@text Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure", Second Edition Chapter 1 - THE BUILDING BLOCKS Modified 070830 for KiNG, kinemage 6 needs 4fxn.pdb Contents of file c1Basics-B-KiNG.kin: *{Kin 1}* Polypeptide fragment: rotatable phi,psi, & chi angles (Fig. 1.2,1.6) *{Kin 6}* Exercise in finding dihedral angles & Calpha handedness (Fig. 1.7,1.2) [A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond immediately: 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. If you need an introduction to those functions, try the Demo5_4a-KiNG.kin file. 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 (by David C. Richardson), which runs on Macintosh, PC, or Unix computers, or use KiNG (by Ian Davis & Vincent Chen) which is a Java application and runs whereever Java is implemented. A utility (called PREKIN) helps authors prepare the kinemages. The kinemages for this Supplement were prepared by Jane S. Richardson and David C. Richardson and are copyrighted by them, but are freely available for educational, research, or personal use. Updated programs and more information are available at http://kinemage.biochem.duke.edu] *{Kinemage 1}* illustrates a 5-residue fragment of polypeptide chain, to show its geometry and atom names and to allow rotation of one residue's worth of the variable dihedral angles Phi, Psi, and Chi. Don't forget to rotate the image often, by dragging with the mouse anywhere in the graphics window. Hydrogen atoms (in brown) are included, so this illustrates the full chemical geometry of a protein. Turn them off (with the "H" button box) to see the heavy atoms alone, more typical of what is directly known for most crystal structures since hydrogen atoms diffract x-rays very weakly. Atoms are depicted in this type of "skeletal" or "stick" representation as the intersections or ends of lines which show the chemical connectivity of the molecule. In this case, non-carbon atoms are shown as colored balls (red for O and blue for N), giving a partial "ball&stick" representation. For a skeletal model, one aspect of the basic physical nature of the molecule - namely the chemical bonding arrangement - is explicitly clear, and the model does not hide parts of itself; on the other hand, another important physical aspect - the packing and steric constraints - can only be inferred by the relative position of the atoms. Choose View3 (on the VIEWS pulldown menu) and turn on the "spheres" button temporarily to see a rough space-filling representation, which has the opposite properties of showing how big the atoms are but of hiding things that are inside. Note that in Mage and KiNG you can click on a sphere and identify it. Now turn off the spheres and go back to View1. Selected atom labels can be turned on, or the angle labels turned off, with the botton box controls on the right side of the screen. They identify the atom names along the backbone, or they label the variable dihedral angles that determine conformation. (Of course, an atom can also be identified just by clicking on it, but then the residues will have specific numbers, such as 45 for the Phe, rather than being called n, n+1, etc.) The dihedral angles Phi (around the N-Calpha bond) and Psi (around the Calpha-C bond) of the central Phe residue can be rotated in both Mage and KiNG. Mage uses sliders in a sparate window that comes up when rotatable axes are defined in the kinemage: Clicking in the bar to right or left of the "thumbmark" will change the angle by 10 degrees at a time; clicking on the right or left arrows will change it by one degree. The lower angle value above the slider changes as you change the angle, while the top one stays at the original value. KiNG constructs a Rotation dial box on demand using menu item Tools: Specialty: Suite Rotation: The Suite Rotation box has one dial and a set of axis choices. Mouse dragging around the dial edge changes the angle freely (left button fast, right button slow). Clicking in the + - boxes to right or