8.345 21.088 2.316
{cb val A23} P 9.673 20.85 1.6 {cg2 val A23} 10.167 19.442 1.954
{ca val A30} P .184 21.71 -4.154 {cb val A30} .49 21.29 -2.708
{cg1 val A30} -.783 21.014 -1.924
{cb val A30} P .49 21.29 -2.708 {cg2 val A30} 1.285 20. -2.74
{ca met B2} P 33.142 16.905 20.93 {cb met B2} 34.172 15.858 21.36
{cg met B2} 34.306 14.67 20.426
{sd met B2} 35.754 13.637 20.782
{ce met B2} 35.522 12.378 19.5
{ca val B9} P 25.022 15.78 13.85 {cb val B9} 26.336 14.944 13.536
{cg1 val B9} 26.186 13.72 12.597
{cb val B9} P 26.336 14.944 13.536 {cg2 val B9} 27.54 15.796 13.117
{ca val B23} P 9.67 15.232 .157 {cb val B23} 11.153 15.505 -.104
{cg1 val B23} 11.506 15.2 -1.554
{cb val B23} P 11.153 15.505 -.104 {cg2 val B23} 11.43 16.974 .18
{ca val B30} P 1.817 16.156 -6.362 {cb val B30} 2.757 17.322 -6.056
{cg1 val B30} 3.265 17.998 -7.32
{cb val B30} P 2.757 17.322 -6.056 {cg2 val B30} 2.024 18.36 -5.224
@group off {zipper sc}
@subgroup {rear zip}
@vectorlist {Leu A} color=hotpink
{ca leu A5} P 32.643 16.6 13.126 {cb leu 5} 32.46 16.42 14.67
{cg leu A5} 32.495 15.02 15.313
{cd1 leu A5} 32.86 15.235 16.79
{cg leu A5} P 32.495 15.02 15.313 {cd2 leu 5} 31.102 14.392 15.26
{ca leu A12} P 24.14 18.084 6.963 {cb leu 12} 23.9 17.347 8.3
{cg leu A12} 24.408 15.918 8.203
{cd1 leu A12} 24.58 15.3 9.56
{cg leu A12} P 24.408 15.918 8.203 {cd2 leu 12} 23.332 15.098 7.556
{ca leu A19} P 15.562 19.515 1.148 {cb leu 19} 15.57 18.356 2.134
{cg leu A19} 16.384 17.163 1.675
{cd1 leu A19} 16.71 16.315 2.883
{cg leu A19} P 16.384 17.163 1.675 {cd2 leu 19} 15.594 16.277 .73
{ca leu A26} P 6.58 21.183 -3.91 {cb leu 26} 6.845 19.727 -3.578
{cg leu A26} 7.913 19.102 -4.402
{cd1 leu A26} 8.753 18.277 -3.443
{cg leu A26} P 7.913 19.102 -4.402 {cd2 leu 26} 7.178 18.174 -5.34
@vectorlist {Asn 16B} color=pink
{ca asn B16} P 17.148 15.287 7.314 {cb asn 16} 18.628 14.868 7.155
{cg asn B16} 19.12 14.552 5.75
{od1 asn B16} 19.236 13.376 5.377
{cg asn B16} P 19.12 14.552 5.75 {nd2 asn 16} 19.58 15.576 5.036
@vectorlist {Val B} color=pink
{ca met B2} P 33.142 16.905 20.93 {cb met 2} 34.172 15.858 21.36
{cg met B2} 34.306 14.67 20.426
{sd met B2} 35.754 13.637 20.782
{ce met B2} 35.522 12.378 19.5
{ca val B9} P 25.022 15.78 13.85 {cb val 9} 26.336 14.944 13.536
{cg1 val B9} 26.186 13.72 12.597
