Contacts of the helix formed by residues 1095 - 1118 (chain A) in PDB entry 5LUQ
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 LEU1095 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094A SER* 1.3 82.5 + - - +
1096A VAL* 1.3 60.5 + - - +
1097A GLU 3.0 1.6 - - - -
1098A GLN* 2.8 43.9 + - + +
1099A PHE* 4.0 5.1 + - + +
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Residues in contact with VAL1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A GLN* 5.6 7.6 - - - +
1056A THR* 5.5 12.1 - - + -
1060A PHE* 5.0 3.4 - - + -
1090A ARG* 2.8 40.6 + - - +
1093A GLU* 3.0 49.1 + - + +
1094A SER* 4.5 0.2 - - - -
1095A LEU* 1.3 84.2 - - - +
1097A GLU* 1.3 59.0 + - - +
1098A GLN 3.0 4.6 + - - -
1099A PHE* 3.5 20.2 - - + -
1100A VAL* 3.3 6.8 - - - +
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Residues in contact with GLU1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A ARG* 3.8 25.1 - - - +
1091A GLU 4.1 6.1 - - - +
1092A GLU* 3.1 9.0 - - - -
1093A GLU* 2.2 39.1 + - + +
1094A SER* 2.5 27.3 + - - +
1096A VAL* 1.3 78.2 - - + +
1098A GLN* 1.3 66.1 + - - +
1100A VAL* 4.1 2.5 - - - -
1101A PHE* 3.0 42.4 - - + -
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Residues in contact with GLN1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A SER 4.6 7.5 + - - -
1095A LEU* 2.8 38.0 + - + +
1096A VAL 3.0 1.6 - - - -
1097A GLU* 1.3 84.0 + - - +
1099A PHE* 1.3 69.1 + - - +
1100A VAL 3.1 1.3 - - - -
1101A PHE* 3.0 21.1 + - - +
1102A GLU* 3.5 11.7 + - - +
1142A HIS* 4.3 17.8 - - - +
1143A VAL* 3.1 42.3 + - + +
1146A ASN* 4.1 7.2 + - - +
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Residues in contact with PHE1099 (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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1057A LYS* 4.9 33.0 - - + -
1060A PHE* 3.3 41.5 - + + -
1064A TYR* 5.8 0.4 - + - -
1095A LEU* 4.0 4.3 + - + +
1096A VAL* 3.5 30.1 - - + -
1098A GLN* 1.3 78.1 - - - +
1100A VAL* 1.3 82.0 + - + +
1102A GLU* 3.0 33.2 + - - +
1103A ALA* 3.1 10.8 + - + +
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Residues in contact with VAL1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A PHE* 3.9 27.8 - - + -
1064A TYR* 3.3 17.5 - - + +
1083A ASN* 6.1 0.7 - - - +
1090A ARG* 3.0 38.8 - - + +
1096A VAL 3.3 8.7 - - - +
1097A GLU 4.0 2.2 - - - +
1099A PHE* 1.3 95.2 - - + +
1101A PHE* 1.3 66.6 + - + +
1103A ALA* 2.9 6.0 + - - +
1104A LEU* 2.3 39.4 + - + +
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Residues in contact with PHE1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090A ARG* 3.7 37.9 - - + -
1091A GLU* 5.1 1.3 - - - -
1097A GLU* 3.0 27.6 - - + -
1098A GLN* 3.0 10.6 + - - +
1100A VAL* 1.3 85.4 - - + +
1102A GLU* 1.3 58.9 + - - +
1104A LEU* 2.8 44.1 + - + +
1105A VAL* 3.2 3.8 + - - +
1137A ILE* 4.3 21.5 - - + -
1138A ILE* 3.3 47.5 - - + +
1142A HIS* 6.3 3.4 - + - -
1150A LYS* 2.8 14.2 + - - +
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Residues in contact with GLU1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1098A GLN 3.5 11.2 + - - +
1099A PHE* 3.0 15.8 + - - +
1101A PHE* 1.3 78.6 - - - +
1103A ALA* 1.3 57.4 + - - +
1105A VAL* 2.9 35.2 + - + +
1106A ILE* 4.2 1.6 - - - +
1145A LEU* 4.9 13.1 - - + +
1146A ASN* 3.1 24.5 - - - +
1149A LYS* 4.9 2.6 - - - +
1150A LYS* 2.8 63.7 + - - +
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Residues in contact with ALA1103 (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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1064A TYR* 2.9 50.4 - - + +
1099A PHE* 3.1 9.6 + - + +
1100A VAL* 2.9 11.5 + - - +
1102A GLU* 1.3 76.6 - - - +
1104A LEU* 1.3 65.5 + - - +
