Contacts of the helix formed by residues 1135 - 1161 (chain D) in PDB entry 5YWB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS1135 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D GLN* 5.5 5.8 - - - -
430D TRP* 4.9 20.6 + + - -
598D ARG* 3.6 32.1 + - - -
599D SER* 5.9 0.2 + - - -
602D LYS* 5.3 5.6 - - - -
1130D ASN* 4.1 5.3 + - + -
1131D THR* 2.7 42.4 + - + +
1134D GLN* 1.3 77.2 - - + +
1136D ILE* 1.3 61.3 + - - +
1137D PRO* 3.4 1.8 - - - -
1138D SER* 3.5 4.2 + - - -
1139D THR* 3.2 31.0 + - - -
1304D ASP* 5.8 1.3 - - - -
1308D GLN* 3.4 19.1 - - - +
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Residues in contact with ILE1136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004D TYR* 4.5 22.4 - - + +
1090D GLY* 5.0 12.1 - - - +
1093D VAL* 5.9 2.0 - - + -
1131D THR* 3.0 5.9 + - + +
1132D ILE* 3.2 40.8 - - + +
1135D HIS* 1.3 76.4 - - - +
1137D PRO* 1.4 67.5 - - + +
1140D LEU* 2.9 42.5 + - + +
1305D MET* 5.8 3.4 - - + +
1308D GLN* 3.2 40.8 + - + +
1309D LEU* 5.0 1.1 - - + +
1312D VAL* 4.3 21.8 - - + -
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Residues in contact with PRO1137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086D VAL* 4.3 12.1 - - + +
1087D GLU* 4.2 24.0 - - - +
1090D GLY* 4.9 16.4 - - - -
1132D ILE 3.8 5.8 - - - +
1133D ASP 4.0 12.3 - - - +
1134D GLN 3.9 5.4 - - - +
1135D HIS 3.4 9.9 - - - +
1136D ILE* 1.4 102.2 - - + +
1138D SER* 1.3 62.8 + - - +
1140D LEU* 3.9 4.2 - - + +
1141D GLU* 2.9 27.5 + - - +
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Residues in contact with SER1138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591D PHE* 6.3 1.3 - - - -
595D SER* 4.1 21.5 - - - -
598D ARG* 4.3 11.5 + - - -
1087D GLU* 6.1 0.2 - - - -
1134D GLN 4.0 11.3 + - - -
1135D HIS* 3.5 10.0 + - - -
1137D PRO* 1.3 81.3 - - - +
1139D THR* 1.3 65.5 + - - +
1141D GLU* 3.8 3.5 - - - +
1142D CYS* 2.9 40.0 + - - -
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Residues in contact with THR1139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135D HIS* 3.2 20.2 + - - +
1138D SER* 1.3 83.0 + - - +
1140D LEU* 1.3 58.3 + - - +
1142D CYS* 3.8 5.3 - - - +
1143D LEU* 2.9 28.2 + - - +
1301D ASN* 3.9 12.2 + - - +
1304D ASP* 2.7 45.3 + - + +
1305D MET* 3.9 15.3 - - + +
1308D GLN* 3.2 13.2 + - - +
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Residues in contact with LEU1140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004D TYR* 4.1 20.2 - - + +
1016D LEU* 5.6 10.5 - - + -
1086D VAL* 5.5 9.2 - - + -
1089D THR* 5.8 6.5 - - + -
1136D ILE* 2.9 28.6 + - + +
1137D PRO* 3.9 3.4 - - + +
1139D THR* 1.3 78.8 - - - +
1141D GLU* 1.3 57.6 + - - +
1143D LEU* 3.3 8.7 + - + +
1144D SER* 3.0 41.0 + - - +
1305D MET* 4.2 31.6 - - + -
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Residues in contact with GLU1141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D ILE* 5.7 3.6 - - + +
591D PHE* 4.4 21.9 - - + -
1016D LEU* 5.6 0.3 - - - +