{cb val B9} P 26.336 14.944 13.536 {cg2 val 9} 27.54 15.796 13.117
{ca val B23} P 9.67 15.232 .157 {cb val 23} 11.153 15.505 -.104
{cg1 val B23} 11.506 15.2 -1.554
{cb val B23} P 11.153 15.505 -.104 {cg2 val 23} 11.43 16.974 .18
{ca val B30} P 1.817 16.156 -6.362 {cb val 30} 2.757 17.322 -6.056
{cg1 val B30} 3.265 17.998 -7.32
{cb val B30} P 2.757 17.322 -6.056 {cg2 val 30} 2.024 18.36 -5.224
@subgroup {front zip}
@vectorlist {Leu B} color=green
{ca leu B5} P 28.993 18.455 17.966 {cb leu 5} 30.46 18.668 17.427
{cg leu B5} 31.045 20.115 17.486
{cd1 leu B5} 32.538 20.142 17.182
{cg leu B5} P 31.045 20.115 17.486 {cd2 leu 5} 30.427 21.023 16.45
{ca leu B12} P 20.537 17.187 11.822 {cb leu 12} 21.825 17.848 11.224
{cg leu B12} 22. 19.29 11.694
{cd1 leu B12} 23.31 19.983 11.275
{cg leu B12} P 22. 19.29 11.694 {cd2 leu 12} 20.78 20.092 11.305
{ca leu B19} P 12.542 16.087 5.334 {cb leu 19} 13.622 17.152 5.14
{cg leu B19} 13.501 18.332 6.097
{cd1 leu B19} 14.723 19.256 5.994
{cg leu B19} P 13.5 18.332 6.097 {cd2 leu 19} 12.203 19.1 5.877
{ca leu B26} P 4.613 15.62 -1.37 {cb leu 26} 5.357 16.95 -1.034
{cg leu B26} 4.935 17.73 .23
{cd1 leu B26} 5.716 19.032 .37
{cg leu B26} P 4.935 17.73 .23 {cd2 leu 26} 3.495 18.16 .132
@vectorlist {Asn 16A} color=sea
{ca asn A16} P 18.92 20.03 4.916 {cb asn 16} 18.758 20.06 6.426
{cg asn A16} 18.773 18.704 7.105
{od1 asn A16} 18.912 17.604 6.512
{cg asn A16} P 18.773 18.704 7.105 {nd2 asn 16} 18.717 18.82 8.413
@vectorlist {Val A} color=sea
{ca met A2} P 36.66 18.155 15.84 {cb met 2} 37.212 19.245 16.74
{cg met A2} 36.06 19.824 17.54
{sd met A2} 36.542 20.556 19.116
{ce met A2} 38.18 21.188 18.664
{ca val A9} P 27.517 19.463 10.67 {cb val 9} 27.758 20.28 12.002
{cg1 val A9} 26.726 21.386 12.216
{cb val A9} P 27.758 20.28 12.002 {cg2 val 9} 27.75 19.406 13.26
{ca val A23} P 9.567 21.098 0.055 {cb val 23} 9.673 20.85 1.6
{cg1 val A23} 8.345 21.088 2.316
{cb val A23} P 9.673 20.85 1.6 {cg2 val 23} 10.167 19.442 1.954
{ca val A30} P .184 21.71 -4.154 {cb val 30} .49 21.29 -2.708
{cg1 val A30} -.783 21.014 -1.924
{cb val A30} P .49 21.29 -2.708 {cg2 val 30} 1.285 20. -2.74
@kinemage 6
@caption

An asparagine sidechain (in gold) as the N-cap of an alpha-helix - Asn 280 of thermolysin (1HYT).  See text for suggestions in trying out the "measure" and "draw new" functions on this structure.


