Contacts of the helix formed by residues 1058 - 1088 (chain A) in PDB entry 5G04
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 SER1058 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A LEU* 1.3 74.2 - - - +
1059A ASP* 1.3 56.1 + - - +
1060A HIS* 3.4 38.2 + - - -
1061A GLU* 3.0 15.1 + - - -
1062A PHE* 2.6 36.5 + - - +
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Residues in contact with ASP1059 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057A LEU 5.4 0.5 - - - +
1058A SER* 1.3 73.3 - - - +
1060A HIS* 1.3 57.9 + - - +
1062A PHE* 3.5 11.4 + - - +
1063A ILE* 3.1 28.2 + - - +
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Residues in contact with HIS1060 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A SER* 3.4 24.7 + - - -
1059A ASP* 1.3 77.2 - - - +
1061A GLU* 1.3 82.8 + - + +
1063A ILE* 3.2 24.8 - - + +
1064A GLU* 3.8 7.1 + - - +
1124A ASN* 5.4 1.6 + - - -
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Residues in contact with GLU1061 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056A GLU 3.5 6.4 - - - +
1057A LEU* 3.3 31.6 - - + +
1058A SER* 3.0 35.7 + - - +
1060A HIS* 1.3 87.4 - - + +
1062A PHE* 1.3 63.8 + - - +
1064A GLU* 3.5 19.3 - - + +
1065A GLU* 3.6 11.1 + - + +
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Residues in contact with PHE1062 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A VAL* 3.8 28.7 - - + -
1053A GLN* 3.7 50.9 - - + -
1057A LEU* 4.2 9.1 - - + +
1058A SER 2.6 20.6 + - - +
1059A ASP* 3.8 10.5 - - - +
1061A GLU* 1.3 71.8 - - - +
1063A ILE* 1.3 66.4 + - + +
1065A GLU* 3.0 27.7 + - + +
1066A LYS* 3.2 43.8 + - + +
1111A ALA* 5.9 3.6 - - + -
1112A PRO 6.1 0.9 - - - -
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Residues in contact with ILE1063 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A ASP 3.1 13.9 + - - +
1060A HIS* 3.2 30.1 - - + +
1062A PHE* 1.3 75.3 - - + +
1064A GLU* 1.3 60.8 + - - +
1066A LYS* 3.3 29.2 - - - +
1067A GLU* 3.2 27.9 + - - +
1118A VAL* 4.0 17.9 - - + -
1124A ASN* 3.9 30.1 - - - +
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Residues in contact with GLU1064 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A HIS 4.2 7.2 - - - +
1061A GLU* 3.5 14.1 + - - +
1063A ILE* 1.3 83.1 - - + +
1065A GLU* 1.3 58.0 + - + +
1067A GLU* 3.5 0.8 + - - -
1068A ASN* 3.1 39.7 + - - +
1124A ASN* 5.3 11.3 + - - +
1125A ILE* 3.4 29.6 + - + +
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Residues in contact with GLU1065 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1051A VAL* 4.6 10.0 - - + +
1052A VAL 5.6 0.7 - - - +
1053A GLN* 4.7 4.2 - - - +
1057A LEU* 3.4 44.4 - - - +
1061A GLU 3.9 8.7 - - - +
1062A PHE* 3.0 25.0 + - + +
1064A GLU* 1.3 81.6 - - + +
1066A LYS* 1.3 61.0 + - - +
1068A ASN* 3.6 9.4 + - - +
1069A ARG* 3.3 20.8 + - - +
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Residues in contact with LYS1066 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A VAL* 3.4 20.7 - - + +
1051A VAL* 3.7 24.1 - - + +
1062A PHE* 3.2 34.4 + - + +
1063A ILE* 3.3 30.2 - - - +
1065A GLU* 1.3 75.8 - - - +
1067A GLU* 1.3 54.2 + - - +
1069A ARG* 3.3 2.2 + - - -
1070A LEU* 2.8 30.9 + - - +
1111A ALA* 4.2 20.1 - - + +
1116A THR* 3.7 22.2 + - - -
1118A VAL* 3.8 31.0 - - + +
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Residues in contact with GLU1067 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A ILE* 3.2 22.2 + - + +
1064A GLU 3.9 0.4 - - - +
1066A LYS* 1.3 74.1 - - - +
