Contacts of the helix formed by residues 1092 - 1122 (chain A) in PDB entry 3IKM
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 PHE1092 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A LYS* 2.9 62.1 - - + +
1030A ARG* 3.8 12.3 - - - -
1045A ALA* 3.3 37.5 - - + -
1048A ALA* 3.0 33.9 - - + -
1049A TRP* 6.0 0.2 - - - -
1090A GLU 3.5 11.2 - - - -
1091A GLU* 1.3 77.9 - - - +
1093A MET* 1.3 64.8 + - + +
1094A THR* 3.5 6.3 - - - +
1095A SER* 2.6 25.5 + - - -
1096A ARG* 2.9 18.0 - - - +
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Residues in contact with MET1093 (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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956A GLY 5.0 2.2 - - - +
995A TYR* 4.6 9.4 - - + +
1007A GLU* 3.0 48.2 - - + +
1011A PRO* 5.9 5.8 - - + -
1092A PHE* 1.3 71.3 - - + +
1094A THR* 1.3 62.7 + - - +
1096A ARG* 2.8 13.6 + - - +
1097A VAL* 2.4 51.8 + - + -
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Residues in contact with THR1094 (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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307A PHE* 5.4 11.7 - - + -
956A GLY* 3.0 37.8 + - - -
957A ALA* 4.0 13.6 - - + +
961A PHE* 5.1 8.0 - - + -
1052A GLY* 5.7 5.2 - - - -
1056A GLU* 4.8 11.7 - - - +
1091A GLU 5.9 0.2 - - - -
1092A PHE* 3.5 5.4 - - - +
1093A MET* 1.3 78.4 - - - +
1095A SER* 1.3 73.6 - - - +
1097A VAL* 3.7 0.2 - - - -
1098A ASN* 2.7 21.4 + - + +
1099A TRP* 6.0 0.4 - - + -
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Residues in contact with SER1095 (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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305A SER* 4.2 17.0 - - - -
307A PHE* 4.9 10.7 - - - -
308A GLN* 4.8 3.6 - - - -
1091A GLU* 3.5 17.9 + - - -
1092A PHE 2.6 23.6 + - - -
1093A MET 3.0 0.2 + - - -
1094A THR* 1.3 85.7 - - - +
1096A ARG* 1.3 64.8 + - - +
1098A ASN 2.7 8.3 + - - -
1099A TRP* 2.8 42.8 + - - -
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Residues in contact with ARG1096 (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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1010A LEU* 2.0 48.1 + - + +
1011A PRO* 3.9 5.7 - - - +
1013A ASP 4.1 0.6 + - - -
1023A GLN* 4.9 1.6 - - - +
1025A LEU 5.0 5.8 - - - +
1027A LYS* 4.0 9.2 - - - +
1028A VAL* 3.1 21.8 - - - +
1029A GLN* 2.5 49.7 + - - +
1091A GLU* 4.7 2.7 - - - -
1092A PHE* 2.9 33.9 - - - +
1093A MET* 2.8 11.0 + - - +
1095A SER* 1.3 82.9 + - - +
1097A VAL* 1.3 63.9 + - + +
1099A TRP* 3.1 7.0 + - - +
1100A VAL* 2.9 27.1 + - + +
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Residues in contact with VAL1097 (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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955A TYR 3.4 6.7 - - - +
956A GLY 4.8 3.6 - - - +
1003A TRP* 3.4 42.2 - - + +
1006A ARG* 4.3 17.0 - - + -
1007A GLU* 5.4 11.4 - - + +
1010A LEU* 6.4 1.8 - - + -
1093A MET* 2.4 51.9 + - + +
1094A THR* 3.7 2.2 - - - +
1096A ARG* 1.3 72.4 - - + +
1098A ASN* 1.3 66.6 + - - +
1100A VAL* 3.2 20.3 + - - +
1101A VAL* 3.7 8.7 + - - +
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Residues in contact with ASN1098 (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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955A TYR* 2.4 65.0 + - - +
