Contacts of the helix formed by residues 1049 - 1075 (chain A) in PDB entry 6DMY
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 ASN1049 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 5.5 7.2 - - + +
1047A LEU* 3.5 5.6 - - + +
1048A LEU* 1.3 77.1 - - - +
1050A PRO* 1.3 74.2 - - - +
1051A TRP* 4.0 7.7 + - - +
1052A THR* 2.4 42.4 + - + +
1053A ALA* 3.5 3.7 + - - +
1105A LEU* 3.4 27.9 - - + +
1180A PRO 2.9 28.1 + - - +
1181A TYR* 4.3 4.8 + - - -
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Residues in contact with PRO1050 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A PHE* 3.8 18.0 - - + -
1044A ALA* 5.4 5.8 - - + -
1048A LEU* 3.0 19.2 - - + +
1049A ASN* 1.3 89.2 - - - +
1051A TRP* 1.3 63.4 + - + +
1053A ALA* 3.2 19.4 + - + +
1054A GLY* 3.3 10.9 + - - -
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Residues in contact with TRP1051 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A ASN* 3.4 8.2 - - - +
1050A PRO* 1.3 82.7 - - + +
1052A THR* 1.3 58.7 + - + +
1053A ALA 3.3 0.4 + - - -
1054A GLY* 3.9 4.9 + - - +
1055A ILE* 3.4 24.4 + - + +
1178A PHE* 3.9 29.0 - + - -
1179A GLY* 2.8 44.0 + - - +
1180A PRO* 4.2 1.6 - - + +
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Residues in contact with THR1052 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A LEU* 3.5 17.4 - - - +
1049A ASN* 2.4 44.2 + - - +
1051A TRP* 1.3 75.4 - - + +
1053A ALA* 1.3 63.1 + - - +
1055A ILE* 3.9 7.8 + - - +
1056A ILE* 3.9 21.3 + - - +
1101A ALA* 4.5 12.5 - - - +
1105A LEU* 3.7 11.9 - - + +
1180A PRO* 3.5 41.3 - - + -
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Residues in contact with ALA1053 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A PHE* 3.7 19.7 - - + -
1043A CYS* 3.3 34.3 - - + +
1044A ALA* 4.4 1.8 - - - +
1047A LEU* 5.3 0.7 - - - -
1049A ASN 3.5 1.3 + - - +
1050A PRO* 3.2 17.0 + - + +
1052A THR* 1.3 78.5 + - - +
1054A GLY* 1.3 59.1 + - - +
1055A ILE 3.1 2.0 - - - -
1056A ILE* 3.0 14.3 + - - +
1057A VAL* 2.9 27.5 + - - +
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Residues in contact with GLY1054 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A PHE* 3.7 13.2 - - - -
1050A PRO 3.3 9.1 + - - -
1051A TRP* 3.9 3.9 + - - -
1052A THR 3.5 0.4 - - - -
1053A ALA* 1.3 77.7 - - - +
1055A ILE* 1.3 62.2 + - - +
1057A VAL* 3.7 9.4 - - - +
1058A MET* 2.9 26.2 + - - +
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Residues in contact with ILE1055 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A TRP* 3.4 26.5 - - + +
1052A THR* 4.3 8.5 - - - +
1053A ALA 3.1 1.0 - - - -
1054A GLY* 1.3 82.0 - - - +
1056A ILE* 1.3 59.1 + - - +
1058A MET* 3.6 16.1 - - + +
1059A VAL* 2.9 33.2 + - + +
1171A LEU* 3.7 11.9 - - + -
1174A LEU* 3.7 12.8 - - + -
1175A LEU* 3.7 31.4 - - + -
1178A PHE* 3.9 30.7 - - + -
1179A GLY* 6.0 1.8 - - - -
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Residues in contact with ILE1056 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039A THR* 5.4 0.2 - - - +
1043A CYS* 4.2 27.4 - - + -
1047A LEU* 5.4 10.1 - - + -
1052A THR 3.9 12.5 + - - +
1053A ALA* 3.0 10.1 + - - +
1055A ILE* 1.3 77.4 - - - +
1057A VAL* 1.3 58.9 + - + +
1059A VAL* 3.9 1.0 - - - +
1060A LEU* 2.9 43.3 + - + +
1094A VAL* 4.5 3.6 - - + -
1097A THR* 3.3 49.5 + - - +
1098A VAL* 3.9 18.6 - - + +
1101A ALA* 3.9 14.6 - - + -
1171A LEU* 5.5 1.3 - - + -
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Residues in contact with VAL1057 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A LEU* 4.1 27.7 - - + +
1039A THR* 4.5 8.5 - - + +
1040A PHE* 3.6 39.5 - - + +
1043A CYS* 6.0 0.2 - - + -
1053A ALA 2.9 15.2 + - - +
1054A GLY* 3.8 8.7 - - - +
1056A ILE* 1.3 79.3 - - + +
1058A MET* 1.3 57.5 + - - +
1060A LEU* 3.6 6.8 - - - +
1061A ALA* 2.8 29.6 + - + +
