Contacts of the helix formed by residues 1079 - 1112 (chain A) in PDB entry 3VF0
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 SER1079 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1077A ASN 4.0 2.0 + - - -
1078A ILE* 1.3 78.3 - - - +
1080A ASP* 1.3 61.3 + - - +
1081A GLU* 4.3 7.5 - - - +
1082A GLU* 3.2 30.0 + - - +
1083A SER* 3.0 25.3 + - - -
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Residues in contact with ASP1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078A ILE 3.9 2.6 + - - +
1079A SER* 1.3 71.5 - - - +
1081A GLU* 1.4 56.4 + - - +
1083A SER* 3.4 6.6 + - - -
1084A GLU* 2.9 52.9 + - - +
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Residues in contact with GLU1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A SER* 3.3 6.8 + - - +
1080A ASP* 1.4 75.4 - - - +
1082A GLU* 1.3 56.8 + - - +
1084A GLU* 3.5 13.1 + - - +
1085A GLN* 3.0 56.7 + - + +
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Residues in contact with GLU1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1072A MET* 3.5 25.0 - - + +
1078A ILE* 3.8 20.5 - - + +
1079A SER* 3.2 29.3 + - - +
1081A GLU* 1.3 75.1 - - - +
1083A SER* 1.3 60.2 + - - +
1085A GLN* 3.5 3.9 + - - +
1086A ALA* 3.0 30.0 + - - +
----------------------------------------------------------
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Residues in contact with SER1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069A LYS* 2.9 37.6 + - - -
1072A MET* 4.1 14.4 - - - +
1073A LEU* 5.8 0.5 - - - +
1078A ILE* 4.0 12.3 - - - +
1079A SER 3.0 16.6 + - - -
1080A ASP* 3.7 9.4 - - - -
1082A GLU* 1.3 75.5 - - - +
1084A GLU* 1.3 61.2 + - - +
1086A ALA* 3.5 2.1 + - - +
1087A THR* 3.2 11.1 + - - -
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Residues in contact with GLU1084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080A ASP* 2.9 36.8 + - - +
1081A GLU* 3.9 13.6 - - - +
1083A SER* 1.3 72.6 - - - +
1085A GLN* 1.4 67.8 + - - +
1087A THR* 3.3 10.0 + - - +
1088A GLU* 3.0 29.4 + - + +
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Residues in contact with GLN1085 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081A GLU* 3.0 43.2 + - + +
1082A GLU* 4.2 4.5 - - - +
1083A SER 3.4 0.2 - - - -
1084A GLU* 1.4 76.1 - - - +
1086A ALA* 1.3 60.2 + - - +
1088A GLU* 3.2 29.5 + - - +
1089A MET* 3.0 40.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A LEU* 5.1 2.4 - - - +
1068A VAL* 4.5 11.9 - - + -
1069A LYS* 4.0 13.9 - - + +
1072A MET* 3.6 28.7 - - + -
1082A GLU 3.0 18.1 + - - +
1083A SER 3.6 4.7 - - - +
1084A GLU 3.3 0.2 - - - -
1085A GLN* 1.3 75.5 - - - +
1087A THR* 1.4 60.6 + - - +
1089A MET* 3.5 18.2 + - + +
1090A LEU* 3.4 23.6 + - - +
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Residues in contact with THR1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASN* 3.4 30.5 - - - +
965A ILE* 5.1 0.9 - - + -
1004A VAL* 4.6 15.6 + - + +
1005A ARG* 6.4 0.9 - - - -
1069A LYS* 2.9 36.3 + - - -
1083A SER 3.2 3.3 + - - -
1084A GLU* 3.4 11.6 - - - +
1085A GLN 3.2 0.2 - - - -
1086A ALA* 1.4 75.1 - - - +
1088A GLU* 1.3 57.1 + - - +
1090A LEU* 3.0 10.9 + - - +
1091A VAL* 2.8 37.9 + - + +
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Residues in contact with GLU1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASN* 5.2 2.4 + - - -
964A PRO* 5.6 3.8 - - - +
1084A GLU* 3.0 17.2 + - + +