956A GLY* 4.0 3.4 - - - +
1056A GLU* 4.4 12.5 + - - -
1074A VAL* 3.1 25.6 - - - +
1094A THR* 2.7 11.4 + - - +
1095A SER 2.7 14.2 + - - +
1097A VAL* 1.3 73.2 - - - +
1099A TRP* 1.3 75.8 + - + +
1101A VAL* 3.6 4.9 + - - +
1102A GLN* 2.9 30.6 + - - -
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Residues in contact with TRP1099 (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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305A SER* 5.0 6.5 - - - -
306A SER* 4.9 14.4 - - - -
307A PHE* 5.4 6.1 - + - -
849A THR* 4.6 1.6 - - + +
850A ILE* 2.7 49.7 - - + +
851A THR* 2.7 38.2 + - - +
1023A GLN* 3.7 15.5 - - - +
1059A ASN* 5.8 3.4 - - - -
1074A VAL* 6.1 2.0 - - + -
1094A THR* 6.0 0.9 - - + -
1095A SER* 2.8 55.3 + - - +
1096A ARG* 3.6 9.9 - - - +
1098A ASN* 1.3 95.2 - - + +
1100A VAL* 1.3 55.7 + - - +
1102A GLN* 4.0 11.6 + - + -
1103A SER* 2.2 44.0 + - - -
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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
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902A LEU* 4.7 10.1 - - + -
1006A ARG* 3.9 31.4 - - + +
1010A LEU* 4.3 31.9 - - + -
1016A GLU 6.4 0.2 - - - -
1017A GLY* 5.3 9.9 - - - -
1023A GLN* 4.0 13.4 + - - +
1096A ARG* 2.9 18.4 + - + +
1097A VAL* 3.2 11.4 + - - +
1099A TRP* 1.3 75.0 - - - +
1101A VAL* 1.3 69.8 + - + +
1103A SER* 3.7 0.9 - - - -
1104A SER* 2.5 39.6 + - - +
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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
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895A GLU* 3.8 26.0 - - + +
898A ILE* 3.2 39.3 - - + +
899A ALA* 5.0 2.5 - - + -
902A LEU* 6.2 1.6 - - + -
954A ILE* 4.3 17.7 - - + +
955A TYR* 4.8 0.4 - - + -
1003A TRP* 3.7 35.4 - - + -
1006A ARG* 5.9 0.2 - - + -
1097A VAL 3.9 10.8 - - - +
1098A ASN 3.6 6.7 - - - +
1099A TRP 3.3 0.2 - - - -
1100A VAL* 1.3 82.1 - - + +
1102A GLN* 1.3 66.4 + - - +
1104A SER 3.2 0.3 + - - -
1105A ALA* 2.9 19.2 + - - +
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Residues in contact with GLN1102 (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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851A THR* 2.9 27.9 + - + +
853A ARG* 2.4 40.3 + - + +
895A GLU* 3.9 8.8 + - - +
955A TYR* 2.6 48.1 - - - -
1074A VAL* 3.2 28.5 - - + +
1098A ASN* 2.9 24.4 + - - +
1099A TRP* 3.1 15.5 + - - +
1101A VAL* 1.3 76.7 - - - +
1103A SER* 1.3 67.0 + - - +
1105A ALA* 2.5 6.7 + - - -
1106A VAL* 3.1 3.8 + - - +
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Residues in contact with SER1103 (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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851A THR* 3.5 7.6 + - - -
852A ARG* 3.7 15.3 + - - +
1016A GLU 5.6 4.3 - - - -
1023A GLN* 2.0 45.3 + - - -
1099A TRP* 2.2 39.5 + - - +
1100A VAL* 3.7 1.8 - - - -
1102A GLN* 1.3 67.6 - - - +
1104A SER* 1.3 52.9 + - - +
1106A VAL* 2.9 27.3 + - - +
1107A ASP* 2.8 23.6 - - - +
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Residues in contact with SER1104 (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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898A ILE* 4.1 12.4 - - - +
902A LEU* 5.8 3.8 - - - +
