Contacts of the helix formed by residues 1114 - 1142 (chain A) in PDB entry 6PUO
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 GLU1114 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A LYS* 4.2 5.5 - - - +
1113A LEU* 1.3 82.9 - - - +
1115A LYS* 1.3 59.2 + - + +
1116A ASN* 3.3 15.9 - - - +
1117A GLU* 3.1 11.4 + - + +
1118A GLU* 2.7 34.9 + - - +
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Residues in contact with LYS1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1113A LEU 4.1 1.2 + - - -
1114A GLU* 1.3 75.8 + - - +
1116A ASN* 1.3 66.7 + - + +
1118A GLU* 3.8 11.6 - - - +
1119A ALA* 2.9 31.4 + - - +
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Residues in contact with ASN1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1114A GLU* 3.4 19.5 - - - +
1115A LYS* 1.3 88.6 - - + +
1117A GLU* 1.3 69.7 + - - +
1119A ALA* 4.1 4.7 + - - +
1120A ALA* 3.8 15.2 + - - +
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Residues in contact with GLU1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A LYS* 2.6 37.1 + - - +
1113A LEU* 3.4 33.0 - - - +
1114A GLU* 3.1 10.9 + - + +
1116A ASN* 1.3 86.8 + - - +
1118A GLU* 1.3 61.4 + - - +
1119A ALA 3.2 0.2 - - - -
1120A ALA* 3.2 8.2 + - + +
1121A LEU* 3.0 29.2 + - - +
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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
----------------------------------------------------------
707A ARG* 2.4 38.9 + - - +
708A VAL 4.1 6.9 - - - +
709A SER* 5.2 0.3 - - - -
710A GLU 5.7 0.7 + - - -
1112A LYS* 5.5 6.2 - - - +
1113A LEU* 4.5 24.0 + - + +
1114A GLU 2.7 19.6 + - - +
1115A LYS* 3.8 13.5 - - - +
1117A GLU* 1.3 80.9 + - - +
1119A ALA* 1.3 56.8 + - - +
1121A LEU* 3.3 6.5 + - + +
1122A LEU* 2.9 40.8 + - + +
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Residues in contact with ALA1119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1115A LYS 2.9 17.4 + - - +
1116A ASN* 4.2 6.5 - - - +
1118A GLU* 1.3 76.6 - - - +
1120A ALA* 1.3 56.1 + - - +
1122A LEU* 3.3 7.1 + - - +
1123A SER* 2.9 30.4 + - - -
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Residues in contact with ALA1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A ARG* 4.6 14.8 + - - +
1116A ASN 3.8 9.9 + - - +
1117A GLU* 3.2 11.5 + - + +
1119A ALA* 1.3 77.6 - - - +
1121A LEU* 1.3 62.4 + - - +
1123A SER* 2.7 20.5 + - - -
1124A TRP* 3.0 14.8 + - - +
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Residues in contact with LEU1121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A ARG* 4.1 25.3 - - + +
703A LYS* 4.5 18.2 - - + -
704A LEU* 3.8 33.7 - - + -
707A ARG* 4.4 13.9 - - - -
1113A LEU* 4.3 24.2 - - + -
1117A GLU* 3.0 16.3 + - - +
1118A GLU* 3.6 10.3 - - + +
1119A ALA 3.3 0.2 - - - -
1120A ALA* 1.3 76.1 - - - +
1122A LEU* 1.3 61.2 + - + +
1124A TRP* 3.3 22.6 + - + +
1125A GLU* 3.0 26.5 + - - +
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Residues in contact with LEU1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A GLN* 4.0 33.3 - - + +
647A ASP* 4.2 11.2 - - + -
707A ARG* 3.5 34.3 - - - +
1118A GLU* 2.9 31.9 + - + +
1119A ALA* 3.9 6.5 - - - +
1121A LEU* 1.3 79.0 - - + +
1123A SER* 1.3 57.9 + - - +
1125A GLU* 3.3 23.6 + - - +
1126A ILE* 2.9 32.3 + - - +
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Residues in contact with SER1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119A ALA 2.9 15.1 + - - -
1120A ALA* 2.7 22.3 + - - -
1122A LEU* 1.3 72.0 - - - +
1124A TRP* 1.3 64.8 + - - +
1126A ILE* 3.3 10.8 + - - +
1127A TYR* 3.0 23.6 + - - +