1068A ASN* 1.3 54.8 + - - +
1070A LEU* 3.1 11.7 + - + +
1071A LEU* 2.8 34.0 + - - +
1118A VAL* 4.0 23.1 - - + +
1119A ASP 3.1 31.6 + - - +
1120A LEU* 3.9 13.6 - - + +
1122A SER* 4.1 3.1 + - - -
1124A ASN* 3.1 44.7 - - - +
1125A ILE* 3.3 20.5 - - + +
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Residues in contact with ASN1068 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064A GLU* 3.1 36.9 + - - +
1065A GLU* 3.7 8.2 - - - +
1066A LYS 3.3 0.2 - - - -
1067A GLU* 1.3 73.7 - - - +
1069A ARG* 1.3 63.7 + - - +
1071A LEU* 3.4 9.8 + - - +
1072A GLN* 3.4 31.1 + - - +
1125A ILE* 3.6 23.4 - - - +
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Residues in contact with ARG1069 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1049A VAL* 3.7 17.9 - - + -
1050A ASN* 4.9 9.0 + - - +
1051A VAL* 3.9 22.7 - - + -
1065A GLU 3.3 11.8 + - - +
1066A LYS 3.5 8.1 - - - +
1068A ASN* 1.3 77.4 - - - +
1070A LEU* 1.3 60.6 + - - +
1072A GLN* 3.2 37.2 + - - +
1073A LEU* 3.3 37.3 + - + +
1546A THR* 3.2 26.6 + - - +
1547A GLY* 4.7 2.6 - - - +
478N GLU 5.9 1.0 + - - -
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Residues in contact with LEU1070 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A VAL* 4.5 8.7 - - + -
1049A VAL* 4.1 6.7 - - + +
1066A LYS 2.8 14.9 + - - +
1067A GLU* 3.1 11.0 + - + +
1069A ARG* 1.3 74.5 - - - +
1071A LEU* 1.3 53.2 + - - +
1073A LEU* 3.1 22.4 + - + +
1074A CYS* 2.8 41.6 + - - -
1108A THR* 4.1 7.6 - - - +
1109A GLY* 3.9 22.0 - - - +
1118A VAL* 3.4 41.7 - - + +
1120A LEU* 3.9 27.4 - - + +
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Residues in contact with LEU1071 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A GLU 2.8 17.2 + - - +
1068A ASN* 3.4 10.0 + - - +
1070A LEU* 1.3 72.7 - - - +
1072A GLN* 1.3 61.1 + - + +
1074A CYS* 3.2 5.2 + - + +
1075A GLN* 2.9 48.4 + - + +
1120A LEU* 3.9 21.5 - - + +
1125A ILE* 3.7 20.2 - - + -
1126A ASP 3.7 22.7 - - - +
1127A VAL* 4.5 8.7 - - + -
1131A MET* 6.1 2.7 - - + -
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Residues in contact with GLN1072 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068A ASN* 3.4 18.7 + - - +
1069A ARG* 3.2 35.7 + - - +
1070A LEU 3.3 0.4 - - - -
1071A LEU* 1.3 79.8 - - + +
1073A LEU* 1.3 60.4 + - - +
1075A GLN* 3.4 22.0 + - - +
1076A ARG* 3.7 3.6 + - - +
1546A THR* 5.1 2.8 - - - -
1547A GLY* 4.0 32.0 - - - +
1548A GLY* 5.1 2.4 - - - +
1555A HIS* 4.4 9.4 - - - -
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Residues in contact with LEU1073 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A VAL* 3.8 31.4 - - + -
1048A ARG 4.3 2.9 - - - +
1049A VAL* 3.9 27.1 - - + -
1069A ARG* 3.3 41.9 + - + +
1070A LEU* 3.1 21.1 + - + +
1072A GLN* 1.3 75.3 - - - +
1074A CYS* 1.3 62.5 + - - +
1076A ARG* 3.3 35.2 + - - +
1077A THR* 3.2 23.5 + - - +
1546A THR* 5.1 2.0 - - + -
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Residues in contact with CYS1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A VAL* 5.8 1.6 - - - -
1070A LEU* 2.8 26.5 + - - -
1071A LEU* 3.2 13.0 + - + +
1073A LEU* 1.3 73.5 - - - +
1075A GLN* 1.3 64.0 + - - +
1077A THR* 2.9 33.3 + - - +
1078A MET* 3.2 24.9 - - + +
1107A LEU* 3.8 22.0 - - + -
1120A LEU* 3.6 31.2 - - + -
1131A MET* 5.0 2.9 - - + -
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Residues in contact with GLN1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A LEU* 2.9 40.9 + - + +
1072A GLN* 3.5 15.0 - - - +
1074A CYS* 1.3 78.9 - - - +