1016A GLU 5.2 1.0 + - - -
1017A GLY* 4.6 16.6 + - - -
1019A TRP* 6.0 1.1 - - - -
1100A VAL* 2.5 36.5 + - - +
1101A VAL* 3.4 6.3 - - - -
1102A GLN 2.8 0.2 + - - -
1103A SER* 1.3 70.1 - - - +
1105A ALA* 1.3 56.1 + - - -
1106A VAL 3.1 4.5 - - - -
1107A ASP* 3.4 19.1 + - - +
1108A TYR* 3.2 19.8 + - - +
1164A PHE* 3.9 11.5 - - - -
1168A LEU* 6.3 2.7 - - - -
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Residues in contact with ALA1105 (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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853A ARG* 2.6 41.2 + - - +
894A GLN* 3.2 17.3 - - + +
895A GLU* 3.9 11.9 - - + -
898A ILE* 4.6 5.6 - - + -
1101A VAL 2.9 9.7 + - - +
1102A GLN 2.5 6.8 + - - +
1104A SER* 1.3 71.9 - - - +
1106A VAL* 1.3 64.7 + - - +
1108A TYR* 3.1 21.3 - - - +
1109A LEU* 3.1 8.7 + - - +
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Residues in contact with VAL1106 (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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430A MET* 5.8 2.0 - - + -
851A THR* 3.2 26.2 - - + +
852A ARG* 3.8 28.5 - - + +
853A ARG* 3.8 21.5 - - - +
1102A GLN 3.1 12.1 - - - +
1103A SER* 2.9 19.3 - - - +
1105A ALA* 1.3 76.3 - - - +
1107A ASP* 1.3 64.8 + - - +
1109A LEU* 2.8 19.9 + - + +
1110A HIS* 3.1 34.5 + - + +
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Residues in contact with ASP1107 (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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423A THR* 4.9 6.7 + - - -
852A ARG* 3.5 14.6 + - - -
1016A GLU 5.2 2.1 - - - +
1017A GLY* 5.3 0.3 - - - +
1019A TRP* 3.7 47.8 - - + +
1020A ILE 3.8 12.5 - - - +
1103A SER 2.8 18.1 - - - +
1104A SER* 3.4 17.7 + - - +
1106A VAL* 1.3 75.0 - - - +
1108A TYR* 1.3 68.2 + - - +
1110A HIS* 3.0 22.6 + - - +
1111A LEU* 3.4 14.8 + - - +
1164A PHE* 4.3 4.0 - - + -
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Residues in contact with TYR1108 (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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891A VAL* 4.4 4.1 - - + +
894A GLN* 4.1 33.2 - - + +
897A TRP* 2.9 33.8 - + - -
898A ILE* 4.4 5.2 - - + -
1104A SER 3.2 2.6 + - - -
1105A ALA* 3.1 20.4 - - - +
1107A ASP* 1.3 80.4 - - - +
1109A LEU* 1.3 67.5 + - - +
1111A LEU 3.0 7.8 + - - -
1112A MET* 3.0 47.1 + - + +
1160A THR* 3.7 12.6 - - + +
1161A ARG* 3.0 39.9 + - + +
1164A PHE* 3.2 33.1 - + + -
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Residues in contact with LEU1109 (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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430A MET* 5.8 0.9 - - - -
853A ARG* 5.5 6.3 - - + +
894A GLN* 4.2 17.5 - - - +
1105A ALA 3.1 5.0 + - - +
1106A VAL* 2.8 17.2 + - + +
1108A TYR* 1.3 75.3 - - - +
1110A HIS* 1.3 60.2 + - + +
1112A MET* 2.8 17.7 - - - +
1113A LEU* 2.8 45.2 - - + +
1132A SER* 3.5 39.0 - - - +
1134A HIS 4.4 10.3 - - - +
1137A VAL* 3.2 33.9 - - + -
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Residues in contact with HIS1110 (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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422A VAL* 4.3 6.1 - - + +
423A THR* 3.7 36.5 + - + +
426A GLY* 3.6 18.7 + - - -
427A MET* 3.9 25.6 - - + +