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Residues in contact with TRP1124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A CYS* 3.5 35.2 - - - -
696A LYS* 4.2 18.9 - - + +
697A ASP* 4.1 15.9 - - + -
700A ARG* 3.3 57.9 - - + +
701A ALA* 4.4 3.4 - - - -
704A LEU* 4.7 3.4 - - + -
1120A ALA 3.0 14.7 + - - +
1121A LEU* 3.4 23.3 - - + +
1123A SER* 1.3 77.3 + - - +
1125A GLU* 1.3 62.6 + - - +
1127A TYR* 3.3 12.9 + + + +
1128A LEU* 3.1 53.5 + - + +
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Residues in contact with GLU1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A GLN 4.4 3.6 - - - +
647A ASP* 3.3 10.7 - - - +
648A CYS* 2.8 45.6 + - - -
649A ILE* 3.6 11.3 + - + +
689A VAL* 5.2 3.4 - - + +
693A CYS* 5.4 3.1 - - - -
704A LEU* 4.1 31.8 - - + +
707A ARG* 5.2 1.9 + - - -
1121A LEU 3.0 11.8 + - - +
1122A LEU* 3.3 26.7 + - - +
1124A TRP* 1.3 79.8 - - + +
1126A ILE* 1.3 57.8 + - - +
1128A LEU* 3.3 6.8 + - - +
1129A LYS* 2.9 28.4 + - - +
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Residues in contact with ILE1126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A SER 3.3 18.4 - - - +
646A GLN* 3.3 32.1 - - + +
648A CYS* 6.1 0.2 - - - -
1122A LEU 2.9 18.8 + - - +
1123A SER* 3.3 13.2 + - - +
1125A GLU* 1.3 75.7 - - - +
1127A TYR* 1.3 64.5 + - - +
1129A LYS* 3.2 20.5 + - - +
1130A GLU* 3.0 23.0 + - + +
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Residues in contact with TYR1127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LYS* 6.5 0.7 - - - -
1123A SER 3.0 12.6 + - - +
1124A TRP* 3.3 16.1 + + + +
1126A ILE* 1.3 77.9 - - - +
1128A LEU* 1.3 82.5 + - + +
1130A GLU* 3.3 11.0 + - + +
1131A ASN* 3.1 30.5 + - + +
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Residues in contact with LEU1128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A VAL* 5.5 4.7 - - + +
692A GLU* 4.1 20.4 - - + +
693A CYS* 3.7 33.4 - - + +
696A LYS* 4.3 23.3 - - + +
1124A TRP* 3.1 51.8 + - + +
1125A GLU* 3.9 4.7 - - - +
1126A ILE 3.3 0.2 - - - -
1127A TYR* 1.3 93.4 - - + +
1129A LYS* 1.3 59.8 + - - +
1131A ASN* 3.3 9.1 + - + +
1132A TYR* 3.0 28.9 + - - +
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Residues in contact with LYS1129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TRP* 4.5 15.9 - - + +
643A ALA* 2.5 34.0 + - - +
644A GLN* 4.4 1.0 - - - +
645A SER 3.7 21.2 + - - -
648A CYS* 3.6 36.3 - - + -
689A VAL* 4.7 15.1 - - + +
1125A GLU 2.9 13.4 + - - +
1126A ILE* 3.2 23.1 + - - +
1128A LEU* 1.3 75.1 - - - +
1130A GLU* 1.3 71.1 + - - +
1132A TYR* 3.2 7.4 + - - +
1133A LEU* 3.0 33.5 + - + +
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Residues in contact with GLU1130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ALA 5.3 1.4 - - - +
1126A ILE* 3.0 13.9 + - + +
1127A TYR* 3.5 15.0 - - + +
1128A LEU 3.3 0.2 - - - -
1129A LYS* 1.3 87.3 + - - +
1131A ASN* 1.3 61.4 + - - +
1133A LEU* 3.3 14.6 + - - +
1134A GLN* 3.1 40.5 + - + +
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Residues in contact with ASN1131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A GLU* 3.2 26.1 + - - -
696A LYS* 5.7 1.6 - - - +
1127A TYR* 3.1 23.9 + - + +
1128A LEU* 3.7 15.2 - - + +
1130A GLU* 1.3 76.3 - - - +
1132A TYR* 1.3 62.8 + - - +
1134A GLN* 3.3 11.1 + - - +
1135A ASN* 3.1 34.7 + - - +
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Residues in contact with TYR1132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TRP* 4.7 7.2 - + - -
684A HIS 4.7 1.4 + - - -
685A ARG* 4.2 16.6 - - + -
688A GLY* 3.5 34.5 - - - +
689A VAL* 3.7 25.6 - - + -