1076A ARG* 1.3 61.6 + - - +
1078A MET* 3.9 9.9 - - - +
1079A ALA* 3.9 5.9 + - - +
1131A MET* 6.0 1.8 - - - +
1550A MET 5.2 1.8 - - - +
1551A ASN* 4.9 2.9 - - - -
1552A TYR* 3.4 58.3 - - + +
1555A HIS* 4.0 9.5 - - + +
1595A HIS* 4.8 7.0 - - + +
1596A SER* 4.2 20.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG1076 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1047A VAL* 4.6 11.3 - - - +
1072A GLN 3.7 1.4 + - - +
1073A LEU* 3.3 51.3 + - - +
1074A CYS 3.2 0.6 - - - -
1075A GLN* 1.3 77.5 - - - +
1077A THR* 1.3 66.1 + - + +
1079A ALA* 3.2 12.8 + - - +
1080A LEU* 3.2 25.2 + - + +
1543A HIS* 3.2 49.5 + - - -
1544A MET* 6.1 0.4 - - - -
1546A THR* 3.6 19.9 - - - +
1555A HIS* 3.6 27.5 + - + +
1559A HIS* 3.8 16.8 - - - +
----------------------------------------------------------
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Residues in contact with THR1077 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042A GLN 5.7 1.1 - - - +
1043A SER* 3.8 14.3 + - - +
1047A VAL* 3.9 26.7 - - + -
1073A LEU 3.2 14.6 + - - +
1074A CYS* 2.9 30.3 + - - -
1076A ARG* 1.3 74.8 - - + +
1078A MET* 1.3 58.2 + - - -
1080A LEU* 3.2 22.0 + - + +
1081A PRO* 3.0 21.3 - - - +
1105A LEU* 4.6 5.0 - - - +
1106A ASN 5.0 8.8 + - - +
1107A LEU* 4.1 16.9 - - - +
----------------------------------------------------------
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Residues in contact with MET1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A CYS* 3.2 26.8 + - + +
1075A GLN* 3.9 19.3 - - - +
1077A THR* 1.3 76.3 + - - +
1079A ALA* 1.3 62.1 + - - +
1081A PRO* 3.3 18.4 - - - +
1082A VAL* 4.8 0.9 + - - +
1105A LEU* 5.1 2.0 - - - -
1107A LEU* 3.7 20.0 - - + -
1131A MET* 3.7 43.3 - - + -
1132A THR* 3.9 2.9 - - - +
1135A ALA* 3.5 38.7 - - + +
1138A HIS* 4.7 4.7 - - - +
1552A TYR* 3.4 19.6 + - + -
1596A SER* 4.0 17.5 - - - +
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Residues in contact with ALA1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075A GLN 3.9 9.6 + - - +
1076A ARG 3.2 10.1 + - - +
1078A MET* 1.3 80.3 - - - +
1080A LEU* 1.3 64.0 + - - +
1082A VAL* 3.2 22.0 + - - +
1083A GLY 3.8 3.1 + - - -
1552A TYR* 3.6 10.6 - - + -
1555A HIS* 3.6 8.3 - - + +
1556A LEU* 3.3 42.3 - - + +
1559A HIS* 4.6 7.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU1080 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LEU 3.5 15.9 - - - +
1041A LEU* 3.8 16.1 - - - +
1042A GLN 3.4 26.5 - - - +
1043A SER* 4.6 1.8 - - - +
1076A ARG* 3.2 24.7 - - + +
1077A THR* 3.6 24.2 - - + +
1079A ALA* 1.3 75.7 - - - +
1081A PRO* 1.4 60.4 - - + +
1083A GLY* 3.2 4.5 + - - -
1084A ARG* 2.8 36.6 + - - +
1543A HIS* 4.8 1.3 - - + +
1559A HIS* 3.4 43.7 - - + +
----------------------------------------------------------
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Residues in contact with PRO1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043A SER* 3.9 12.3 - - - +
1077A THR 3.0 25.8 - - - +
1078A MET 3.3 9.9 - - - +
1080A LEU* 1.4 79.8 - - + +
1082A VAL* 1.3 61.8 - - - +
1084A ARG* 3.9 23.1 - - + +
1085A GLY* 3.0 20.4 + - - -
1105A LEU* 4.2 3.6 - - + -
1135A ALA 4.2 3.4 - - - +
1138A HIS* 3.7 9.6 - - + -
1139A ASN* 3.5 37.9 - - + +
1142A ALA* 3.3 12.1 - - + +
1608A HIS* 4.7 0.2 - - - -
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Residues in contact with VAL1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078A MET 4.9 1.6 - - - +
1079A ALA* 3.2 10.6 + - - +
1081A PRO* 1.3 74.5 - - - +
1083A GLY* 1.3 62.0 + - - +
1085A GLY* 3.6 6.6 + - - -