1085A GLN* 3.2 35.8 + - - +
1087A THR* 1.3 77.2 - - - +
1089A MET* 1.3 56.3 + - + +
1091A VAL* 3.3 23.1 + - - +
1092A HIS* 2.9 30.5 + - - +
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Residues in contact with MET1089 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1065A LEU* 3.6 35.6 - - + +
1068A VAL* 5.3 8.3 - - + -
1085A GLN* 3.0 27.3 + - + +
1086A ALA* 3.6 19.7 - - + +
1087A THR 3.2 0.2 - - - -
1088A GLU* 1.3 76.5 - - + +
1090A LEU* 1.4 55.6 + - - +
1092A HIS* 3.5 6.5 + - - +
1093A ASN* 3.0 28.6 + - - +
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Residues in contact with LEU1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ILE* 4.3 11.0 - - + -
1000A MET* 4.2 6.4 - - + +
1004A VAL* 3.7 24.2 - - + -
1014A LEU* 4.7 2.5 - - + -
1062A LEU* 3.7 27.3 - - + +
1065A LEU* 3.8 22.7 - - + +
1066A SER* 3.7 17.9 - - - +
1069A LYS* 3.7 32.1 - - + -
1086A ALA 3.4 8.6 + - - +
1087A THR* 3.0 10.2 + - - +
1089A MET* 1.4 72.9 - - - +
1091A VAL* 1.3 57.5 + - - +
1093A ASN* 3.3 3.7 + - - +
1094A ALA* 2.8 37.9 + - - +
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Residues in contact with VAL1091 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASN* 3.5 34.3 - - - +
964A PRO* 3.6 26.2 - - + -
965A ILE* 3.7 13.2 - - + +
1087A THR* 2.8 20.6 + - + +
1088A GLU* 3.4 26.9 - - - +
1090A LEU* 1.3 74.5 - - - +
1092A HIS* 1.4 57.6 + - - +
1094A ALA* 3.4 1.6 + - - +
1095A GLN* 2.9 48.9 + - + +
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Residues in contact with HIS1092 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1088A GLU 2.9 16.0 + - - +
1089A MET* 3.8 7.2 - - - +
1091A VAL* 1.4 75.1 - - - +
1093A ASN* 1.3 60.5 + - + +
1095A GLN* 3.5 14.0 + - - +
1096A ASN* 3.0 69.1 + - - +
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Residues in contact with ASN1093 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A ILE* 3.0 31.5 + - - +
1061A GLN* 3.4 26.5 + - - +
1062A LEU* 3.2 35.7 - - + +
1065A LEU* 3.9 10.9 - - + +
1089A MET 3.0 18.1 + - - +
1090A LEU* 3.7 5.2 - - - +
1092A HIS* 1.3 75.9 - - + +
1094A ALA* 1.3 54.6 + - - +
1096A ASN* 3.1 11.1 + - - +
1097A LEU* 2.8 33.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA1094 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ILE* 4.2 19.5 - - + -
968A ALA* 4.5 2.2 - - + -
997A MET* 3.6 38.1 - - + -
1000A MET* 4.6 2.5 - - + -
1062A LEU* 4.7 1.1 - - + +
1090A LEU 2.8 21.4 + - - +
1091A VAL 3.6 3.1 - - - +
1093A ASN* 1.3 72.4 + - - +
1095A GLN* 1.4 56.0 + - - +
1097A LEU* 3.3 2.0 + - - +
1098A MET* 2.9 37.1 + - - +
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Residues in contact with GLN1095 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A PRO* 4.2 16.6 + - - +
968A ALA* 4.2 20.9 - - + -
1091A VAL* 2.9 40.1 + - + +
1092A HIS* 3.8 16.1 + - - +
1094A ALA* 1.4 73.1 - - + +
1096A ASN* 1.4 59.6 + - - +
1098A MET* 3.5 1.6 + - - +
1099A GLN* 3.0 30.7 + - - +
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Residues in contact with ASN1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A ILE* 3.8 18.3 - - + +
1092A HIS* 3.0 54.1 + - - +
1093A ASN* 3.1 9.5 + - - +
1095A GLN* 1.4 76.0 - - - +
1097A LEU* 1.3 61.8 + - - +
1099A GLN* 3.5 6.3 + - - +
1100A SER* 3.1 27.7 + - - -
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Residues in contact with LEU1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993A MET* 3.8 15.0 - - + -