@onewidth
@zoom 1.54
@zslab 170
@ztran 0
@center 48.137 56.073 -18.953
@matrix
0.547168 -0.258899 0.795977 -0.023188 -0.955285 -0.294776 0.836702 0.142835 -0.528705
@2viewid {closeup}
@2zoom 2.42
@2zslab 200
@2ztran 0
@2center 47.076 53.338 -18.773
@2matrix
0.437281 -0.442741 0.782793 -0.080977 -0.886272 -0.456032 0.895672 0.136026 -0.423402
@3viewid {end}
@3zoom 2.23
@3zslab 310
@3ztran 0
@3center 47.857 57.544 -18.260
@3matrix
0.461943 -0.884632 0.063516 -0.221859 -0.184596 -0.957446 0.858714 0.428194 -0.281536
@4viewid {2 helices}
@4zoom 1.10
@4zslab 200
@4ztran 0
@4center 44.508 58.334 -14.292
@4matrix
0.974233 -0.128440 -0.185402 -0.051655 -0.927227 0.370921 -0.219550 -0.351787 -0.909970
@group {TLN helix}
@subgroup {main ch} dominant
@balllist {mc N hb} color= sky radius= 0.100
{n gln 283}48.411 53.377 -20.964
@vectorlist {mc} color= white
{ca ser 279}P 42.845 51.174 -21.537
{c ser 279}43.787 50.205 -20.859
{o ser 279}43.351 49.441 -19.995
{c ser 279}P 43.787 50.205 -20.859
{n asn 280}45.092 50.327 -21.147
{ca asn 280}46.091 49.475 -20.467
{c asn 280}46.930 50.294 -19.504
{o asn 280}46.684 51.489 -19.350
{c asn 280}P 46.930 50.294 -19.504
{n phe 281}47.921 49.676 -18.843
{ca phe 281}48.656 50.460 -17.829
{c phe 281}49.322 51.696 -18.436
{o phe 281}49.398 52.759 -17.840
{c phe 281}P 49.322 51.696 -18.436
{n ser 282}49.906 51.494 -19.606
{ca ser 282}50.586 52.565 -20.270
{c ser 282}49.632 53.712 -20.602
{o ser 282}49.925 54.891 -20.425
{c ser 282}P 49.632 53.712 -20.602
{n gln 283}48.411 53.377 -20.964
{ca gln 283}47.429 54.419 -21.187
{c gln 283}46.977 55.091 -19.894
{o gln 283}46.730 56.292 -19.870
{c gln 283}P 46.977 55.091 -19.894
{n leu 284}46.906 54.323 -18.794
{ca leu 284}46.566 54.909 -17.535
{c leu 284}47.636 55.962 -17.152
{o leu 284}47.389 57.032 -16.613
{c leu 284}P 47.636 55.962 -17.152
{n arg 285}48.876 55.632 -17.415
{ca arg 285}49.897 56.597 -17.042
{c arg 285}49.691 57.918 -17.801
{o arg 285}49.837 59.000 -17.240
{c arg 285}P 49.691 57.918 -17.801
{n ala 286}49.369 57.822 -19.112
{ca ala 286}49.168 59.006 -19.954
{c ala 286}47.978 59.790 -19.498
{o ala 286}47.991 61.006 -19.415
{c ala 286}P 47.978 59.790 -19.498
{n ala 287}46.994 59.049 -19.026
{ca ala 287}45.796 59.665 -18.508
{c ala 287}46.053 60.414 -17.240
{o ala 287}45.580 61.541 -17.027
{c ala 287}P 46.053 60.414 -17.240
{n ala 288}46.793 59.772 -16.355
{ca ala 288}47.060 60.410 -15.091
{c ala 288}47.935 61.627 -15.270
{o ala 288}47.751 62.636 -14.647
{c ala 288}P 47.935 61.627 -15.270
{n val 289}48.853 61.561 -16.192
{ca val 289}49.698 62.727 -16.444
{c val 289}48.882 63.872 -17.054
{o val 289}48.987 65.027 -16.675
{c val 289}P 48.882 63.872 -17.054
{n gln 290}48.028 63.536 -18.005
{ca gln 290}47.194 64.561 -18.620
{c gln 290}46.281 65.218 -17.639
{o gln 290}46.079 66.434 -17.684
{c gln 290}P 46.281 65.218 -17.639
{n ser 291}45.729 64.411 -16.724
{ca ser 291}44.849 64.941 -15.675
{c ser 291}45.553 65.922 -14.745
{o ser 291}44.990 66.935 -14.340
