Contacts of the helix formed by residues 1108 - 1129 (chain C) in PDB entry 2ZM3
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 SER1108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106C PRO 3.7 2.4 + - - -
1107C PRO* 1.3 76.3 - - - +
1109C LEU* 1.3 66.3 + - - +
1110C SER* 3.8 9.7 + - - -
1111C LYS* 3.1 33.2 + - - +
1112C MET* 3.0 22.6 + - - +
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Residues in contact with LEU1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108C SER* 1.3 73.2 - - - +
1110C SER* 1.3 58.0 + - - +
1112C MET* 3.1 6.5 + - - +
1113C ILE* 2.9 39.2 + - + +
1238C PRO* 3.7 37.5 - - + -
1240C MET* 3.7 33.2 - - + -
1241C LEU* 4.1 9.4 - - + -
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Residues in contact with SER1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108C SER* 3.8 9.0 + - - -
1109C LEU* 1.3 79.1 - - - +
1111C LYS* 1.3 59.5 + - - +
1113C ILE* 3.8 11.5 - - - +
1114C GLN* 3.2 23.4 + - - +
1269C GLU* 4.7 23.1 - - - +
1271C GLU* 5.3 2.3 - - - +
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Residues in contact with LYS1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105C ALA 5.7 3.0 + - - +
1106C PRO 5.9 0.4 + - - -
1107C PRO* 4.2 10.7 - - + +
1108C SER* 3.1 34.7 + - - +
1110C SER* 1.3 77.6 + - - +
1112C MET* 1.3 61.1 + - - +
1113C ILE 3.2 0.4 - - - -
1114C GLN* 3.8 6.7 - - + +
1115C MET* 3.1 38.6 + - + +
1271C GLU* 5.6 5.6 - - - +
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Residues in contact with MET1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107C PRO* 3.7 31.2 - - + +
1108C SER 3.0 15.9 + - - +
1109C LEU* 3.5 9.2 - - - +
1111C LYS* 1.3 78.1 - - - +
1113C ILE* 1.3 57.3 + - - +
1115C MET* 3.6 7.9 + - - +
1116C ALA* 3.1 28.2 + - - +
1202C LEU* 5.3 0.2 - - - +
1205C ILE* 3.3 45.9 - - + +
1206C ALA* 3.9 12.3 - - + +
1208C LEU* 5.4 1.6 - - + -
1238C PRO* 4.7 13.9 - - + -
1241C LEU* 3.6 33.6 - - + +
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Residues in contact with ILE1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C LEU* 2.9 31.8 + - + +
1110C SER* 3.9 8.7 - - - +
1112C MET* 1.3 75.8 - - - +
1114C GLN* 1.3 59.4 + - - +
1116C ALA* 3.2 5.0 + - + +
1117C GLY* 2.9 25.8 + - - -
1240C MET* 3.4 42.2 - - + -
1241C LEU* 3.9 13.9 - - + -
1244C LEU* 5.9 0.7 - - + -
1266C ILE* 3.9 34.2 - - + +
1269C GLU* 3.9 25.6 - - + +
1270C MET* 3.6 7.5 - - - +
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Residues in contact with GLN1114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110C SER 3.2 16.6 + - - +
1111C LYS* 3.8 8.3 - - - +
1112C MET 3.4 0.2 - - - -
1113C ILE* 1.3 79.9 - - - +
1115C MET* 1.3 63.8 + - + +
1117C GLY 3.5 0.2 + - - -
1118C GLU* 2.9 60.2 + - - +
1147C PHE 6.1 0.2 - - - +
1269C GLU 4.5 1.2 + - - +
1270C MET* 3.6 24.2 - - - +
1271C GLU* 2.9 60.6 + - - +
1274C PHE* 4.9 6.5 - - - +
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Residues in contact with MET1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087C LEU* 4.2 22.7 - - + -
1090C TYR* 5.0 8.7 - - + -
1091C LEU* 4.7 9.0 - - + -
1107C PRO* 3.7 29.6 - - + -
1111C LYS* 3.1 33.8 + - + +
1112C MET* 3.7 9.4 - - - +
1113C ILE 3.3 0.2 - - - -
1114C GLN* 1.3 76.5 - - + +
1116C ALA* 1.3 63.0 + - - +
1118C GLU* 3.4 9.3 + - - +
1119C ILE* 3.1 32.5 + - + +
1143C VAL* 6.1 0.2 - - - -