1106A ILE* 2.9 26.8 + - + +
1107A TYR 3.2 0.7 + - - -
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Residues in contact with LEU1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A TYR* 4.1 3.8 - - - +
1083A ASN* 3.1 33.4 - - - +
1090A ARG* 6.2 2.2 - - + -
1100A VAL* 2.3 25.6 + - + +
1101A PHE* 2.8 45.5 + - + +
1103A ALA* 1.3 70.8 - - - +
1105A VAL* 1.3 55.6 + - - +
1107A TYR* 2.8 30.9 + - + +
1108A MSE 3.6 3.8 + - - +
1134A LEU* 4.3 8.3 - - + +
1135A CYS* 3.6 40.3 - - + +
1137A ILE* 6.0 0.7 - - + -
1138A ILE* 3.8 19.5 - - + -
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Residues in contact with VAL1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101A PHE 3.3 11.7 - - - +
1102A GLU* 2.9 21.9 + - + +
1104A LEU* 1.3 72.1 - - + +
1106A ILE* 1.3 74.0 + - + +
1108A MSE 3.8 16.5 - - + +
1109A GLU* 3.3 17.8 + - - +
1138A ILE* 5.1 1.6 - - + -
1150A LYS* 3.3 26.7 - - + +
1153A LEU* 3.4 43.7 - - + -
1157A PHE* 4.2 3.8 - - - -
1172A LEU* 6.0 0.2 - - + -
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Residues in contact with ILE1106 (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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1064A TYR* 3.3 35.7 - - + -
1068A LEU* 6.1 0.9 - - + -
1102A GLU 4.2 0.7 - - - +
1103A ALA* 2.9 30.8 + - + +
1105A VAL* 1.3 85.6 - - + +
1107A TYR* 1.3 51.7 - - - +
1109A GLU* 2.9 12.9 - - + +
1110A SER* 2.1 46.9 + - - +
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Residues in contact with TYR1107 (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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1063A LEU* 6.0 1.9 - - + +
1064A TYR* 4.5 15.7 - + + -
1067A ALA* 3.9 4.3 - - + -
1079A SER* 2.3 58.5 + - - -
1082A PHE* 4.9 3.6 - + - +
1083A ASN* 3.1 44.2 + - + +
1103A ALA 3.2 6.8 + - - +
1104A LEU* 2.8 26.9 + - + +
1106A ILE* 1.3 76.8 - - - +
1108A MSE 1.3 49.4 + - - +
1110A SER* 2.6 10.1 - - - -
1111A LEU* 2.3 57.2 + - + -
1131A ILE* 4.0 16.6 - - + -
1135A CYS* 5.3 0.2 - - - -
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Residues in contact with MSE1108 (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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1104A LEU 3.6 4.1 + - - +
1105A VAL* 3.8 25.4 - - + +
1107A TYR* 1.3 75.1 - - - +
1109A GLU* 1.3 62.3 + - - +
1111A LEU 2.9 1.0 + - - -
1112A ALA* 2.3 42.4 + - + +
1131A ILE* 4.3 2.9 - - - +
1132A ASP* 3.2 38.1 + - + +
1135A CYS* 4.6 10.5 - - + -
1157A PHE* 3.5 19.7 - - + -
1165A LEU* 3.5 18.6 - - + -
1168A LEU* 4.4 11.0 - - + -
1172A LEU* 3.4 39.9 - - + -
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Residues in contact with GLU1109 (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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1068A LEU* 5.1 1.6 - - - +
1105A VAL 3.3 14.4 + - - +
1106A ILE* 2.9 21.0 + - + +
1108A MSE 1.3 76.1 - - - +
1110A SER* 1.3 63.5 + - - +
1113A LEU* 3.6 27.9 - - - +
1153A LEU* 6.1 0.9 - - + -
1157A PHE* 4.0 21.5 - - + -
1160A SER* 5.0 2.1 + - - +
1162A SER* 4.1 5.5 + - - -
1165A LEU* 3.5 29.7 - - - +
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Residues in contact with SER1110 (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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1064A TYR* 4.6 1.4 - - - -
1067A ALA* 4.3 1.1 - - - +
1068A LEU* 3.3 42.1 - - - +
1106A ILE* 2.1 46.7 + - - +
1107A TYR* 2.6 21.5 - - - -
1108A MSE 3.0 0.4 - - - -
1109A GLU* 1.3 75.1 - - - +
1111A LEU* 1.3 58.5 + - - -
1114A ALA* 2.7 34.4 + - - +
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Residues in contact with LEU1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A ALA* 3.3 23.1 - - + +