997A MET* 4.0 10.5 - - + -
1021A ILE* 3.5 32.5 - - + -
1025A SER* 3.7 15.3 - - - +
1055A ILE* 4.2 13.5 - - + -
1058A ILE* 3.7 22.9 - - + -
1059A SER* 3.7 17.0 - - - +
1062A LEU* 4.0 9.6 - - + -
1093A ASN* 2.8 20.7 + - - +
1094A ALA* 3.3 5.8 + - - +
1096A ASN* 1.3 71.4 - - - +
1098A MET* 1.3 66.1 + - + +
1100A SER* 3.3 1.7 + - - -
1101A VAL* 3.2 33.2 + - + +
----------------------------------------------------------
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Residues in contact with MET1098 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A ALA* 3.5 35.4 - - + +
969A ALA* 4.1 2.7 - - - -
972A LEU* 3.7 31.5 - - + +
993A MET* 3.6 33.4 - - + -
994A ALA* 4.8 1.1 - - - -
997A MET* 3.6 44.2 - - + -
1094A ALA 2.9 21.9 + - - +
1095A GLN* 4.1 3.1 - - - +
1097A LEU* 1.3 77.3 - - + +
1099A GLN* 1.4 56.0 + - - +
1101A VAL* 3.6 3.5 + - - +
1102A LYS* 3.0 38.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095A GLN 3.0 18.8 + - - +
1096A ASN* 3.7 6.7 - - - +
1098A MET* 1.4 77.1 - - - +
1100A SER* 1.3 56.6 + - - +
1102A LYS* 3.4 24.1 + - - +
1103A GLU* 2.8 69.1 + - - +
1106A ARG* 4.6 11.7 + - - +
----------------------------------------------------------
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Residues in contact with SER1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A VAL* 3.9 6.0 - - - +
1054A ARG* 3.4 20.8 + - - +
1055A ILE* 3.7 22.0 - - - -
1058A ILE* 3.5 16.8 - - - +
1096A ASN 3.1 17.5 + - - -
1097A LEU* 3.3 4.9 + - - -
1099A GLN* 1.3 73.9 - - - +
1101A VAL* 1.3 56.5 + - - +
1103A GLU* 3.5 11.3 + - - +
1104A THR* 2.7 37.1 + - - -
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Residues in contact with VAL1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A LEU* 3.7 24.9 - - + -
990A ALA* 3.9 20.0 - - + -
993A MET* 3.5 32.8 - - + -
1028A VAL* 4.5 12.6 - - + -
1055A ILE* 4.2 12.8 - - + -
1097A LEU* 3.2 24.5 + - + +
1098A MET 4.0 3.8 - - - +
1100A SER* 1.3 73.5 - - - +
1102A LYS* 1.3 64.4 + - - +
1104A THR* 3.2 6.3 + - - -
1105A VAL* 3.0 31.9 + - + +
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Residues in contact with LYS1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A SER* 2.8 43.2 + - - +
972A LEU* 3.8 18.4 - - + +
975A GLU* 4.0 13.0 - - + +
1098A MET* 3.0 25.3 + - - +
1099A GLN* 3.4 26.8 + - - +
1101A VAL* 1.3 77.2 - - - +
1103A GLU* 1.3 55.1 + - - +
1105A VAL* 3.4 6.5 + - - +
1106A ARG* 2.9 64.8 + - - +
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Residues in contact with GLU1103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A VAL* 3.3 25.1 - - + +
1054A ARG* 2.8 31.2 + - - -
1099A GLN* 2.8 54.6 + - - +
1100A SER* 3.6 1.9 - - - +
1102A LYS* 1.3 72.9 - - - +
1104A THR* 1.3 60.1 + - - +
1106A ARG* 3.3 12.8 + - - +
1107A GLU* 2.9 34.3 + - + +
----------------------------------------------------------
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Residues in contact with THR1104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A ILE* 4.5 6.1 - - + -
1028A VAL* 3.9 19.1 - - + -
1032A ALA* 3.6 30.7 - - + -
1048A LEU* 3.9 7.0 - - + +
1051A VAL* 3.6 16.0 + - - +
1052A CYS* 3.8 7.8 - - + +
1055A ILE* 3.4 15.7 - - - +
1100A SER 2.7 22.4 + - - -
1101A VAL* 3.2 6.5 + - - -
1103A GLU* 1.3 72.1 - - - +
1105A VAL* 1.3 57.5 + - - +
1107A GLU 3.3 0.5 + - - -
