@text coordinates from file: 1doz.pdb A dozen residues from T4 Lysozyme illustrates the solvent accessible surface in relation to the actual molecular surface at the van der Waals interaction distance. The CPK space filling representation shows the actual volume occupied by the atoms themselves. The molecular surface as shown is that part of the individual atom's van der Waals surface that a water molecule (standardly taken to be a ball of radius 1.4 Angstroms, the size of an oxygen atom) could actually touch given the structure of the molecule. The solvent accessible surface (as defined by Lee and Richards) is that surface swept out by the center of such a ball, of radius 1.4, as it rolls over the actual molecular surface. The area of the accessible surface is about 4 times the area of the actual contact area on the van der Waals surface of the atoms of the molecule, but in as much as the solvent accessible surface describes the area of possible coverage by water, it is used as a standard to scale interaction energies as a bulk phenomenon. If one is interested in the actual details of which atoms contact each other in the interface between two molecules, then the molecular surface as shown here is a convenient representation. To appreciate the continuous molecular surface, such as shown by the Connelly algorithm (for instance as shown by a GRASP display), use the "draw new" drawline tool in Mage to make dots (two clicks make a zero length line, a dot) on the probe dots that span two atoms when the probe is a special positon of being in contact with two or three atoms. @kinemage 1 @caption Probe V2.1.0 (12/06/99), run Tue Dec 7 11:34:15 1999 command: newprobe -drop -name 1doz.EVS -den16 -rad1.4 -outcol gold -out "not water" 1doz.pdb Probe V2.1.0 (12/06/99), run Tue Dec 7 11:37:59 1999 command: newprobe -drop -name SAS -den16 -rad0 -vdwo1.4 -out "not water" 1doz.pdb @1viewid {overview} @1zoom 1.0 @1zslab 210 @1ztran 0 @1center 42.026 4.732 9.172 @1matrix 0.98110 -0.03418 -0.19047 -0.05002 -0.99561 -0.07906 -0.18693 0.08710 -0.97851 @2viewid {probe roll} @2zoom 3.39 @2zslab 10 @2ztran 0 @2center 41.538 -2.913 9.364 @2matrix 0.99069 0.04573 -0.12818 -0.02847 -0.85134 -0.52383 -0.13308 0.52261 -0.84212 @5matrix {index} 1 0 0 0 1 0 0 0 1 @group {1doz aa} dominant @subgroup {mainchain} @spherelist {n met} color= blue radius= 0.2 { n met 1 B25.34} P 44.078, -3.150, 8.939 @spherelist {o met} color= red radius= 0.2 { o met 1 B22.12} L 41.538, -2.913, 9.364 @vectorlist {mc} color= white { n met 1 B25.34} P 44.078, -3.150, 8.939 { n met 1 B25.34} L 44.078, -3.150, 8.939 { ca met 1 B17.31} L 43.598, -1.791, 9.029 { c met 1 B27.05} L 42.190, -1.891, 9.569 { o met 1 B22.12} L 41.538, -2.913, 9.364 { c met 1 B27.05} P 42.190, -1.891, 9.569 { n asn 2 B21.49} L 41.752, -0.869, 10.290 { ca asn 2 B10.56} L 40.400, -0.803, 10.845 { c asn 2 B18.47} L 40.009, 0.672, 10.869 { o asn 2 B11.01} L 40.851, 1.514, 10.597 { c asn 2 B18.47} P 40.009, 0.672, 10.869 { n ile 3 B11.70} L 38.780, 0.978, 11.232 { ca ile 3 B17.14} L 38.257, 2.328, 11.266 { c ile 3 B22.46} L 39.103, 3.293, 12.113 { o ile 3 B17.10} L 39.324, 4.469, 11.768 { c ile 3 B22.46} P 39.103, 3.293, 12.113 { n phe 4 B9.82} L 39.552, 2.802, 13.266 { ca phe 4 B12.18} L 40.368, 3.616, 14.135 { c phe 4 B16.11} L 41.674, 4.039, 13.500 { o phe 4 B15.81} L 42.056, 5.218, 13.578 { c phe 4 B16.11} P 41.674, 4.039, 13.500 { n glu 5 B13.54} L 42.378, 3.069, 