692A GLU* 4.4 17.3 - - + -
1128A LEU 3.0 17.0 + - - +
1129A LYS* 3.2 6.9 + - + +
1131A ASN* 1.3 80.1 - - - +
1133A LEU* 1.3 81.2 + - + +
1135A ASN* 3.3 7.2 + - + +
1136A ARG* 2.9 63.2 + - + +
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Residues in contact with LEU1133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A TRP* 4.5 12.6 - - + -
643A ALA* 4.0 35.2 - - + +
685A ARG* 5.4 2.0 - - - +
1129A LYS* 3.0 29.0 + - + +
1130A GLU* 3.7 15.9 - - - +
1132A TYR* 1.3 95.8 - - + +
1134A GLN* 1.3 65.8 + - - +
1136A ARG* 3.9 14.8 - - - +
1137A GLN* 3.0 28.5 + - - +
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Residues in contact with GLN1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130A GLU* 3.1 32.3 + - + +
1131A ASN* 3.5 10.5 - - - +
1132A TYR 3.3 0.2 - - - -
1133A LEU* 1.3 78.0 - - - +
1135A ASN* 1.3 65.3 + - - +
1137A GLN* 3.9 16.3 + - - +
1138A PHE* 3.0 25.9 + - - +
229D SER 3.7 9.4 + - - +
230D SER* 2.4 34.9 + - - -
231D TYR* 4.7 1.0 - - - +
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Residues in contact with ASN1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A GLU* 4.3 11.9 + - - +
1131A ASN* 3.1 36.5 + - - +
1132A TYR* 3.3 9.3 + - + +
1134A GLN* 1.3 78.2 - - - +
1136A ARG* 1.3 58.1 + - - +
1138A PHE* 3.4 8.8 + - - +
1139A GLN* 3.0 46.9 + - - +
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Residues in contact with ARG1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A GLU* 5.0 13.7 + - - +
684A HIS* 6.2 1.6 - - - +
685A ARG* 3.3 40.7 - - - +
1132A TYR* 2.9 50.3 + - + +
1133A LEU* 3.9 12.9 - - - +
1134A GLN 3.3 0.2 - - - -
1135A ASN* 1.3 77.9 - - - +
1137A GLN* 1.3 56.7 + - - +
1139A GLN* 3.4 8.9 + - - +
1140A GLN* 2.9 57.9 + - + +
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Residues in contact with GLN1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A LEU 3.0 17.6 + - - +
1134A GLN* 3.9 17.2 + - - +
1136A ARG* 1.3 77.0 - - - +
1138A PHE* 1.3 65.4 + - - +
1140A GLN* 3.2 9.8 + - - +
1141A LYS* 3.0 38.6 + - - +
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Residues in contact with PHE1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A GLN 3.0 18.3 + - - +
1135A ASN* 3.9 8.3 - - - +
1137A GLN* 1.3 79.6 - - - +
1139A GLN* 1.3 71.6 + - + +
1141A LYS* 3.3 20.1 + - + +
1142A GLN* 3.5 37.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A ASN* 3.0 34.2 + - - +
1136A ARG* 3.9 6.7 - - - +
1138A PHE* 1.3 89.4 - - + +
1140A GLN* 1.3 63.2 + - + +
1142A GLN* 3.3 18.0 + - - +
1143A ARG* 4.0 8.5 + - - +
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Residues in contact with GLN1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1136A ARG* 2.9 57.7 + - + +
1137A GLN* 3.2 7.6 + - - +
1139A GLN* 1.3 75.9 - - + +
1141A LYS* 1.3 64.4 + - - +
1142A GLN 3.5 0.2 + - - -
1143A ARG* 3.1 40.2 + - - +
1146A GLN* 4.4 6.9 - - - +
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Residues in contact with LYS1141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137A GLN* 3.0 30.6 + - - +
1138A PHE* 3.5 15.7 - - + +
1139A GLN 3.2 0.6 - - - -
1140A GLN* 1.3 78.7 - - - +
1142A GLN* 1.3 74.1 + - - +
1143A ARG 3.2 10.0 + - - +
1146A GLN* 3.9 21.4 - - - +
1147A LYS* 4.6 9.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A PHE* 3.5 37.2 - - + +
1139A GLN* 3.3 11.3 + - - +
1140A GLN 3.3 1.6 - - - -
1141A LYS* 1.3 99.9 - - - +
1143A ARG* 1.3 63.0 + - - +
1144A PRO* 3.7 5.2 - - - +
1147A LYS* 4.0 25.6 + - - +
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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