1020D GLN* 2.8 34.0 + - - +
1082D THR* 5.0 3.1 + - - -
1083D SER* 5.1 9.4 + - - +
1086D VAL* 3.2 29.7 - - + +
1137D PRO 2.9 18.5 + - - +
1138D SER* 3.9 3.6 - - - +
1140D LEU* 1.3 77.8 - - - +
1142D CYS* 1.3 58.1 + - - +
1144D SER* 3.3 5.6 + - - +
1145D ARG* 2.9 35.6 + - + +
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Residues in contact with CYS1142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591D PHE* 3.4 34.1 - - - -
592D LEU* 5.7 3.4 - - - -
595D SER* 5.5 2.2 - - - -
1138D SER* 2.9 30.1 + - - +
1139D THR* 3.9 4.5 - - - +
1141D GLU* 1.3 76.5 - - - +
1143D LEU* 1.3 57.8 + - - +
1145D ARG* 3.4 13.1 + - - +
1146D SER* 2.9 33.8 + - - -
1297D TRP* 4.5 11.2 - - - +
1301D ASN* 3.2 20.2 - - - +
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Residues in contact with LEU1143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139D THR 2.9 17.7 + - - +
1140D LEU* 3.5 9.9 - - + +
1141D GLU 3.2 0.2 - - - -
1142D CYS* 1.3 76.6 - - - +
1144D SER* 1.3 63.7 + - - +
1146D SER* 3.3 1.4 + - - -
1147D THR* 2.9 24.5 + - + +
1298D MET* 3.5 33.5 - - + +
1301D ASN* 3.6 12.7 + - + +
1302D LEU* 3.4 36.6 - - + +
1305D MET* 3.5 44.0 - - + -
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Residues in contact with SER1144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016D LEU* 5.0 9.4 - - - +
1020D GLN* 4.6 13.7 - - - -
1140D LEU* 3.0 27.5 + - - +
1141D GLU* 3.7 13.9 - - - -
1143D LEU* 1.3 77.5 - - - +
1145D ARG* 1.3 62.6 + - - +
1147D THR* 3.0 12.3 - - - +
1148D LEU* 3.0 31.8 + - - +
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Residues in contact with ARG1145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D VAL* 5.8 4.9 - - - +
588D THR* 4.9 9.3 + - - +
591D PHE* 3.6 49.9 - - - +
592D LEU* 5.7 0.4 - - - +
1020D GLN* 4.8 3.0 + - - +
1024D HIS* 3.8 19.1 + - + +
1141D GLU* 2.9 26.5 + - + +
1142D CYS* 3.7 10.6 + - - +
1144D SER* 1.3 76.7 - - - +
1146D SER* 1.3 57.2 + - - +
1148D LEU* 3.4 0.8 + - - -
1149D LEU* 2.9 49.9 + - + +
1294D TYR* 4.1 25.7 + - - -
1297D TRP* 4.1 29.5 - - - +
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Residues in contact with SER1146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142D CYS 2.9 17.8 + - - -
1143D LEU* 3.8 0.9 - - - -
1144D SER 3.3 0.2 - - - -
1145D ARG* 1.3 79.5 + - - +
1147D THR* 1.3 57.8 + - - +
1149D LEU* 3.2 11.0 + - - +
1150D CYS* 2.9 33.1 + - - -
1294D TYR* 4.2 11.6 - - - +
1297D TRP* 3.3 24.5 + - - -
1298D MET* 3.6 33.2 - - - -
1301D ASN* 3.6 1.1 + - - -
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Residues in contact with THR1147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143D LEU* 2.9 13.3 + - + +
1144D SER* 3.0 25.6 - - - +
1146D SER* 1.3 76.1 - - - +
1148D LEU* 1.3 67.4 + - + +
1150D CYS* 3.3 6.8 + - - +
1151D VAL* 3.0 35.5 + - + +
1298D MET* 3.3 28.7 - - - +
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Residues in contact with LEU1148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020D GLN* 3.4 36.8 - - + +