12.916 { ca glu 5 B14.83} L 43.655, 3.360, 12.282 { c glu 5 B23.09} L 43.429, 4.191, 11.042 { o glu 5 B20.52} L 44.236, 4.995, 10.652 { c glu 5 B23.09} P 43.429, 4.191, 11.042 { n met 6 B13.62} L 42.319, 3.973, 10.379 { ca met 6 B10.84} L 42.026, 4.732, 9.172 { c met 6 B27.45} L 41.840, 6.214, 9.512 { o met 6 B14.28} L 42.414, 7.124, 8.886 { c met 6 B27.45} P 41.840, 6.214, 9.512 { n leu 7 B15.26} L 40.985, 6.461, 10.496 { ca leu 7 B16.62} L 40.698, 7.830, 10.925 { c leu 7 B16.82} L 41.906, 8.514, 11.575 { o leu 7 B17.15} L 42.081, 9.723, 11.517 { c leu 7 B16.82} P 41.906, 8.514, 11.575 { n arg 8 B15.80} L 42.739, 7.734, 12.222 { ca arg 8 B18.35} L 43.936, 8.293, 12.834 { c arg 8 B17.23} L 44.899, 8.790, 11.745 { o arg 8 B17.81} L 45.555, 9.806, 11.886 { c arg 8 B17.23} P 44.899, 8.790, 11.745 { n ile 9 B15.76} L 44.917, 8.128, 10.613 { ca ile 9 B13.06} L 45.720, 8.571, 9.490 { c ile 9 B24.43} L 45.127, 9.838, 8.847 { o ile 9 B17.15} L 45.790, 10.812, 8.546 { c ile 9 B24.43} P 45.127, 9.838, 8.847 { n asp 10 B16.82} L 43.829, 9.871, 8.677 { ca asp 10 B13.39} L 43.143, 11.024, 8.072 { c asp 10 B18.15} L 43.089, 12.308, 8.906 { o asp 10 B19.19} L 43.095, 13.402, 8.405 { c asp 10 B18.15} P 43.089, 12.308, 8.906 { n glu 11 B11.68} L 43.016, 12.172, 10.202 { ca glu 11 B22.91} L 42.854, 13.305, 11.072 { c glu 11 B23.19} L 44.102, 13.762, 11.818 { o glu 11 B21.24} L 44.159, 14.914, 12.226 { c glu 11 B23.19} P 44.102, 13.762, 11.818 { n gly 12 B13.78} L 45.045, 12.843, 12.066 { ca gly 12 B16.51} L 46.276, 13.104, 12.809 { c gly 12 B23.28} L 45.959, 13.168, 14.297 { o gly 12 B18.84} L 44.848, 12.855, 14.708 @vectorlist {Calphas} color= white off { ca met 1 B17.31} P 43.598, -1.791, 9.029 { ca met 1 B17.31} L 43.598, -1.791, 9.029 { ca asn 2 B10.56} L 40.400, -0.803, 10.845 { ca ile 3 B17.14} L 38.257, 2.328, 11.266 { ca phe 4 B12.18} L 40.368, 3.616, 14.135 { ca glu 5 B14.83} L 43.655, 3.360, 12.282 { ca met 6 B10.84} L 42.026, 4.732, 9.172 { ca leu 7 B16.62} L 40.698, 7.830, 10.925 { ca arg 8 B18.35} L 43.936, 8.293, 12.834 { ca ile 9 B13.06} L 45.720, 8.571, 9.490 { ca asp 10 B13.39} L 43.143, 11.024, 8.072 { ca glu 11 B22.91} L 42.854, 13.305, 11.072 { ca gly 12 B16.51} L 46.276, 13.104, 12.809 @subgroup {sidechain} @vectorlist {sc} color= cyan { ca met 1 B17.31} P 43.598, -1.791, 9.029 { cb met 1 B19.45} L 43.639, -1.263, 7.589 { cg met 1 B30.24} L 43.029, 0.088, 7.385 { sd met 1 B38.45} L 44.125, 1.384, 7.934 { ce met 1 B39.75} L 45.585, 0.974, 6.978 { ca asn 2 B10.56} P 40.400, -0.803, 10.845 { cb asn 2 B12.29} L 40.303, -1.495, 12.247 { cg asn 2 B23.72} L 41.276, -0.920, 13.234 { od1 asn 2 B15.47} L 41.224, 0.273, 13.538 { cg asn 2 B23.72} P 41.276, -0.920, 13.234 { nd2 asn 2 B15.88} L 42.141, -1.760, 13.760 { ca ile 3 B17.14} P 38.257, 2.328, 11.266 { cb ile 3 B19.90} L 36.735, 2.339, 11.578 { cg1 ile 3 B11.60} L 36.160, 3.753, 11.439 { cd1 ile 3 B9.93} L 36.373, 4.423, 10.061 { cb ile 3 B19.90} P 36.735, 2.339, 11.578 { cg2 ile 3 B9.37} L 36.462, 1.779, 12.984 { ca phe 4 B12.18} P 40.368, 3.616, 14.135 { cb phe 4 B11.01} L 40.617, 2.925, 15.476 { cg phe 4 B19.39} L 39.355, 2.903, 16.322 { cd1 phe 4 B15.83} L 38.482, 1.803, 16.270 { ce1 phe 4 B21.92} L 37.339, 1.764, 17.084 { cz phe 4 B16.53} L 37.061, 2.826, 17.949 { cg phe 4 B19.39} P 39.355, 2.903, 16.322 { cd2 phe 4 B17.67} L 39.051, 3.960, 17.191 { ce2 phe 4 B27.56} L 37.921, 3.920, 18.005 { cz phe 4 B16.53} L 37.061, 2.826, 17.949 { ca glu 5 B14.83} P 43.655, 3.360, 12.282 { cb glu 5 B15.23} L 44.332, 2.082, 11.828 { cg glu 5 B21.28} L 44.642, 1.141, 12.998 { cd glu 5 B37.56} L 45.208, -0.200, 12.531 { oe1 glu 5 B44.63} L 45.319, -0.524, 11.358 { cd glu 5 B37.56} P 45.208, -0.200, 12.531 { oe2 glu 5 B52.26} L 45.557, -0.983, 13.522 { ca met 6 B10.84} P 42.026, 4.732, 9.172 { cb met 6 B9.75} L 40.725, 4.209, 8.586 { cg met 6 B8.11} L 40.327, 4.828, 7.254 { sd met 6 B14.20} L 38.527, 4.587, 6.940 { ce met 6 B11.23} L 38.424, 4.639, 5.136 { ca leu 7 B16.62} P 40.698, 7.830, 10.925 { cb leu 7 B10.97} L 39.460, 7.891, 11.822 { cg leu 7 B13.94} L 38.160, 7.872, 11.041 { cd1 leu 7 B17.62} L 36.974, 7.578, 11.986 { cg leu 7 B13.94} P 38.160, 7.872, 11.041 { cd2 leu 7 B17.88} L 37.953, 9.242, 10.385 { ca arg 8 B18.35} P 43.936, 8.293, 12.834 { cb arg 8 B19.95} L 44.575, 7.332, 13.808 { cg arg 8 B27.22} L 46.012, 7.698, 14.100 { cd arg 8 B43.45} L 46.149, 8.617, 15.311 { ne arg 8 B48.98} L 47.512, 9.082, 15.623 { cz arg 8 B100.00} L 48.333, 9.782, 14.812 { nh1 arg 8 B33.75} L 48.014, 10.123, 13.555 { cz arg 8 B100.00} P 48.333, 9.782, 14.812 { nh2 arg 8 B71.28} L 49.535, 10.146, 15.278 { ca ile 9 B13.06} P 45.720, 8.571, 9.490 { cb ile 9 B20.39} L 45.804, 7.459, 8.460 { cg1 ile 9 B18.53} L 46.802, 6.396, 8.912 { cd1 ile 9 B19.25} L 46.651, 5.155, 8.066 { cb ile 9 B20.39} P 45.804, 7.459, 8.460 { cg2 ile 9 B13.74} L 46.190, 8.000, 7.078 { ca asp 10 B13.39} P 43.143, 11.024, 8.072 { cb asp 10 B13.15} L 41.728, 10.598, 7.628 { cg asp 10 B16.46} L 41.769, 9.853, 6.314 { od1 asp 10 B14.23} L 42.680, 9.965, 5.501 { cg asp 10 B16.46} P 41.769, 9.853, 6.314 { od2 asp 10 B17.55} L 40.763, 9.046, 6.158 { ca glu 11 B22.91} P 42.854, 13.305, 11.072 { cb glu 11 B13.87} L 41.834, 12.899, 12.133 { cg glu 11 B16.41} L 40.458, 12.664, 11.528 { cd glu 11 B25.64} L 39.764, 13.889, 10.995 { oe1 glu 11 B18.90} L 38.725, 13.835, 10.383 { cd glu 11 B25.64} P 39.764, 13.889, 10.995 { oe2 glu 11 B26.27} L 40.351, 15.009, 11.288 @group {1doz CPK} dominant nobutton off master= {CPK} @subgroup {mainchain} @spherelist {mc C} color= green radius= 1.75 nobutton { ca met 1 } L 43.598, -1.791, 9.029 { c met 1 } L 42.190, -1.891, 9.569 { ca asn 2 } L 40.400, -0.803, 10.845 { c asn 2 } L 40.009, 0.672, 10.869 { ca ile 3 } L 38.257, 2.328, 11.266 { c ile 3 } L 39.103, 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42.739, 7.734, 12.222 { n ile 9 } L 44.917, 8.128, 10.613 { n asp 10 } L 43.829, 9.871, 8.677 { n glu 11 } L 43.016, 12.172, 10.202 { n gly 12 } L 45.045, 12.843, 12.066 @spherelist {mc O} color= red radius= 1.4 nobutton { o met 1 } L 41.538, -2.913, 9.364 { o asn 2 } L 40.851, 1.514, 10.597 { o ile 3 } L 39.324, 4.469, 11.768 { o phe 4 } L 42.056, 5.218, 13.578 { o glu 5 } L 44.236, 4.995, 10.652 { o met 6 } L 42.414, 7.124, 8.886 { o leu 7 } L 42.081, 9.723, 11.517 { o arg 8 } L 45.555, 9.806, 11.886 { o ile 9 } L 45.790, 10.812, 8.546 { o asp 10 } L 43.095, 13.402, 8.405 { o glu 11 } L 44.159, 14.914, 12.226 { o gly 12 } L 44.848, 12.855, 14.708 @subgroup {sidechain} @spherelist {sc C} color= green radius= 1.75 nobutton { cb met 1 } L 43.639, -1.263, 7.589 { cg met 1 } L 43.029, 0.088, 7.385 { ce met 1 } L 45.585, 0.974, 6.978 { cb asn 2 } L 40.303, -1.495, 12.247 { cg asn 2 } L 41.276, -0.920, 13.234 { cb ile 3 } L 36.735, 2.339, 11.578 { cg1 ile 3 } L 36.160, 3.753, 11.439 { cd1 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