{c ser 291}P 45.553 65.922 -14.745
{n ala 292}46.731 65.513 -14.262
{ca ala 292}47.489 66.347 -13.371
@subgroup {mc Hbonds} dominant
@vectorlist {mc Hb} color= purple
{leu 284 hn} <1.976>P U 47.076 53.338 -18.773
{asn 280 o}U 46.802 52.044 -19.177
{arg 285 hn} <2.038>P U 49.190 54.786 -17.845
{phe 281 o}U 49.336 53.367 -17.841
{ala 286 hn} <2.325>P U 49.247 56.953 -19.591
{ser 282 o}U 49.722 55.510 -20.175
{ala 287 hn} <1.983>P U 47.003 58.050 -18.993
{gln 283 o}U 46.812 56.819 -19.607
{ala 288 hn} <1.848>P U 47.195 58.865 -16.481
{leu 284 o}U 47.331 57.582 -16.573
{val 289 hn} <1.991>P U 49.040 60.761 -16.762
{arg 285 o}U 49.598 59.528 -17.097
{gln 290 hn} <1.924>P U 47.896 62.609 -18.355
{ala 286 o}U 47.963 61.487 -19.097
{ser 291 hn} <1.933>P U 45.871 63.422 -16.689
{ala 287 o}U 45.667 62.105 -16.926
{ala 292 hn} <2.091>P U 47.155 64.633 -14.476
{ala 288 o}U 47.572 63.235 -14.596
@subgroup {Cbetas} dominant off
@vectorlist {Cb} color= yellowtint
{ca phe 281}P 48.656 50.460 -17.829
{cb phe 281}49.745 49.572 -17.228
{ca ser 282}P 50.586 52.565 -20.270
{cb ser 282}51.415 52.035 -21.422
{ca gln 283}P 47.429 54.419 -21.187
{cb gln 283}46.250 53.862 -21.968
{ca leu 284}P 46.566 54.909 -17.535
{cb leu 284}46.589 53.795 -16.466
{ca arg 285}P 49.897 56.597 -17.042
{cb arg 285}51.282 56.046 -17.280
{ca ala 286}P 49.168 59.006 -19.954
{cb ala 286}48.965 58.560 -21.368
{ca ala 287}P 45.796 59.665 -18.508
{cb ala 287}44.656 58.625 -18.358
{ca ala 288}P 47.060 60.410 -15.091
{cb ala 288}47.691 59.431 -14.137
{ca val 289}P 49.698 62.727 -16.444
{cb val 289}50.884 62.348 -17.356
{ca gln 290}P 47.194 64.561 -18.620
{cb gln 290}46.409 64.002 -19.795
{ca ser 291}P 44.849 64.941 -15.675
{cb ser 291}44.227 63.859 -14.772
{ca ala 292}P 47.489 66.347 -13.371
{cb ala 292}48.780 65.634 -12.871
@subgroup {Asn 280} dominant
@balllist {sc O} color= red radius= 0.100
{od1 asn 280}48.049 50.898 -21.965
@balllist {sc N} color= sky radius= 0.100
{nd2 asn 280}47.964 49.358 -23.567
@vectorlist {sc} color= gold
{ca asn 280}P 46.091 49.475 -20.467
{cb asn 280}46.962 48.783 -21.496
{cg asn 280}47.732 49.773 -22.350
{od1 asn 280}48.049 50.898 -21.965
{cg asn 280}P 47.732 49.773 -22.350
{nd2 asn 280}47.964 49.358 -23.567
@group {new helix} off
@subgroup {} nobutton
@vectorlist {Calphas} color= white
{ ca gly 259 }P 48.890 63.989 -0.636
{ ca arg 260 }45.552 62.104 -0.693
{ ca asp 261 }43.339 64.884 -1.880
{ ca lys 262 }45.330 65.534 -5.019
{ ca leu 263 }45.683 61.792 -5.613
{ ca gly 264 }41.865 61.512 -5.580
{ ca lys 265 }41.432 64.509 -7.851
{ ca ile 266 }43.843 63.257 -10.394
{ ca phe 267 }42.507 59.708 -10.447
{ ca tyr 268 }38.877 60.788 -10.566
{ ca arg 269 }39.638 63.030 -13.494
{ ca ala 270 }41.486 60.311 -15.316
{ ca leu 271 }38.668 57.874 -14.717
{ ca thr 272 }35.860 60.135 -15.773
{ ca gln 273 }37.567 61.945 -18.600
@vectorlist {axis} color= green
{hlx N-t 260}P 46.905 64.748 0.087
{hlx mid} blue 42.087 62.097 -9.079
{hlx C-t 272} red 37.268 59.446 -18.245