1147C PHE 5.1 3.8 - - - +
1149C VAL* 3.3 20.9 - - + -
1205C ILE* 4.2 22.7 - - + -
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Residues in contact with ALA1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C MET 3.1 18.9 + - - +
1113C ILE* 3.2 7.6 + - + +
1115C MET* 1.3 74.3 - - - +
1117C GLY* 1.3 64.9 + - - +
1119C ILE* 3.6 3.5 + - - -
1120C ALA* 3.0 25.5 + - - +
1198C PHE* 3.4 16.0 - - + -
1202C LEU* 3.6 28.5 - - + -
1205C ILE* 4.9 1.5 - - + +
1241C LEU* 5.2 4.0 - - + -
1244C LEU* 5.8 3.4 - - + -
1266C ILE* 4.5 8.5 - - + -
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Residues in contact with GLY1117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113C ILE 2.9 15.4 + - - -
1116C ALA* 1.3 76.0 - - - +
1118C GLU* 1.3 52.4 + - - +
1120C ALA* 3.3 4.8 + - - +
1121C ASP* 2.8 36.8 + - - +
1263C ILE* 4.1 7.0 - - - +
1266C ILE* 3.8 17.8 - - - +
1270C MET* 3.8 17.0 - - - -
1274C PHE* 4.3 2.3 - - - -
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Residues in contact with GLU1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C HIS* 3.4 37.6 + - + +
1114C GLN* 2.9 53.8 + - - +
1115C MET* 3.8 4.6 - - - +
1116C ALA 3.3 0.2 - - - -
1117C GLY* 1.3 76.6 - - - +
1119C ILE* 1.3 60.1 + - - +
1121C ASP* 3.4 2.2 + - - -
1122C GLY* 3.2 17.0 + - - -
1147C PHE 4.3 1.4 - - - +
1148C THR* 3.8 19.2 + - - +
1149C VAL* 2.9 49.8 + - - +
1150C LYS* 5.6 0.2 - - - -
1270C MET* 4.0 4.5 - - + +
1274C PHE* 5.1 0.2 - - + -
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Residues in contact with ILE1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087C LEU* 4.0 18.4 - - + -
1115C MET* 3.1 21.4 + - + +
1116C ALA* 4.0 5.2 - - - +
1117C GLY 3.3 0.2 - - - -
1118C GLU* 1.3 73.0 - - - +
1120C ALA* 1.3 65.1 + - - +
1122C GLY 3.3 0.2 + - - -
1123C MET* 3.1 22.8 + - + +
1136C LEU* 4.1 24.5 - - + -
1141C CYS* 4.2 8.7 - - - -
1149C VAL* 3.7 28.0 - - + -
1151C ILE* 3.2 17.3 - - + +
1198C PHE* 4.0 18.6 - - + -
1201C VAL* 4.2 17.9 - - + -
1205C ILE* 4.5 6.1 - - + -
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Residues in contact with ALA1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C ALA 3.0 18.9 + - - +
1117C GLY* 3.6 4.3 - - - +
1119C ILE* 1.3 77.1 - - - +
1121C ASP* 1.3 58.3 + - - +
1123C MET* 3.2 1.9 + - - +
1124C ALA* 2.8 31.5 + - - +
1198C PHE* 3.8 14.7 - - + -
1259C PHE* 3.7 22.4 - - + +
1262C ILE* 4.3 10.1 - - + -
1263C ILE* 3.7 18.8 - - + -
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Residues in contact with ASP1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C CYS* 4.2 3.6 - - - -
1061C HIS* 2.7 32.3 + - + +
1117C GLY 2.8 20.9 + - - +
1118C GLU 3.6 1.1 - - - +
1119C ILE 3.3 0.2 - - - -
1120C ALA* 1.3 74.0 - - - +
1122C GLY* 1.3 62.0 + - - +
1124C ALA* 3.5 2.9 + - - +
1125C TYR* 3.1 21.5 + - - +
1263C ILE* 3.5 9.9 - - + +
1274C PHE* 3.8 4.7 - - + -
1278C SER* 3.2 11.3 - - - -
1279C PHE* 2.8 23.6 + - - +
1280C TYR* 2.9 34.7 + - - +
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Residues in contact with GLY1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C CYS* 4.5 1.1 - - - -
1061C HIS* 3.9 19.2 - - - +
1062C VAL* 4.4 5.6 - - - +
1118C GLU 3.2 8.3 + - - -
1119C ILE 3.3 0.2 + - - -
1120C ALA 3.2 0.2 - - - -
1121C ASP* 1.3 78.5 - - - +
1123C MET* 1.3 56.2 + - - +
1125C TYR* 3.2 10.2 - - - +
1126C LEU* 3.0 28.8 + - - +
