Contacts of the helix formed by residues 1164 - 1186 (chain A) in PDB entry 4DDG
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 ASP1164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU* 4.9 0.4 - - - -
1160A ALA 3.6 7.7 + - - +
1161A SER* 3.2 14.5 + - - +
1163A ASN* 1.3 77.9 - - - +
1165A GLN* 1.3 70.0 + - - +
1166A SER* 3.2 12.0 + - - -
1167A THR* 2.9 39.7 + - - +
1168A SER* 3.3 22.3 + - - -
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Residues in contact with GLN1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU* 3.9 10.1 - - - +
1086A ARG* 3.2 27.8 + - - +
1163A ASN 3.7 3.2 + - - -
1164A ASP* 1.3 76.0 - - - +
1166A SER* 1.3 62.6 + - - +
1168A SER* 3.8 0.9 - - - -
1169A ASP* 2.9 63.7 + - - +
62B PHE* 5.7 4.0 - - + -
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Residues in contact with SER1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A ASP* 3.2 7.7 + - - -
1165A GLN* 1.3 78.9 - - - +
1167A THR* 1.3 61.0 + - - +
1169A ASP* 4.3 5.6 - - - -
1170A TYR* 2.9 43.9 + - - +
1B MET* 4.1 36.7 - - - +
62B PHE* 4.5 9.4 - - - -
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Residues in contact with THR1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A THR* 3.3 30.1 + - + +
1145A LEU* 4.1 22.7 - - + -
1148A GLN* 5.6 0.9 - - - +
1161A SER* 3.9 20.2 - - - +
1164A ASP* 2.9 22.8 + - - +
1166A SER* 1.3 74.6 + - - +
1168A SER* 1.3 67.0 + - - +
1170A TYR* 3.2 2.4 + - - -
1171A LEU* 3.0 19.2 + - - +
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Residues in contact with SER1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU* 4.2 2.0 - - - -
1094A ARG* 2.4 39.2 + - - +
1145A LEU* 5.6 1.3 - - - -
1161A SER 4.4 1.5 + - - -
1162A PHE* 3.2 38.8 + - - +
1164A ASP 3.3 12.5 + - - -
1165A GLN 3.8 1.1 - - - -
1167A THR* 1.3 79.1 - - - +
1169A ASP* 1.3 59.7 + - - +
1171A LEU* 3.1 10.6 + - - +
1172A VAL* 2.9 28.1 + - - +
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Residues in contact with ASP1169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU* 4.4 0.2 - - - +
1090A ASN* 5.3 0.4 + - - -
1094A ARG* 3.3 25.7 + - - -
1165A GLN* 2.9 47.2 + - - +
1166A SER 4.1 0.2 - - - +
1168A SER* 1.3 76.4 - - - +
1170A TYR* 1.3 56.3 + - - +
1172A VAL* 3.1 7.6 + - - +
1173A VAL* 2.9 34.0 + - - +
1211A MET* 4.0 17.4 - - + +
62B PHE* 3.8 29.9 - - + -
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Residues in contact with TYR1170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A ASP* 3.9 30.3 + - + -
1138A PHE* 3.5 36.3 - + + +
1141A THR* 3.8 25.8 - - + +
1166A SER* 2.9 35.7 + - - +
1167A THR 3.5 4.7 - - - +
1169A ASP* 1.3 74.9 - - - +
1171A LEU* 1.3 64.1 + - - +
1173A VAL* 3.2 5.0 + - - +
1174A TYR* 3.0 21.7 + - - +
1B MET* 3.9 29.6 + - + +
5B ARG* 4.9 4.2 + - - +
60B TYR 4.6 1.1 + - - -
61B PRO* 3.9 18.1 - - + +
62B PHE* 3.6 29.4 - + - -
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Residues in contact with LEU1171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A TYR 4.5 4.7 - - - +
1094A ARG* 5.1 0.7 - - - -
1097A GLY* 4.8 3.8 - - - -
1101A LEU* 4.7 3.8 - - + -
1138A PHE 5.3 0.9 - - - -
1141A THR* 3.8 5.0 - - - +
1142A PHE* 3.6 34.0 - - + +
1145A LEU* 3.6 29.4 - - + -
1162A PHE* 3.6 33.4 - - + -
1167A THR 3.0 12.4 + - - +
1168A SER* 3.2 11.4 - - - +
1170A TYR* 1.3 76.7 - - - +
1172A VAL* 1.3 70.1 + - + +
1174A TYR* 3.1 8.6 + - - +
1175A LEU* 2.9 42.5 + - + +
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Residues in contact with VAL1172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A ASN* 3.7 30.5 - - + -