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Residues in contact with MET1058 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054A GLY 2.9 19.2 + - - +
1055A ILE* 3.2 23.5 + - - +
1057A VAL* 1.3 77.9 - - - +
1059A VAL* 1.3 60.9 + - + +
1061A ALA* 3.2 4.6 + - - +
1062A LEU* 3.0 54.4 + - + +
1174A LEU* 5.0 19.3 - - + -
1178A PHE* 5.7 3.8 - - + -
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Residues in contact with VAL1059 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055A ILE* 2.9 19.9 + - + +
1058A MET* 1.3 76.4 - - + +
1060A LEU* 1.3 54.3 + - - +
1062A LEU* 4.7 3.6 - - - +
1063A MET* 2.6 40.2 + - + +
1097A THR* 3.8 25.4 - - + -
1166A ASN* 3.7 34.8 + - + +
1167A GLY* 4.4 4.3 - - - -
1170A LEU* 3.9 15.9 - - + -
1171A LEU* 3.7 23.3 - - + -
1174A LEU* 5.5 1.6 - - + -
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Residues in contact with LEU1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A LEU* 3.8 11.7 - - + -
1039A THR* 3.7 29.6 - - + +
1056A ILE* 2.9 37.3 + - + +
1057A VAL* 3.6 5.6 - - - +
1059A VAL* 1.3 77.5 - - - +
1061A ALA* 1.3 56.5 + - - +
1063A MET* 3.3 5.0 + - + +
1064A THR* 2.9 37.6 + - + +
1090A VAL* 3.3 37.0 - - + +
1093A GLY* 3.5 27.1 - - - +
1094A VAL* 3.8 13.2 - - + -
1097A THR* 4.9 1.1 - - - +
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Residues in contact with ALA1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A LEU* 3.9 21.8 - - + -
1057A VAL* 2.8 23.3 + - + +
1058A MET* 3.6 5.8 - - - +
1060A LEU* 1.3 72.9 - - - +
1062A LEU* 1.3 64.5 + - + +
1064A THR* 3.2 5.3 + - - -
1065A VAL* 3.0 35.6 + - + +
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Residues in contact with LEU1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A LEU* 3.7 33.2 - - + -
765A LEU* 5.9 0.2 - - + -
1058A MET* 3.0 49.0 + - + +
1059A VAL* 4.6 3.1 - - - +
1061A ALA* 1.3 82.4 - - + +
1063A MET* 1.3 56.8 + - - +
1065A VAL* 3.9 9.3 - - + +
1066A GLU* 3.0 42.6 + - - +
1166A ASN* 4.7 2.9 - - - +
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Residues in contact with MET1063 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A VAL* 2.6 25.4 + - + +
1060A LEU* 3.3 10.1 - - + +
1061A ALA 3.2 0.2 - - - -
1062A LEU* 1.3 76.3 - - - +
1064A THR* 1.3 62.4 + - + +
1066A GLU* 3.4 6.7 + - - +
1067A LEU* 3.0 28.4 + - + +
1089A SER 5.6 0.9 - - - +
1093A GLY* 5.2 12.6 - - - +
1159A LEU* 3.7 30.3 - - + -
1162A LEU* 3.6 26.9 - - + +
1163A GLY* 3.4 28.9 - - - +
1166A ASN* 2.9 28.9 - - - +
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Residues in contact with THR1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A ILE* 4.6 20.4 - - - +
1036A LEU* 4.9 2.1 - - + +
1060A LEU* 2.9 15.6 + - + +
1061A ALA* 3.2 11.6 + - - -
1063A MET* 1.3 78.2 - - + +
1065A VAL* 1.3 65.2 + - - +
1067A LEU* 3.8 7.3 - - - +
1068A PHE* 2.9 30.8 + - - +
1086A LEU* 4.4 8.0 - - - +
1089A SER* 4.3 10.1 - - - +
1090A VAL* 3.6 41.3 - - + +
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Residues in contact with VAL1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A LEU* 4.7 4.9 - - + -
764A SER* 4.4 1.1 - - - -
765A LEU* 3.7 29.8 - - + -
768A THR* 4.1 12.5 - - + +
1032A ILE* 6.4 1.3 - - + -
1061A ALA* 3.0 23.0 + - + +
1062A LEU* 3.9 11.4 - - + +
1064A THR* 1.3 79.7 - - - +
1066A GLU* 1.3 58.1 + - - +
1068A PHE* 3.9 6.1 - - + +
1069A GLY* 3.0 26.3 + - - -
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Residues in contact with GLU1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A PHE* 4.2 6.6 - - - +
760A LEU* 3.5 23.2 - - + +
761A LEU* 3.3 30.3 + - + +
764A SER* 3.3 27.8 - - - +
1062A LEU* 3.0 27.3 + - - +
1063A MET* 3.7 4.3 - - - +
1064A THR 3.3 0.2 - - - -
1065A VAL* 1.3 77.3 - - - +
1067A LEU* 1.3 56.9 + - - +
1070A MET* 3.0 34.4 + - - +
1162A LEU* 4.4 15.0 - - + +
1166A ASN* 3.9 18.5 + - - -
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Residues in contact with LEU1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A MET* 3.0 21.2 + - + +