1108A ALA* 2.8 34.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL1105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A LEU* 5.4 2.2 - - + -
975A GLU* 4.7 16.4 - - + +
976A ALA* 5.5 1.3 - - + -
979A TRP* 4.3 11.9 - - + +
986A ILE* 3.7 26.2 - - + -
987A ILE* 3.8 26.0 - - + -
990A ALA* 4.5 13.9 - - + -
1101A VAL* 3.0 23.5 + - + +
1102A LYS* 3.6 7.4 - - - +
1104A THR* 1.3 74.0 - - - +
1106A ARG* 1.3 62.0 + - + +
1108A ALA* 4.6 1.6 - - - -
1109A GLU* 3.2 24.0 + - + +
1125A TRP* 3.5 14.8 - - + -
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Residues in contact with ARG1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A GLU* 3.1 42.1 + - - +
978A LYS* 5.4 0.2 - - - +
1099A GLN* 4.6 15.6 + - - +
1102A LYS* 2.9 50.7 + - - +
1103A GLU* 3.3 9.5 + - - +
1104A THR 3.2 0.2 - - - -
1105A VAL* 1.3 78.3 - - + +
1107A GLU* 1.3 60.2 + - + +
1109A GLU* 3.5 9.6 + - - +
1110A ALA* 3.0 27.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU1107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A ILE* 3.6 26.6 - - + +
1047A ASN* 3.6 40.9 + - + +
1048A LEU* 3.9 27.6 - - + +
1051A VAL* 4.8 9.0 - - + +
1103A GLU* 2.9 20.6 + - + +
1104A THR* 4.8 0.4 - - - -
1106A ARG* 1.3 75.6 - - + +
1108A ALA* 1.4 60.6 + - - +
1110A ALA* 3.3 6.4 + - - +
1111A ALA* 3.0 28.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA1108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A ILE* 4.2 20.6 - - + -
1032A ALA* 5.5 0.2 - - + -
1035A VAL* 4.2 10.6 - - + +
1048A LEU* 3.8 18.1 - - + +
1104A THR 2.8 22.5 + - - +
1105A VAL* 3.9 1.1 - - - +
1107A GLU* 1.4 71.4 - - - +
1109A GLU* 1.3 60.4 + - - +
1111A ALA* 3.4 5.2 + - - +
1112A SER* 3.3 16.6 + - - -
1123A LEU* 4.4 6.0 - - + +
1125A TRP* 3.7 25.6 + - + -
----------------------------------------------------------
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Residues in contact with GLU1109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A TRP* 3.4 28.6 - - + -
1105A VAL 3.2 18.1 + - - +
1106A ARG* 3.7 7.9 - - - +
1108A ALA* 1.3 76.3 - - - +
1110A ALA* 1.3 65.7 + - - +
1112A SER* 2.6 26.2 + - - -
1113A ILE* 5.1 2.1 - - - +
1125A TRP* 3.6 42.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA1110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044A ILE* 3.8 25.2 - - + +
1106A ARG 3.0 17.8 + - - +
1107A GLU* 3.3 11.4 + - - +
1109A GLU* 1.3 80.1 + - - +
1111A ALA* 1.4 60.2 + - - +
1113A ILE* 3.4 23.3 - - - +
1114A LYS* 4.4 6.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA1111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A VAL* 4.0 18.2 - - + -
1039A CYS* 3.9 16.8 - - - -
1044A ILE* 3.7 17.2 - - + +
1048A LEU* 4.3 5.2 - - + -
1107A GLU 3.0 13.9 + - - +
1108A ALA 3.5 10.8 - - - +
1109A GLU 3.2 0.2 - - - -
1110A ALA* 1.4 73.1 - - - +
1112A SER* 1.3 53.0 + - - +
1113A ILE 3.1 5.8 - - - -
1114A LYS* 2.8 26.5 + - - +
1115A ILE* 3.0 16.8 - - + +
----------------------------------------------------------
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Residues in contact with SER1112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035A VAL* 6.0 0.4 - - - -
1108A ALA 3.3 5.3 + - - -
1109A GLU* 2.6 23.8 + - - +
1111A ALA* 1.3 75.1 - - - +
1113A ILE* 1.3 69.5 + - - +
1115A ILE* 3.7 18.8 - - - +
1123A LEU 4.7 4.5 - - - -
1125A TRP* 3.5 35.0 - - - +
----------------------------------------------------------
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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