1093A TYR* 4.0 10.7 - - + +
1094A ARG* 3.8 43.5 - - - +
1168A SER* 2.9 19.6 + - - +
1169A ASP* 3.1 9.6 + - - +
1171A LEU* 1.3 82.6 - - + +
1173A VAL* 1.3 64.8 + - - +
1175A LEU* 3.2 6.5 + - - +
1176A ARG* 2.9 31.5 + - - +
1211A MET* 3.8 11.2 - - + -
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Residues in contact with VAL1173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A PHE* 3.7 38.1 - - + -
1169A ASP 2.9 20.9 + - - +
1170A TYR* 3.4 7.4 - - - +
1172A VAL* 1.3 74.8 - - - +
1174A TYR* 1.3 57.2 + - - +
1176A ARG* 3.2 9.7 + - - +
1177A LEU* 2.9 36.2 + - + +
1209A GLU 5.7 1.6 - - - +
1211A MET* 3.6 24.7 - - + -
62B PHE* 4.5 5.4 - - + -
94B SER* 5.6 0.7 - - - +
95B PRO* 3.9 28.7 - - + -
96B ALA* 4.9 2.2 - - + +
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Residues in contact with TYR1174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121A SER* 2.7 24.9 + - - -
1122A LYS* 3.4 11.4 + - - -
1125A LEU* 4.0 14.1 - - + +
1135A ILE* 4.3 7.6 - - + -
1138A PHE* 3.9 22.0 - - + +
1139A HIS* 3.1 44.5 + - + -
1142A PHE* 3.4 38.6 - + + -
1170A TYR 3.0 13.2 + - - +
1171A LEU 3.1 8.0 + - - +
1173A VAL* 1.3 76.2 - - - +
1175A LEU* 1.3 58.2 + - - +
1177A LEU* 3.1 13.2 + - + +
1178A LEU* 2.9 51.9 + - + +
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Residues in contact with LEU1175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A TYR* 3.4 43.5 - - + +
1096A PHE* 4.8 5.4 - - + -
1097A GLY* 4.1 11.9 - - - +
1142A PHE* 4.4 15.3 - - + -
1171A LEU* 2.9 37.3 + - + +
1172A VAL 3.2 6.7 + - - +
1174A TYR* 1.3 75.9 - - - +
1176A ARG* 1.3 53.3 + - - +
1178A LEU* 3.4 13.3 + - + +
1179A THR* 2.6 37.5 + - - -
1223A LEU* 3.7 23.9 - - + +
1227A LEU* 4.2 16.2 - - + -
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Residues in contact with ARG1176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089A GLY 3.5 8.7 + - - -
1090A ASN* 2.7 30.3 + - - -
1093A TYR* 3.3 43.5 + - + -
1172A VAL* 2.9 21.2 + - - +
1173A VAL* 3.4 9.4 - - - +
1175A LEU* 1.3 77.3 - - - +
1177A LEU* 1.3 58.4 + - + +
1179A THR* 3.2 8.4 + - - -
1180A SER* 2.9 26.5 + - - -
1207A GLU 4.4 1.6 + - - -
1208A VAL* 3.1 42.4 + - - +
1209A GLU* 3.9 12.3 - - - +
1210A PRO 3.6 18.0 + - - -
1211A MET* 4.0 11.3 - - - +
1212A CYS 3.6 4.0 - - - +
1213A LYS 2.8 29.2 + - - -
1214A GLU 5.0 0.4 + - - -
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Residues in contact with LEU1177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125A LEU* 3.7 17.8 - - + +
1130A PHE* 3.8 29.6 - - + -
1135A ILE* 3.9 24.0 - - + -
1138A PHE* 4.5 5.8 - - + -
1173A VAL* 2.9 27.3 + - + +
1174A TYR* 3.1 17.4 + - + +
1176A ARG* 1.3 74.7 - - + +
1178A LEU* 1.3 60.3 + - - +
1180A SER* 3.4 3.6 + - - -
1181A GLY* 2.9 26.3 + - - -
1209A GLU* 4.4 15.0 - - + +
94B SER* 4.8 2.7 - - - +
96B ALA* 3.7 33.9 - - + -
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Residues in contact with LEU1178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1121A SER* 3.6 31.9 - - - +
1125A LEU* 3.9 17.3 - - + -
1142A PHE* 4.4 2.7 - - + -
1174A TYR* 2.9 41.2 + - + +
1175A LEU* 3.6 21.3 - - + +
1177A LEU* 1.3 72.0 - - - +
1179A THR* 1.3 67.5 + - - +
1181A GLY* 3.1 1.6 + - - -
1182A TYR* 2.9 26.3 + - - +
1185A ARG* 5.4 1.0 + - - +
1223A LEU* 4.2 6.3 - - + -
1226A ALA* 4.2 12.8 - - + +
1227A LEU* 3.7 30.3 - - + -