left of the dial will change the angle by 0.1 degrees at a time for fine control. One angle number below the dial center changes as you change the angle, while the other stays at the original value. A double-click on the dial resets the current angle to its original value. As you change one of the angles, look for positions at which atoms on either side are too close together (that is what determines the allowed conformations). For instance, try setting phi to 0 and psi to 180 - does that look possible? What bumps? The central Phe (residue n) is shown in cyan with a full side chain and a green ball at its Calpha. The Calpha-Cbeta bonds are grouped separately and colored seagreen, both to better illustrate the tetrahedral geometry of the Calpha atom and also to point out that the Cbeta position is fixed with respect to the polypeptide backbone. Were it not for the unique amino acid glycine which lacks a Cbeta, one would probably consider the Cbeta as part of the main chain rather than the side chain. View2 looks down the Cbeta-Calpha bond, showing that the starting conformation is one of the three staggered positions of Chi1 (the first side-chain dihedral angle) expected from simple steric considerations around a carbon-carbon single bond. (One can always return to the startup view by choosing View1.) Try rotating Chi1 and Chi2. *{Kinemage 6}* uses a short segment from flavodoxin, for practice with dihedral angles, the "measure" tool, and amino-acid handedness. The startup view shows just 4 backbone atoms and the bonds between them - this is the minimum for defining a single dihedral angle. Imagine it as a mechanical linkage with stiff bonds and rigid angles of about 120 degrees connecting each pair of bonds, but with something like a rotating sleeve that allows rotation around the central bond. To see this rotation, in Mage: click and hold down the mouse in the horizontal scrollbar in the rotation window (on the arrow for slow motion, and on the scrollbar just inside the arrow for rapid motion); then click and hold at the opposite end to rotate back. In KiNG: select menu item "Tools: Specialty: Suite Rotation to get its dial box on screen. Select the ro1 dihedral, and drag in the dial region to change it. Choose View2 to look down the central bond (move the image back and forth a bit to see both ends of that bond) and rotate the dihedral angle again. This is a "phi" conformational angle, since it is rotation around the N-Calpha bond. Watch the numerical value of phi change as you rotate, and see what the geometry looks like near 180 degrees and near 0 degrees; which one is most extended? Turn on "measures ..." under the "Tools" pulldown menu; the measure function reports the geometry of 4 successive atoms picked, including angles and dihedrals. Choose View1 again. Click on the bottom C atom, then on the 'N' atom (the "dist" part will give the distance between those last 2 atoms picked), then on the 'Calpha' atom (now "angle" will give the in-plane angle defined by the last 3 atoms picked), and finally on the 'C' atom (now "dhdrl" will give the dihedral angle defined by all 4 atoms). In Mage turn the "measure" button on the righthand panel off and then on again, in KiNG type the "m" keyboard key twice (to restart the white lines), and then click on the 4 atoms in the opposite order to verify that the dihedral angle is the same when measured from either direction. Now press the "m" key on the keyboard to get rid of the white measure lines, and click here: *{Kin 6 v=3, m={flavodoxin} on, m={dihedral} off}* to put up a short portion of flavodoxin, including some alpha helix, some extended strand, and the connection between them. Practice identifying backbone atom types N, Calpha, C and O by their geometry and relationships (first with the "side ch" button turned on, and then with it turned off). The biggest clues are that the CO (or "carbonyl") sticks out, and that each entire peptide (the group of 5 atoms from one Calpha to the