1076A LEU* 3.5 28.7 - - + +
1079A SER* 3.8 0.7 - - - -
1080A LEU* 3.6 33.4 - - + +
1107A TYR* 2.3 48.4 + - + +
1110A SER* 1.3 67.1 - - - +
1112A ALA* 1.3 69.9 + - - +
1114A ALA* 2.9 3.8 - - - +
1115A HIS* 2.7 27.1 + - - -
1128A CYS* 3.4 28.0 - - + -
1131A ILE* 3.7 15.5 - - + -
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Residues in contact with ALA1112 (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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1108A MSE 2.3 33.6 + - + +
1111A LEU* 1.3 74.2 - - - +
1113A LEU* 1.3 52.1 + - - +
1115A HIS* 3.4 16.9 - - - -
1116A ALA* 2.7 34.7 + - - +
1128A CYS* 5.0 0.6 - - - +
1132A ASP* 5.2 0.7 - - - +
1164A CYS* 5.2 0.9 - - - -
1165A LEU* 3.4 28.7 - - + +
1168A LEU* 3.8 22.0 - - + -
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Residues in contact with LEU1113 (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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1068A LEU* 6.6 0.2 - - + -
1108A MSE 3.8 0.8 + - - -
1109A GLU* 3.6 29.3 + - - +
1110A SER 3.5 1.6 + - - -
1112A ALA* 1.3 77.0 - - - +
1114A ALA* 1.3 67.6 + - - +
1116A ALA* 2.9 16.6 + - - +
1117A ASP* 3.2 28.9 + - + +
1162A SER* 3.9 37.5 - - - +
1163A LEU* 5.2 1.6 - - + -
1165A LEU* 4.5 2.2 - - + +
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Residues in contact with ALA1114 (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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1067A ALA 5.0 2.2 - - - +
1068A LEU* 5.3 5.4 - - + -
1071A ASN* 5.1 4.1 - - - +
1072A ALA* 3.1 40.1 - - + +
1076A LEU* 3.5 10.1 - - + -
1110A SER 2.7 22.5 + - - +
1111A LEU* 2.9 22.0 - - + +
1112A ALA 2.9 0.8 + - - -
1113A LEU* 1.3 76.9 - - - +
1115A HIS* 1.3 58.0 + - - +
1117A ASP* 5.1 0.5 - - - +
1118A GLU* 4.1 9.7 + - - +
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Residues in contact with HIS1115 (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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1072A ALA 5.4 0.2 - - - -
1076A LEU* 3.3 5.1 - - + +
1111A LEU 2.7 30.1 + - - -
1112A ALA* 3.4 16.7 + - - +
1114A ALA* 1.3 74.2 - - - +
1116A ALA* 1.3 72.0 + - - +
1118A GLU* 2.6 9.9 - - - +
1119A LYS* 2.2 39.7 + - - -
1124A ILE* 3.4 28.0 - - + -
1125A GLN* 3.5 35.5 + - + +
1128A CYS* 3.1 41.5 - - + -
1129A ASP 5.1 0.4 - - - -
1164A CYS* 4.1 13.0 - - - -
1168A LEU* 5.3 4.2 - - + +
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Residues in contact with ALA1116 (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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1112A ALA 2.7 23.7 + - - +
1113A LEU* 2.9 16.2 + - - +
1115A HIS* 1.3 72.9 - - - +
1117A ASP* 1.3 58.3 + - - +
1119A LYS* 2.9 34.9 - - - +
1162A SER 3.6 13.5 - - - +
1163A LEU* 4.9 4.9 - - - +
1164A CYS* 3.3 33.5 - - + +
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Residues in contact with ASP1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113A LEU* 3.2 22.4 + - + +
1114A ALA 5.1 0.9 - - - +
1116A ALA* 1.3 81.4 - - - +
1118A GLU* 1.3 77.2 + - + +
1119A LYS* 3.3 9.0 + - - +
1163A LEU* 3.6 27.2 - - - +
1252A ALA* 5.7 2.9 - - - +
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Residues in contact with GLU1118 (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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1071A ASN* 5.0 15.6 + - - +
1072A ALA 4.2 20.9 - - - +
1073A PHE* 6.2 0.4 - - + -
1114A ALA 4.1 6.6 + - - +
1115A HIS* 2.6 14.7 + - - +
1117A ASP* 1.3 95.8 - - + +
1119A LYS* 1.3 54.0 + - - +
1120A SER* 2.7 25.8 + - - -
1124A ILE* 5.6 4.2 - - - +
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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