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Residues in contact with THR1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093A TYR* 3.4 20.5 - - - +
1175A LEU 2.6 21.1 + - - -
1176A ARG* 3.3 10.3 - - - -
1178A LEU* 1.3 76.8 - - - +
1180A SER* 1.3 57.6 + - - +
1182A TYR* 3.5 0.7 + - - -
1183A LEU* 2.9 37.5 + - + +
1208A VAL* 4.1 12.3 - - + -
1219A HIS* 3.7 32.3 - - + +
1222A ALA* 3.9 14.5 - - + +
1223A LEU* 3.7 15.8 - - - +
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Residues in contact with SER1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130A PHE* 4.2 2.3 - - - -
1176A ARG 2.9 13.4 + - - -
1177A LEU* 3.7 4.9 - - - -
1179A THR* 1.3 77.1 - - - +
1181A GLY* 1.3 58.0 + - - +
1183A LEU* 3.3 1.4 + - - +
1184A GLN* 2.9 44.4 + - - +
1204A CYS* 3.2 17.0 - - - +
1208A VAL* 3.7 9.2 - - - +
1209A GLU* 2.9 42.2 + - - -
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Residues in contact with GLY1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125A LEU* 3.9 11.7 - - - -
1128A GLN* 2.8 41.8 + - - -
1130A PHE* 4.4 6.0 - - - -
1177A LEU 2.9 15.7 + - - -
1178A LEU 3.1 3.5 + - - -
1180A SER* 1.3 76.9 - - - +
1182A TYR* 1.3 56.3 + - - +
1184A GLN* 3.2 2.2 + - - -
1185A ARG* 2.9 13.8 + - - -
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Residues in contact with TYR1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1178A LEU 2.9 14.5 + - - +
1179A THR 4.2 0.9 - - - +
1181A GLY* 1.3 75.9 - - - +
1183A LEU* 1.3 63.2 + - - +
1185A ARG* 3.9 29.3 - - - +
1186A GLU* 3.1 54.3 + - + +
1190A PHE* 3.8 22.7 - + - -
1222A ALA* 3.7 18.4 - - - +
1225A GLN* 3.5 46.4 + - + +
1226A ALA* 3.8 22.0 - - + -
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Residues in contact with LEU1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A THR* 2.9 32.0 + - + +
1180A SER 3.4 5.2 - - - +
1181A GLY 3.2 0.2 - - - -
1182A TYR* 1.3 79.3 - - - +
1184A GLN* 1.3 57.2 + - - +
1187A SER* 3.2 25.5 + - - -
1190A PHE* 3.6 46.4 - - + -
1200A VAL* 3.6 10.3 - - + +
1203A PHE* 4.2 15.0 - - + -
1204A CYS* 3.6 20.9 - - - -
1208A VAL* 4.1 17.9 - - + -
1218A ILE* 4.1 12.8 - - + +
1219A HIS* 5.3 2.5 - - - -
1222A ALA* 3.7 15.3 - - + -
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Residues in contact with GLN1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128A GLN* 3.9 12.0 - - + +
1130A PHE* 4.1 13.7 - - - -
1180A SER* 2.9 37.8 + - - +
1181A GLY* 3.9 3.4 - - - +
1183A LEU* 1.3 73.6 - - - +
1185A ARG* 1.3 66.3 + - - +
1186A GLU 3.4 0.2 - - - -
1187A SER* 3.1 23.7 + - - -
1200A VAL* 4.2 2.7 - - + -
1201A LYS* 3.4 46.0 - - + +
1204A CYS* 3.8 15.7 - - - +
1209A GLU* 3.6 10.7 + - - -
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Residues in contact with ARG1185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124A ASP* 3.9 29.5 + - - +
1125A LEU* 5.2 2.4 - - - +
1128A GLN* 2.9 44.8 + - - +
1178A LEU* 5.4 1.2 + - - +
1181A GLY* 2.9 10.9 + - - +
1182A TYR* 3.7 40.9 - - - +
1183A LEU 3.3 0.2 - - - -
1184A GLN* 1.3 79.3 - - - +
1186A GLU* 1.3 71.8 + - + +
1187A SER* 3.2 3.3 + - - -
1188A LYS* 5.7 3.1 - - - +
1226A ALA* 5.5 5.1 + - - +
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Residues in contact with GLU1186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A TYR* 3.1 45.3 + - + +
1183A LEU 3.8 2.0 - - - -
1185A ARG* 1.3 87.5 - - + +
1187A SER* 1.3 52.2 + - - +
1188A LYS* 3.2 5.1 - - - +
1189A PHE* 2.6 43.8 + - + +
1190A PHE* 3.6 23.0 + - + -
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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