1151C ILE* 3.3 20.0 - - - -
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Residues in contact with MET1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119C ILE* 3.1 16.6 + - + +
1120C ALA 3.6 4.5 - - - +
1122C GLY* 1.3 73.7 - - - +
1124C ALA* 1.3 57.0 + - - +
1126C LEU* 2.9 16.4 + - + +
1127C ASN* 2.7 40.5 + - - +
1133C HIS* 3.7 17.3 - - + -
1136C LEU* 3.8 29.4 - - + -
1151C ILE* 3.2 17.2 - - + +
1194C ASP* 3.3 42.0 - - + +
1259C PHE* 3.5 33.0 - - + -
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Residues in contact with ALA1124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C ALA 2.8 21.2 + - - +
1121C ASP 3.7 5.8 - - - +
1123C MET* 1.3 72.2 - - - +
1125C TYR* 1.3 57.1 + - - +
1127C ASN* 3.9 3.2 - - - +
1128C ALA* 2.9 31.5 + - - +
1259C PHE* 3.8 18.2 - - + +
1260C LEU* 3.7 30.9 - - + +
1263C ILE* 4.3 6.3 - - + -
1279C PHE* 3.7 8.2 - - + -
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Residues in contact with TYR1125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056C GLU 3.4 7.1 + - - -
1057C PHE* 3.3 30.7 - + + -
1058C ASN* 2.7 41.0 + - - +
1059C CYS* 3.7 26.2 - - + -
1062C VAL* 4.3 5.8 - - + -
1121C ASP 3.1 13.1 + - - +
1122C GLY 3.2 11.7 - - - +
1123C MET 3.1 0.6 - - - -
1124C ALA* 1.3 76.6 - - - +
1126C LEU* 1.3 67.6 + - + +
1128C ALA* 3.3 1.7 + - - +
1129C ASN* 2.8 56.5 + - - -
1279C PHE* 3.8 31.8 - + + -
1284C GLU* 3.9 14.1 - - - -
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Residues in contact with LEU1126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057C PHE* 3.7 36.1 - - + -
1062C VAL* 5.0 2.0 - - + -
1122C GLY 3.0 16.8 + - - +
1123C MET* 2.9 30.4 + - + +
1125C TYR* 1.3 82.0 - - + +
1127C ASN* 1.3 65.7 + - - +
1129C ASN* 3.1 11.5 + - - +
1130C LYS 3.3 0.2 + - - -
1131C PHE* 2.9 36.1 + - + +
1133C HIS* 4.1 10.5 - - + -
1151C ILE* 4.4 3.4 - - + -
1154C PHE* 3.2 40.6 - - + -
1157C THR* 5.3 1.3 - - + -
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Residues in contact with ASN1127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123C MET* 2.7 23.0 + - - +
1124C ALA* 4.2 4.5 - - - +
1126C LEU* 1.3 75.9 - - - +
1128C ALA* 1.3 56.9 + - - +
1130C LYS* 2.9 26.3 + - - +
1131C PHE 2.8 22.2 + - - -
1132C VAL* 4.4 0.2 - - - +
1191C THR* 2.9 43.2 - - + +
1194C ASP* 3.4 17.8 + - - -
1259C PHE* 3.3 23.9 - - + -
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Residues in contact with ALA1128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124C ALA 2.9 20.6 + - - +
1125C TYR 3.6 3.4 - - - +
1126C LEU 3.2 0.2 - - - -
1127C ASN* 1.3 72.6 - - - +
1129C ASN* 1.3 59.5 + - - +
1130C LYS* 3.1 14.7 + - - +
1260C LEU* 6.5 0.9 - - + -
1279C PHE* 3.4 28.0 - - + -
1284C GLU* 5.6 1.6 - - + +
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Residues in contact with ASN1129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056C GLU* 4.6 12.6 - - - +
1057C PHE* 5.5 2.9 - - + -
1125C TYR* 2.8 64.2 + - + +
1126C LEU* 3.1 6.8 + - - +
1128C ALA* 1.3 77.8 - - - +
1130C LYS* 1.3 70.3 + - - +
1131C PHE* 3.1 27.1 - - + -
1159C ASP* 5.0 1.0 - - - +
1284C GLU* 3.5 14.8 + - - +
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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) + - + + + + + -
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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