430A MET* 4.7 17.0 - - + -
852A ARG* 5.4 2.1 + - - -
1106A VAL* 3.7 36.2 - - + +
1107A ASP* 3.0 13.9 + - - +
1109A LEU* 1.3 77.7 - - + +
1111A LEU* 1.3 66.1 + - + +
1113A LEU* 3.5 8.8 - - - +
1114A VAL* 2.6 35.0 + - - +
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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
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139A PHE* 3.2 36.8 - - + -
422A VAL* 3.3 29.6 - - + -
1019A TRP* 3.1 44.9 - - + +
1107A ASP* 3.5 12.1 - - - +
1108A TYR 3.0 2.5 + - - +
1109A LEU 3.0 0.2 + - - -
1110A HIS* 1.3 78.9 - - + +
1112A MET* 1.3 72.2 + - - +
1113A LEU 2.8 2.4 + - - -
1114A VAL* 2.9 2.9 + - - +
1115A ALA* 2.8 27.7 + - - +
1156A THR* 4.5 1.6 - - - +
1160A THR* 3.2 25.1 - - + -
1163A MET* 4.0 2.0 - - - -
1164A PHE* 4.3 1.8 - - + -
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Residues in contact with MET1112 (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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891A VAL* 4.2 11.2 - - + -
894A GLN* 4.6 5.8 - - - -
1108A TYR* 3.0 48.0 - - + +
1109A LEU* 2.8 35.0 - - + +
1111A LEU* 1.3 75.7 - - - +
1113A LEU* 1.3 65.3 + - + +
1116A MET* 2.8 30.7 + - + +
1137A VAL* 4.1 12.1 - - + -
1139A TYR* 4.1 5.4 - - - +
1153A LEU* 5.8 2.2 - - + -
1156A THR* 3.0 23.0 - - + +
1157A ASN* 3.1 30.3 - - - +
1160A THR* 4.0 4.8 - - + +
1180A PHE* 5.1 0.4 - - + -
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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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426A GLY 4.2 11.0 - - - +
429A GLU* 5.7 0.4 - - + -
430A MET* 5.1 5.8 - - + +
1109A LEU* 2.8 42.8 - - + +
1110A HIS* 3.5 7.6 - - - +
1111A LEU 2.8 0.2 + - - -
1112A MET* 1.3 76.6 - - + +
1114A VAL* 1.3 63.8 + - - +
1116A MET* 3.0 4.2 + - - +
1117A LYS* 2.7 54.4 + - - +
1130A CYS* 3.9 14.4 - - - +
1132A SER* 3.5 21.8 - - - +
1137A VAL* 3.5 3.4 - - + -
1139A TYR* 3.0 28.9 - - + +
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Residues in contact with VAL1114 (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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139A PHE* 4.7 2.5 - - + +
142A LEU* 3.7 27.6 - - + -
143A ALA* 4.2 7.9 - - - +
146A GLN* 3.7 16.7 + - - +
422A VAL* 3.6 26.2 - - + +
425A ALA* 4.6 2.2 - - + -
426A GLY* 3.8 14.1 - - - +
1110A HIS 2.6 31.3 + - - +
1111A LEU* 2.9 6.2 + - + +
1113A LEU* 1.3 70.9 - - - +
1115A ALA* 1.3 57.3 + - - +
1117A LYS* 2.7 20.5 - - - +
1118A TRP* 3.0 29.6 + - - +
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Residues in contact with ALA1115 (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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139A PHE* 5.1 6.3 - - + -
142A LEU* 4.4 14.1 - - + -
1111A LEU 2.8 20.0 + - - +
1114A VAL* 1.3 73.4 - - - +
1116A MET* 1.3 52.0 + - - +
1118A TRP* 2.8 8.8 - - - +
1119A LEU* 2.6 42.3 + - + +
1156A THR* 3.1 22.7 - - + +
1159A LEU* 4.3 17.5 - - + -
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Residues in contact with MET1116 (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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887A VAL* 6.5 0.7 - - + -
1112A MET 2.8 23.8 + - - +
1113A LEU* 3.0 5.3 + - - +
1115A ALA* 1.3 76.2 - - - +