next) lies in one plane. Practice telling N-to-C-terminal polypeptide chain direction from the fact that the peptide N atom precedes the Calpha, while the CO follows it. Check yourself by clicking on an atom to get its atom name (just "ca" for the Calpha), residue name, and residue number on the information line at the bottom of the screen. The backbone atom type at which the chain turns the most definite corner in 3 dimensions is the Calpha, which is the join between two successive planar peptides. Click on atoms to find the residue numbers for the start and end of this entire segment of structure. Now click on successive Calphas along the chain, and notice the distance between each Calpha pair: to within about 0.1 Angstrom, it is always 3.8A. Choose View4 for a closeup of the extended, or beta-strand, part of the structure. Turn "measures" back on, and starting at the first N (at the very beginning of the chain), click on the first 4 atoms in order along the backbone: N, Calpha, C, and N (but not the O, which sticks out from the continuous line); the dihedral angle displayed after that 4th atom-click is a psi angle (rotation around the Calpha-C bond) for Trp 6, and should read 132.9. Then click on the next atom in order (the next Calpha) to get the near-180 omega dihedral angle around the 6-7 peptide bond: what is its actual value? Then click on the next atom in order (a C) to get the phi angle for Ser 7. [Notice that at each step the white lines produced by the measures function show you which 4 atoms define the currently-displayed dihedral angle. To measure the dihedral around a given bond, you must start one atom BEFORE that bond and finish one atom AFTER the bond.] Choose View5 for a closeup of the helical part. By clicking your way along the backbone (starting at the C atom of residue Gly 10), measure the phi and psi angles of the fully-helical residues 11 to 13. They should be close to -60, -40, and in between each phi,psi pair you should see a near-180 omega angle. Choose View6, to concentrate on the connection between the strand and helix (residues Gly 8, Thr 9, and Gly 10). Because they are not fully in any piece of secondary-structure, their conformations are more variable. Measure their phi,psi angles, looking for one with a positive phi value; which residue is it? what is that phi value? Gly is uniquely able to adopt such conformations, because it has only an H in place of a Cbeta atom; to see why that is true in this particular case, let's construct a hypothetical Cbeta onto this Gly. Mage (using construction tools): First, with measures on, pick the N, C, Calpha, and Cbeta atoms of Thr 9, in that zigzag order, to define normal Cbeta geometry. Now choose "draw new" under the "Edit" menu and turn on the new "construct4" button. Click on the N, C, and then Calpha of the Gly you found with positive phi (Gly 10), and accept the "last measures" default in the resulting dialog box. The construct-line tool draws a Cbeta for the Gly with the same geometry as the reference one you measured for Thr 9. KiNG (using the mutation tool): Mutate the Gly to an Ala. First, type "m" to turn off the measure highlights. Then under the "Tools" menu select "Structural Biology" then "Sidechain mutator". A dialog box comes up in which you need to navigate to where you downloaded the flavodoxin coordinate file 4fxn.pdb, choose this file. Now a full model of flavodoxin overlays the original fragment. Ctrl-click, option-click, or middle-click the Gly Calpha atom: select "Ala". Now there are 2 more little dialog boxes: a ÒModel managerÓ and a box labeled with this mutation. Turn off "refit H's" in the button panel in order to see just the heavy atoms like the Cbeta. That hypothetical Cbeta is just 2.3 A away from another atom (an impossibly close bump distance): which atom is too close? (In KiNG, select "Probe dots" in the "Model manager" dialog box to visualize this collision.) We will now make what would be the Cbeta of a D-amino acid. Mage: Click the "eraselast" button to get rid of the new Cbeta, and click on the N, C, and Calpha of the Gly again, but this time in the construct dialog-box change the 125 dihedral value to -125 and then accept. Turn the "construct" button back off, and press the 'm' key to get rid of the measure lines. KiNG: Under "Tools" menu select "Kin editing":"Fudge Kins" which produces a "Fudge Kins" dialog box. Select "Adjust Dihedral" and "Move One Point". Turn on markers so you can see the atom picking steps. Click in succession 4 particular points of Gly 10: n, c, ca, cb. This last atom picked will be the moved one point. You now have, in effect, a D-Ala residue at position 10. Rotate to look at the D-Ala from its Calpha H direction (the 4th, now-empty, tetrahedral direction from the Calpha); the Calpha should hump slightly toward you. If you have trouble identifying that direction, choose View7. From there, turn on the "corncrib, D" button for labels, and try the "corn crib" test for amino-acid handedness: the 3 branches leaving the Calpha atom should read CO, then R ("r group" of the side chain, in this case your new green Cbeta), and then N around in a clockwise direction for a normal biological L-amino acid, but counter-clockwise for a D-amino acid such as this one you just made. For comparison, try the same thing for the normal L-Thr at position 9: center on its Calpha (turn "pickcenter" on, click that Calpha, and turn pickcenter back off), rotate to look from its H direction, and read off the CO, R, N branches, this time clockwise. If it doesn't seem obvious at first, choose View8 and turn on the "corncrib, L" button for labels. Practice identifying both L and D forms, until you can do it without the help of preset views and labels. Remember that amino-acid handedness has strong effects on larger-scale structures: if we were made of D-amino acids, our alpha helices would be lefthanded, our beta sheets would twist the other way, and our enzymes would be specific for molecules of the opposite chirality. Copyright 1999,2007 Jane S. and David C. Richardson. Permission freely granted for educational, research, and personal use. For program updates and more information, see http://kinemage.biochem.duke.edu. @kinemage 1 @caption (B&T Fig. 1.2, 1.5, 1.6, 1.8) Polypeptide fragment with rotatable Phi, Psi, and Chi angles. Main chain is white, Calpha-Cbeta bonds are seagreen, the Phe side chain is cyan, and H atoms are brown. N and O atoms are marked in blue and red. 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14.415 3.905 @labellist {atom labels} color= yellowtint master= {atom labels} off { O}25.953 13.520 4.118 @labellist {angle labels} color= pinktint master= {angle label} { PSI}27.330 14.240 3.110 @balllist {mc O} color= red radius= 0.140 master= {balls} {o phe 45}25.853 13.421 4.017 @balllist {mc N} color= blue radius= 0.155 master= {balls} {n ala 46}26.658 15.521 4.330 @vectorlist {mc} color= yellowtint {c phe 45}P 26.649 14.315 3.805 {o phe 45}25.853 13.421 4.017 {c phe 45}P 26.649 14.315 3.805 {n ala 46}26.658 15.521 4.330 @spherelist {mc O} color= red master= {spheres} off radius= 1.400 {o phe 45}25.853 13.421 4.017 @spherelist {mc C} color= sea master= {spheres} off radius= 1.650 {c phe 45}26.649 14.315 3.805 @group {Ala n+1} dominant @subgroup {mainchain} @balllist {mc N} color= blue radius= 0.155 master= {balls} {n ala 46}26.658 15.521 4.330 {n ser 47}24.346 16.743 3.630 @balllist {mc O} color= red radius= 0.140 master= {balls} {o ala 46}23.392 16.231 5.655 @vectorlist {mc} color= yellowtint {n ala 46}P 26.658 15.521 4.330 {ca ala 46}25.675 15.808 5.404 {c ala 46}24.367 16.296 4.882 {o ala 46}23.392 16.231 5.655 {c ala 46}P 24.367 16.296 4.882 {n ser 47}24.346 16.743 3.630 @labellist {angle labels} color= pinktint master= {angle label} { Omega}26.652 14.769 4.002 @vectorlist {H} color= brown master= {H} {n ala 46}P 26.658 15.521 4.330 {h ala 46}27.351 16.217 4.054 {ca ala 46}P 25.675 15.808 5.404 {ha ala 46}25.459 14.848 