1021D LEU* 3.5 31.6 - - + -
1024D HIS* 3.4 45.1 - - + +
1144D SER* 3.0 21.1 + - - +
1145D ARG 3.8 0.2 - - - +
1147D THR* 1.3 83.0 - - + +
1149D LEU* 1.3 61.2 + - - +
1151D VAL* 3.3 12.1 + - + +
1152D SER* 2.9 29.5 + - - -
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Residues in contact with LEU1149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584D HIS* 4.7 13.9 - - + +
1024D HIS* 4.0 18.4 - - + +
1027D LEU* 4.7 14.6 - - + -
1145D ARG* 2.9 38.0 + - + +
1146D SER* 3.5 4.7 - - - +
1148D LEU* 1.3 76.8 - - - +
1150D CYS* 1.3 57.4 + - - +
1152D SER* 3.3 7.3 + - - -
1153D ALA* 2.9 29.9 + - - +
1287D TYR* 5.3 0.5 - - - -
1290D MET* 4.8 11.2 - - + -
1291D VAL* 5.3 1.1 - - - -
1294D TYR* 3.5 52.0 - - + +
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Residues in contact with CYS1150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146D SER 2.9 18.3 + - - -
1147D THR* 3.6 9.9 - - - +
1148D LEU 3.3 0.2 - - - -
1149D LEU* 1.3 77.0 - - - +
1151D VAL* 1.3 62.1 + - + +
1153D ALA* 3.3 1.4 + - - +
1154D LEU* 3.0 25.8 + - - +
1291D VAL* 4.1 25.9 - - + +
1294D TYR* 4.1 22.0 - - - -
1295D LEU* 4.5 11.2 - - - -
1298D MET* 4.1 15.3 - - - -
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Residues in contact with VAL1151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147D THR* 3.0 28.0 + - - +
1148D LEU* 3.6 14.1 - - + +
1149D LEU 3.3 0.2 - - - -
1150D CYS* 1.3 77.1 - - + +
1152D SER* 1.3 62.5 + - - +
1154D LEU* 3.4 4.5 + - - +
1155D THR* 2.9 37.7 + - - +
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Residues in contact with SER1152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024D HIS* 5.2 10.8 - - - -
1027D LEU* 5.9 3.0 - - - +
1028D VAL* 3.4 26.9 + - - +
1148D LEU 2.9 17.6 + - - -
1149D LEU* 3.6 9.0 - - - -
1151D VAL* 1.3 78.7 - - - +
1153D ALA* 1.3 57.0 + - - +
1155D THR* 3.3 4.6 + - - -
1156D VAL* 2.9 34.3 + - - +
1287D TYR* 3.1 21.7 + - - -
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Residues in contact with ALA1153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149D LEU 2.9 17.3 + - - +
1150D CYS 3.8 2.2 - - - +
1151D VAL 3.3 0.2 - - - -
1152D SER* 1.3 73.7 - - - +
1154D LEU* 1.3 65.7 + - - +
1156D VAL* 3.3 1.4 + - - +
1157D ILE* 3.0 31.0 + - + +
1287D TYR* 3.5 28.9 - - + +
1290D MET* 5.8 0.9 - - + -
1291D VAL* 3.5 35.7 - - + +
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Residues in contact with LEU1154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150D CYS 3.0 17.4 + - - +
1151D VAL* 3.9 4.7 - - - +
1153D ALA* 1.3 76.3 - - - +
1155D THR* 1.3 68.5 + - - +
1157D ILE* 3.4 5.9 + - - +
1158D SER* 2.9 31.7 + - - +
1164D PHE* 6.0 2.5 - - + -
1165D LEU* 5.5 3.6 - - + -
1168D LEU* 4.0 38.4 - - + -
1291D VAL* 5.6 0.2 - - - +
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Residues in contact with THR1155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028D VAL* 6.0 4.3 - - + -