1086A MET* 3.8 14.8 + - - +
1138A HIS* 3.5 36.6 - - + +
1552A TYR* 5.2 0.9 - - - +
1556A LEU* 3.7 29.2 - - + -
1560A MET* 4.0 10.3 - - + -
1607A ARG* 3.8 30.3 - - + +
1608A HIS* 4.0 17.5 - - + +
1610A TYR* 4.2 7.1 + - + -
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Residues in contact with GLY1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041A LEU* 3.8 9.0 - - - -
1079A ALA 3.8 3.8 + - - -
1080A LEU 3.2 5.2 + - - -
1082A VAL* 1.3 74.9 - - - +
1084A ARG* 1.3 63.6 + - - +
1086A MET* 3.3 23.4 + - - +
1087A PHE* 3.5 5.2 + - - +
1559A HIS* 3.9 26.7 - - - -
1560A MET* 4.3 8.4 - - - +
1563A GLY* 3.7 8.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG1084 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014A ASP 4.3 9.4 + - - -
1015A GLY* 5.6 0.9 - - - -
1016A MET* 3.7 34.1 - - + +
1041A LEU* 3.6 24.0 + - + +
1043A SER* 3.7 22.8 - - - +
1080A LEU 2.8 21.5 + - - +
1081A PRO* 3.3 14.9 + - + +
1083A GLY* 1.3 69.6 - - - +
1085A GLY* 1.3 65.1 + - - +
1087A PHE* 3.2 7.8 + - - +
1088A THR* 3.0 32.8 - - + +
1103A PRO* 3.5 27.2 - - - +
1139A ASN* 2.7 32.1 + - - -
1142A ALA* 3.5 25.5 - - - +
1143A ALA* 4.1 6.3 - - - +
1146A LYS* 5.9 1.7 - - - +
----------------------------------------------------------
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Residues in contact with GLY1085 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1081A PRO 3.0 14.9 + - - -
1082A VAL 3.6 1.3 + - - -
1083A GLY 3.3 0.4 - - - -
1084A ARG* 1.3 72.7 - - - +
1086A MET* 1.3 66.3 + - - +
1087A PHE 3.2 0.7 + - - -
1088A THR* 3.2 20.6 - - - +
1089A LEU* 3.3 8.8 + - - +
1142A ALA* 4.0 28.0 - - - +
1145A LEU* 4.5 1.9 - - - +
1608A HIS* 6.0 0.7 - - - -
1610A TYR* 3.3 14.1 - - - -
----------------------------------------------------------
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Residues in contact with MET1086 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082A VAL* 3.8 9.8 + - + +
1083A GLY* 3.3 8.9 + - - +
1085A GLY* 1.3 75.1 - - - +
1087A PHE* 1.3 60.6 + - - +
1089A LEU* 3.2 9.2 - - - +
1560A MET* 3.3 47.8 - - + +
1563A GLY* 3.6 14.1 - - - +
1564A LEU* 3.0 41.7 - - + -
1567A LEU* 3.7 7.4 - - + +
1568A GLY 2.9 23.6 + - - -
1588A LEU* 5.2 1.3 - - + -
1607A ARG 4.9 0.2 - - - +
1610A TYR* 3.1 53.1 + - + -
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Residues in contact with PHE1087 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A MET* 3.8 31.2 - - - -
1019A MET* 3.7 30.1 - - + +
1024A MET* 4.6 2.0 - - + -
1034A VAL* 4.5 19.3 - - + -
1037A VAL* 3.7 24.9 - - + -
1038A ARG* 4.2 12.6 - - + -
1041A LEU* 3.8 19.5 - - + -
1083A GLY 3.5 2.2 + - - +
1084A ARG 3.2 8.7 + - - +
1085A GLY 3.1 0.2 - - - -
1086A MET* 1.3 78.7 - - - +
1088A THR* 1.3 65.6 + - + +
1563A GLY* 4.4 3.6 - - - -
1566A PHE* 3.3 36.8 - - + -
1568A GLY 3.2 4.3 - - - -
1569A GLY* 2.7 35.7 + - - -
----------------------------------------------------------
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Residues in contact with THR1088 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A MET* 4.2 16.6 - - + -
1018A ASP 4.3 1.2 + - - -
1019A MET* 3.7 24.1 - - - -
1084A ARG* 3.0 26.0 + - + +
1085A GLY* 3.2 8.3 - - - +
1087A PHE* 1.3 87.9 - - + +
1089A LEU* 1.3 56.2 + - - +
1091A SER* 3.7 12.5 + - - -
1142A ALA 4.3 3.8 - - - +
1146A LYS* 3.1 48.3 + - - +
----------------------------------------------------------
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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