5.823 @subgroup {mc H} master= {H} @labellist {atom labels} color= yellowtint master= {atom labels} off { H n+1}27.351 16.217 4.054 @spherelist {mc H} color= gray master= {spheres} off radius= 1.000 {h ala 46}27.351 16.217 4.054 @spherelist {mc H} color= gray master= {spheres} off radius= 1.170 {ha ala 46}25.459 14.848 5.823 @subgroup {sidechain} master= {side chain} @vectorlist {ca-cb} color= sea {ca ala 46}P 25.675 15.808 5.404 {cb ala 46}26.196 16.712 6.521 @vectorlist {H} color= brown master= {H} {cb ala 46}P 26.196 16.712 6.521 {hb1 ala 46}26.470 17.594 6.138 {cb ala 46}P 26.196 16.712 6.521 {hb2 ala 46}26.985 16.282 6.959 {cb ala 46}P 26.196 16.712 6.521 {hb3 ala 46}25.476 16.855 7.200 @spherelist {sc H} color= gray master= {spheres} master= {H} off radius= 1.170 {hb1 ala 46}26.470 17.594 6.138 {hb2 ala 46}26.985 16.282 6.959 {hb3 ala 46}25.476 16.855 7.200 @subgroup {spheres} master= {spheres} off @spherelist {mc N} color= blue radius= 1.550 {n ala 46}26.658 15.521 4.330 {n ser 47}24.346 16.743 3.630 @spherelist {mc O} color= red radius= 1.400 {o ala 46}23.392 16.231 5.655 @spherelist {mc CA} color= sea radius= 1.750 {ca ala 46}25.675 15.808 5.404 @spherelist {mc CO} color= sea radius= 1.650 {c ala 46}24.367 16.296 4.882 @spherelist {CB} color= sea master= {side chain} radius= 1.750 {cb ala 46}26.196 16.712 6.521 @subgroup {asn 46} master= {mutations} master= {side chain} off @vectorlist {asn 46} color= sea {cb asn 46}P 26.196 16.712 6.521 {cg asn 46} 27.396 16.058 7.187 {cg asn 46}P 27.396 16.058 7.187 {od1 asn 46} 28.526 16.263 6.781 {cg asn 46}P 27.396 16.058 7.187 {nd2 asn 46} 27.079 15.274 8.216 @vectorlist {leu 44 H} color= brown master= {H} {nd2 asn 46}P 27.079 15.274 8.216 {hd21 asn 46} 26.124 15.125 8.529 {nd2 asn 46}P 27.079 15.274 8.216 {hd22 asn 46} 27.770 14.768 8.763 @group {to n+2} dominant @subgroup {mainchain} @balllist {mc N} color= blue radius= 0.155 master= {balls} {n ser 47}24.346 16.743 3.630 @vectorlist {mc} color= yellowtint {n ser 47}P 24.346 16.743 3.630 {ca ser 47}23.079 17.207 3.070 @subgroup {mc H} master= {H} @vectorlist {mc H} color= brown {n ser 47}P 24.346 16.743 3.630 {d ser 47}25.189 16.759 3.061 @spherelist {mc H} color= gray master= {spheres} off radius= 1.000 {d ser 47}25.189 16.759 3.061 @subgroup {spheres} master= {spheres} off @spherelist {mc N} color= blue radius= 1.550 {n ser 47}24.346 16.743 3.630 @spherelist {mc CA} color= sea radius= 1.750 {ca ser 47}23.079 17.207 3.070 @kinemage 6 @caption A short segment modified from flavodoxin for practice with dihedral angles, the "measure" tool, and amino-acid handedness. Follow directions in text window. @listcolordominant @onewidth @perspective @viewid {dihedral} @zoom 4.30 @zslab 170 @ztran 0 @center 37.350 10.122 11.378 @matrix -0.546780 0.152090 0.823350 -0.284180 -0.958710 -0.011620 0.787580 -0.240330 0.567420 @2viewid {down bond} @2zoom 4.30 @2zslab 170 @2center 37.350 10.122 11.378 @2matrix 0.259620 -0.947900 0.184640 -0.599050 -0.308050 -0.739090 0.757460 0.081270 -0.647810 @3viewid {overview} @3zoom 1.00 @3zslab 183 @3center 32.810 8.600 9.210 @3matrix -0.994955 0.076319 0.065110 -0.099660 -0.826220 -0.554462 0.011480 -0.558153 0.829658 @4viewid {close beta} @4zoom 2.00 @4zslab 200 @4center 34.587 7.758 9.183 @4matrix -0.983302 0.075400 0.165625 -0.156482 -0.814943 -0.558015 0.092900 -0.574614 0.813135 @5viewid {close hlx} @5zoom 2.00 @5zslab 220 @5center 29.164 10.492 8.803 @5matrix -0.798970 0.102180 0.592630 -0.245680 -0.954930 -0.166570 0.548900 -0.278680 0.788060 @6viewid {close turn} @6zoom 2.00 @6zslab 200 @6center 31.399 6.755 6.501 @6matrix -0.990994 0.082282 0.105640 -0.125150 -0.849710 -0.512182 0.047620 -0.520790 0.852355 @7viewid {Gly 10 H} @7zoom 3.23 @7zslab 200 @7center 29.941 8.048 6.480 @7matrix -0.215050 -0.723040 -0.656480 -0.965360 0.259080 0.030880 0.147750 0.640380 -0.753710 @8viewid {Thr 9 H} @8zoom 3.23 @8zslab 200 @8center 31.247 4.572 5.606 @8matrix -0.781350 -0.483060 0.395150 -0.515050 0.856670 