1064A THR* 3.8 8.3 - - - +
1065A VAL 3.3 0.4 - - - -
1066A GLU* 1.3 75.7 - - - +
1068A PHE* 1.3 59.4 + - - +
1070A MET* 3.8 10.8 - - + -
1071A MET* 2.9 47.1 + - + +
1085A ILE 5.1 0.2 - - - +
1086A LEU* 3.7 20.4 - - + -
1089A SER* 3.9 20.6 - - - +
1155A VAL* 4.0 15.9 - - + +
1158A ILE* 3.7 36.6 - - + +
1159A LEU* 4.5 9.2 - - + -
1162A LEU* 5.1 2.7 - - + +
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Residues in contact with PHE1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768A THR* 3.9 29.4 - - + -
771A VAL* 4.1 24.0 - - + +
1025A ARG* 4.9 12.3 - - - -
1028A LEU* 4.1 27.4 - - + -
1064A THR 2.9 16.8 + - - +
1065A VAL* 4.0 4.9 - - + +
1067A LEU* 1.3 77.4 - - - +
1069A GLY* 1.3 55.6 + - - +
1071A MET* 3.3 11.3 - - - +
1072A GLY* 3.0 20.1 + - - -
1078A LEU* 4.0 25.6 - - + -
1086A LEU* 3.9 28.7 - - + +
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Residues in contact with GLY1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A SER* 3.3 22.7 - - - -
767A GLY* 3.2 14.0 - - - -
768A THR* 3.6 15.7 - - - -
1065A VAL 3.0 12.2 + - - -
1066A GLU 4.1 0.2 - - - -
1068A PHE* 1.3 76.9 - - - +
1070A MET* 1.3 56.2 + - - +
1072A GLY* 2.6 26.0 + - - -
1073A LEU 2.9 5.2 + - - -
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Residues in contact with MET1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A SER* 4.5 8.0 + - - +
1066A GLU 3.0 14.8 + - - +
1067A LEU* 3.8 22.7 - - + -
1069A GLY* 1.3 72.3 - - - +
1071A MET* 1.3 61.8 + - - +
1073A LEU* 4.0 13.5 - - + +
1074A ILE* 3.0 50.6 + - + +
1158A ILE* 3.6 38.8 - - + -
1162A LEU* 3.7 28.0 - - + -
----------------------------------------------------------
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Residues in contact with MET1071 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A VAL* 5.3 0.7 - - + -
1067A LEU* 2.9 36.1 + - + +
1068A PHE* 3.3 9.9 - - - +
1070A MET* 1.3 78.6 - - - +
1072A GLY* 1.3 60.1 + - - +
1074A ILE* 4.4 2.9 - - - -
1075A GLY* 3.1 15.2 + - - -
1076A ILE* 3.1 45.1 + - + +
1078A LEU* 4.5 12.3 - - + -
1082A PRO* 3.6 33.0 - - + +
1086A LEU* 4.2 18.6 - - + -
1155A VAL* 3.8 32.5 - - + -
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Residues in contact with GLY1072 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A GLY 3.5 13.7 - - - -
770A ARG* 3.6 21.3 + - - +
771A VAL* 3.7 16.8 - - - +
1068A PHE 3.0 7.7 + - - -
1069A GLY 2.6 17.6 + - - -
1071A MET* 1.3 70.8 - - - +
1073A LEU* 1.3 60.8 + - - -
1075A GLY* 3.1 16.0 + - - -
1076A ILE 4.9 2.0 - - - -
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Residues in contact with LEU1073 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A VAL* 3.6 39.9 - - + +
764A SER* 5.3 0.2 - - - -
766A TYR* 4.3 11.0 - - + -
767A GLY* 3.6 22.2 - - - +
770A ARG* 3.4 37.2 + - - +
1069A GLY 2.9 9.7 + - - +
1070A MET* 3.1 14.7 + - + +
1072A GLY* 1.3 71.0 - - - +
1074A ILE* 1.3 69.2 + - + +
----------------------------------------------------------
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Residues in contact with ILE1074 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A MET* 3.0 51.5 + - + +
1071A MET* 4.6 2.5 - - - +
1073A LEU* 1.3 81.1 - - + +
1075A GLY* 1.3 58.5 + - - +
1076A ILE* 3.8 26.6 - - + +
1150A ARG* 5.9 3.1 - - - +
1154A ALA* 5.9 5.6 - - + +
1158A ILE* 5.8 2.7 - - + -
----------------------------------------------------------
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Residues in contact with GLY1075 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A ARG* 6.3 0.4 - - - -
1071A MET 3.1 2.2 + - - -
1072A GLY 3.1 17.3 + - - -
1074A ILE* 1.3 79.0 - - - +
1076A ILE* 1.3 60.0 + - - +
1077A LYS* 2.6 34.8 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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