1117A LYS* 1.3 57.0 + - - +
1119A LEU* 3.0 5.4 + - - +
1120A PHE* 2.7 77.4 + - + -
1139A TYR* 4.4 25.1 - - + +
1149A ALA* 4.4 4.0 - - + +
1152A ALA* 3.1 19.1 - - + -
1153A LEU* 3.2 45.1 - - + +
1156A THR* 3.3 13.7 - - + +
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Residues in contact with LYS1117 (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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146A GLN* 3.4 24.7 - - - +
426A GLY* 3.0 31.2 + - - +
429A GLU* 3.7 40.4 - - + +
1113A LEU* 2.7 46.5 + - - +
1114A VAL* 2.7 27.7 - - - +
1116A MET* 1.3 73.3 - - + +
1118A TRP* 1.3 68.7 + - - +
1120A PHE* 3.2 8.1 + - - +
1121A GLU* 2.9 24.8 + - - +
1129A PHE 6.1 1.3 - - - +
1139A TYR* 6.1 2.7 - - + -
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Residues in contact with TRP1118 (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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130A LEU* 6.2 1.3 - - + -
131A TYR* 6.3 1.2 - - - -
141A LEU 5.8 0.2 - - - -
142A LEU* 3.1 49.3 - - + +
145A LYS* 2.9 58.6 - - + -
146A GLN* 4.5 7.9 - - + -
1114A VAL 3.0 13.0 + - - +
1115A ALA* 2.8 16.6 - - - +
1117A LYS* 1.3 85.3 - - - +
1119A LEU* 1.3 65.7 + - + -
1121A GLU* 2.7 41.3 - - - +
1122A GLU* 2.8 52.7 + - - +
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Residues in contact with LEU1119 (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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129A PRO* 6.1 4.5 - - + -
130A LEU* 5.0 18.6 - - + -
1115A ALA* 2.6 30.0 + - + +
1116A MET* 3.0 5.1 + - - +
1118A TRP* 1.3 81.6 - - + +
1120A PHE* 1.3 68.0 + - - +
1122A GLU* 2.8 41.4 + - + +
1123A PHE 3.6 2.8 - - - +
1152A ALA* 4.7 23.6 - - + +
1155A ILE* 5.5 11.2 - - + -
1156A THR* 4.6 8.7 - - - +
1159A LEU* 5.5 4.9 - - + -
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Residues in contact with PHE1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116A MET* 2.7 54.6 + - + +
1117A LYS* 3.6 8.1 - - - +
1119A LEU* 1.3 74.9 - - - +
1121A GLU* 1.3 66.5 + - + +
1123A PHE 3.1 9.5 - - - +
1125A ILE* 2.9 38.8 - - + +
1126A ASP* 3.8 18.8 - - + -
1127A GLY 3.2 40.4 - - - -
1128A ARG* 3.7 8.1 - - - -
1139A TYR* 4.6 11.2 - + + -
1140A LEU 3.9 1.3 - - - -
1141A VAL* 4.2 6.5 - - + -
1149A ALA* 3.9 20.9 - - + -
1152A ALA* 4.6 2.9 - - + -
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Residues in contact with GLU1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLN* 3.9 14.4 - - - +
290A ARG* 5.2 7.8 + - - -
429A GLU* 5.3 1.6 - - - +
1117A LYS* 2.9 15.6 - - - +
1118A TRP* 2.7 47.8 - - - +
1120A PHE* 1.3 76.8 - - - +
1122A GLU* 1.3 58.3 + - - +
1123A PHE* 2.4 21.7 + - - -
1125A ILE* 4.1 9.6 - - - +
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Residues in contact with GLU1122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 5.4 7.6 + - - -
1118A TRP* 2.8 58.4 + - - +
1119A LEU* 2.8 40.6 + - + +
1121A GLU* 1.3 79.8 - - - +
1123A PHE* 1.3 88.6 + - + +
1124A ALA* 4.9 1.2 - - - +
1231A LEU 4.9 2.4 - - - +
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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) + - + + + + + -
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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