1151D VAL* 2.9 28.4 + - - +
1152D SER* 3.7 5.2 - - - -
1154D LEU* 1.3 81.1 - - - +
1156D VAL* 1.3 58.9 + - + +
1158D SER* 2.6 23.5 + - - +
1159D TYR* 2.9 17.6 + - + +
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Residues in contact with VAL1156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028D VAL* 3.6 28.3 - - + -
1032D TYR* 6.3 1.3 - - + -
1152D SER 2.9 21.2 + - - +
1153D ALA 3.8 4.0 - - - +
1154D LEU 3.3 0.2 - - - -
1155D THR* 1.3 77.1 - - + +
1157D ILE* 1.3 63.9 + - - +
1159D TYR* 3.1 7.6 + - - +
1160D VAL* 2.9 32.2 + - + +
1283D LEU* 3.9 30.1 - - + +
1284D GLY* 4.4 0.4 - - - +
1287D TYR* 3.5 38.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE1157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153D ALA 3.0 22.7 + - - +
1154D LEU* 4.0 4.9 - - - +
1156D VAL* 1.3 75.5 - - - +
1158D SER* 1.3 62.2 + - - +
1160D VAL* 3.2 21.3 - - + +
1161D THR* 3.2 14.7 + - - +
1164D PHE* 3.9 39.0 - - + -
1259D VAL* 5.7 4.9 - - + -
1260D VAL* 6.2 0.2 - - - -
1263D ALA* 4.2 15.3 - - + -
1284D GLY* 4.1 16.6 - - - +
1287D TYR* 4.7 3.6 - - + -
1288D ALA* 3.8 34.1 - - + +
1291D VAL* 5.1 5.6 - - + -
----------------------------------------------------------
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Residues in contact with SER1158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154D LEU* 2.9 20.7 + - - +
1155D THR* 2.6 28.6 + - - +
1157D ILE* 1.3 78.4 - - - +
1159D TYR* 1.3 60.6 + - - +
1161D THR 3.2 20.9 - - - +
1162D PRO* 3.5 9.4 - - - +
1164D PHE* 5.2 6.5 - - - -
1165D LEU* 4.5 26.0 - - - +
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Residues in contact with TYR1159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032D TYR* 6.6 0.2 - - + -
1155D THR* 2.9 19.2 + - + +
1156D VAL* 3.1 6.9 + - - +
1158D SER* 1.3 79.3 + - - +
1160D VAL* 1.3 68.8 + - + +
1161D THR 3.5 0.2 + - - -
1162D PRO* 4.1 9.9 - - - +
1280D LEU* 4.4 23.2 - - + +
1283D LEU* 6.2 2.2 - - + -
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Residues in contact with VAL1160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156D VAL* 2.9 21.8 + - + +
1157D ILE* 3.2 21.8 - - + +
1159D TYR* 1.3 81.7 - - + +
1161D THR* 1.3 77.4 + - + +
1162D PRO* 3.9 4.2 - - - +
1267D SER* 5.0 4.9 - - - +
1271D SER* 5.5 2.8 - - - -
1275D GLU* 5.1 7.3 - - - +
1280D LEU* 3.5 59.6 - - + +
1283D LEU* 4.3 5.8 - - + -
1284D GLY* 4.1 20.6 - - - +
----------------------------------------------------------
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Residues in contact with THR1161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157D ILE* 3.2 16.6 + - - +
1158D SER* 3.2 9.8 - - - +
1160D VAL* 1.3 93.5 - - + +
1162D PRO* 1.3 61.9 - - - +
1163D VAL* 2.9 24.5 + - + -
1164D PHE* 3.1 21.7 + - - +
1165D LEU 4.8 0.3 + - - -
1263D ALA* 5.5 0.5 + - - -
1266D THR* 4.6 10.2 + - - +
1267D SER* 4.2 29.8 + - - +
1270D ASN* 5.3 4.3 - - + -
1271D SER* 5.2 8.3 - - - -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il