0.028810 -0.352430 -0.181020 -0.918160 @master {flavodoxin} @master {dihedral} @group {flavodoxin} master= {flavodoxin} off @subgroup {main ch} dominant @vectorlist {mc} color= pink {n trp 6}P 37.231 10.664 11.864 {ca trp 6}37.469 9.581 10.893 {c trp 6}36.171 8.792 10.724 {o trp 6}35.403 8.667 11.710 {c trp 6}P 36.171 8.792 10.724 {n ser 7}35.799 8.529 9.488 {ca ser 7}34.587 7.758 9.183 {c ser 7}34.829 6.799 8.020 {o ser 7}35.492 7.188 7.029 {c ser 7}P 34.829 6.799 8.020 {n gly 8}34.398 5.568 8.174 {ca gly 8}34.677 4.503 7.201 {c gly 8}33.588 4.343 6.149 {o gly 8}33.884 4.044 4.967 {c gly 8}P 33.588 4.343 6.149 {n thr 9}32.374 4.649 6.542 {ca thr 9}31.247 4.572 5.606 {c thr 9}30.392 5.839 5.587 {o thr 9}29.334 5.854 4.911 {c thr 9}P 30.392 5.839 5.587 {n gly 10}30.655 6.755 6.501 {ca gly 10}29.941 8.048 6.480 {c gly 10}29.148 8.400 7.740 {o gly 10}28.482 9.465 7.770 {c gly 10}P 29.148 8.400 7.740 {n asn 11}28.988 7.415 8.601 {ca asn 11}28.141 7.556 9.800 {c asn 11}28.647 8.612 10.783 {o asn 11}27.860 9.468 11.260 {c asn 11}P 28.647 8.612 10.783 {n thr 12}29.905 8.477 11.151 {ca thr 12}30.544 9.453 12.043 {c thr 12}30.713 10.781 11.321 {o thr 12}30.539 11.865 11.930 {c thr 12}P 30.713 10.781 11.321 {n glu 13}30.795 10.677 10.017 {ca glu 13}30.869 11.903 9.232 {c glu 13}29.558 12.684 9.314 {o glu 13}29.576 13.931 9.469 {c glu 13}P 29.558 12.684 9.314 {n lys 14}28.454 11.958 9.242 {ca lys 14}27.136 12.605 9.358 {c lys 14}26.970 13.227 10.742 {o lys 14}26.501 14.386 10.860 @subgroup {side ch} dominant @labellist {gly} color= cyan {Gly} <8>34.677 4.503 7.201 {"} <10>29.941 8.048 6.480 @vectorlist {sc} color= cyan {ca trp 6}P 37.469 9.581 10.893 {cb trp 6}38.599 8.640 11.338 {cg trp 6}38.946 7.624 10.223 {cd1 trp 6}39.862 7.727 9.239 {ne1 trp 6}39.803 6.591 8.402 {ce2 trp 6}38.909 5.807 8.859 {ne1 trp 6}39.803 6.591 8.402 {cg trp 6}P 38.946 7.624 10.223 {cd2 trp 6}38.364 6.362 10.045 {ce2 trp 6}38.909 5.807 8.859 {cz2 trp 6}38.492 4.596 8.330 {ch2 trp 6}37.497 3.946 9.058 {cd2 trp 6}P 38.364 6.362 10.045 {ce3 trp 6}37.375 5.702 10.761 {cz3 trp 6}36.957 4.481 10.231 {ch2 trp 6}37.497 3.946 9.058 {ca ser 7}P 34.587 7.758 9.183 {cb ser 7}33.478 8.735 8.813 {og ser 7}32.266 8.027 8.592 {ca thr 9}P 31.247 4.572 5.606 {cb thr 9}30.355 3.365 5.895 {og1 thr 9}29.479 3.665 6.971 {cb thr 9}P 30.355 3.365 5.895 {cg2 thr 9}31.122 2.071 6.170 {ca asn 11}P 28.141 7.556 9.800 {cb asn 11}27.941 6.212 10.506 {cg asn 11}27.136 5.243 9.636 {od1 asn 11}27.070 4.024 9.917 {cg asn 11}P 27.136 5.243 9.636 {nd2 asn 11}26.521 5.764 8.600 {ca thr 12}P 30.544 9.453 12.043 {cb thr 12}31.911 8.975 12.528 {og1 thr 12}31.772 7.711 13.165 {cb thr 12}P 31.911 8.975 12.528 {cg2 thr 12}32.549 9.957 13.509 {ca glu 13}P 30.869 11.903 9.232 {cb glu 13}31.239 11.611 7.781 {cg glu 13}31.308 12.901 6.968 {cd glu 13}31.768 12.631 5.538 {oe1 glu 13}31.648 11.482 5.047 {cd glu 13}P 31.768 12.631 5.538 {oe2 glu 13}32.207 13.594 4.862 {ca lys 14}P 27.136 12.605 9.358 {cb lys 14}25.992 11.620 9.106 {cg lys 14}24.607 12.280 9.129 {cd lys 14}24.282 13.051 7.849 {ce lys 14}23.010 13.888 7.992 {nz lys 14}22.967 14.919 6.945 @group {corncrib L} dominant off @subgroup {} nobutton @labellist {crib,l} color= white {N} <9>32.374 4.649 6.542 {'R'} <9>30.355 3.365 5.895 {CO} <9>30.392 5.839 5.587 @group {corncrib D} dominant off @subgroup {} nobutton @labellist {crib,d} color= yellow {N} <10>30.655 6.755 6.501 {'R'} <10>30.918 9.180 6.165 {CO} <10>29.148 8.400 7.740 @group {dihedral} master= {dihedral} @subgroup {rotation} dominant @labellist {st lbl} color= greentint {C}36.171 8.792 10.724 {Calpha}37.469 9.581 10.893 {N}37.231 10.664 11.864 @vectorlist {rot} color= green {c trp 6}P 36.171 8.792 10.724 {ca trp 6}37.469 9.581 10.893 @vectorlist {ro1} color= green 1bondrot -125.2 {ca trp 6}P 37.469 9.581 10.893 {n trp 6}37.231 10.664 11.864 @vectorlist {ro} color= green {n trp 6}P 37.231 10.664 11.864 {c tyr 5}37.479 11.931 11.580 @labellist {rot lbl} color= greentint {C}37.479 11.931 11.580