Contacts of the helix formed by residues 1139 - 1169 (chain A) in PDB entry 5UAK
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 ILE1139 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A ILE* 5.5 2.0 - - + +
1001A VAL* 4.2 29.8 - - + +
1004A ALA* 3.9 28.0 - - + -
1005A ILE* 4.8 5.4 - - + +
1107A PHE* 3.5 31.0 - - + -
1135A LEU 3.3 14.9 + - - +
1136A ALA* 3.5 12.1 - - - +
1137A MET 3.4 0.2 - - - -
1138A ASN* 1.3 74.7 - - - +
1140A MET* 1.3 58.1 + - - +
1141A SER 3.2 3.1 - - - -
1142A THR* 2.6 51.2 + - - +
1143A LEU* 3.3 4.5 + - + -
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Residues in contact with MET1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 5.2 0.4 - - - +
131A PHE* 3.4 31.2 - - + -
134A ARG* 3.9 20.0 - - - +
1104A GLU* 4.2 16.8 - - + +
1107A PHE* 3.6 37.9 - - + -
1111A PHE* 5.5 0.7 - - + -
1136A ALA 4.9 0.2 - - - +
1137A MET* 3.2 24.8 + - - +
1138A ASN* 5.1 1.1 - - - -
1139A ILE* 1.3 81.4 - - - +
1141A SER* 1.3 62.3 + - - +
1143A LEU* 3.1 11.6 + - + +
1144A GLN* 2.9 41.4 + - + +
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Residues in contact with SER1141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 5.6 0.9 - - - +
348A MET* 3.7 31.3 - - - +
1138A ASN* 3.4 20.3 + - - -
1140A MET* 1.3 85.1 - - - +
1142A THR* 1.3 67.2 + - - +
1144A GLN* 3.8 10.0 + - - +
1145A TRP* 3.1 35.7 + - - -
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Residues in contact with THR1142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 5.8 2.0 - - + -
347A ARG* 6.3 0.4 - - - +
924A ASP* 5.1 4.7 - - - +
997A LEU* 4.1 14.0 - - + +
1000A ILE* 4.3 30.6 - - + +
1001A VAL* 3.6 8.0 - - - +
1138A ASN 5.3 2.0 - - - +
1139A ILE* 2.6 40.7 + - - +
1141A SER* 1.3 77.6 + - - +
1143A LEU* 1.3 52.3 + - - -
1145A TRP* 3.0 24.0 + - + +
1146A ALA* 2.8 35.0 + - - +
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Residues in contact with LEU1143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001A VAL* 4.2 30.5 - - + -
1026A PHE* 3.8 34.8 - - + -
1103A ILE* 4.9 3.5 - - + +
1107A PHE* 3.4 38.1 - - + -
1139A ILE* 3.3 5.6 + - + +
1140A MET* 3.1 14.5 + - + +
1142A THR* 1.3 81.5 + - - +
1144A GLN* 1.3 62.2 + - + +
1146A ALA* 3.6 4.6 + - + +
1147A VAL* 3.3 33.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN1144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 4.9 8.9 - - - -
1100A GLN* 4.5 19.7 + - - +
1103A ILE* 4.8 20.9 - - + +
1104A GLU* 4.5 29.9 + - - +
1140A MET* 2.9 26.4 + - + +
1141A SER* 4.0 9.8 - - - +
1143A LEU* 1.3 77.5 - - + +
1145A TRP* 1.3 61.4 + - + +
1147A VAL* 3.5 1.6 + - - +
1148A ASN* 2.8 33.1 + - - +
----------------------------------------------------------
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Residues in contact with TRP1145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A PHE* 4.1 13.7 - + - -
311A PHE* 5.6 3.6 - + - -
347A ARG* 4.9 2.9 - - - -
348A MET* 3.6 41.7 - - + -
352A ARG* 3.3 41.3 - - - -
356A TRP* 6.0 4.0 - + - -
993A ASP* 4.9 1.1 - - - +
997A LEU* 3.5 34.3 - - + +
1141A SER* 3.1 19.0 + - - -
1142A THR* 3.0 20.4 + - + +
1144A GLN* 1.3 81.1 + - + +
1146A ALA* 1.3 54.2 + - - +
1148A ASN* 3.8 11.3 - - + +
1149A SER* 2.8 36.4 + - - -
----------------------------------------------------------
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Residues in contact with ALA1146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A PHE* 4.0 9.9 - - + +
997A LEU* 3.8 31.6 - - + +
998A LEU* 4.7 9.0 - - + +
1001A VAL* 4.8 3.4 - - + -
1142A THR 2.8 19.7 + - - +
1143A LEU* 3.7 11.4 - - + +
1145A TRP* 1.3 72.7 - - - +
1147A VAL* 1.3 62.6 + - + +
1149A SER* 2.7 21.5 + - - -
1150A SER* 3.4 10.6 + - - -
----------------------------------------------------------
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Residues in contact with VAL1147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A PHE* 4.7 14.6 - - + +
1030A ARG* 3.9 17.0 - - + +
1099A PHE* 3.6 24.2 - - + -
1103A ILE* 3.5 32.8 - - + -
1143A LEU* 3.3 27.8 + - + +
1144A GLN 4.1 0.4 - - - +
1146A ALA* 1.3 75.1 - - + +
1148A ASN* 1.3 62.7 + - - +
1150A SER* 2.7 21.5 + - - -
1151A ILE* 3.8 9.9 - - - +
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Residues in contact with ASN1148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A PHE* 6.0 0.2 - - - -
1100A GLN* 4.6 18.3 - - - +
1144A GLN 2.8 22.4 + - - +
1145A TRP* 3.8 12.2 - - + +
1147A VAL* 1.3 77.6 - - - +
1149A SER* 1.3 60.9 + - - +
1151A ILE* 3.7 19.5 + - - +
1152A ASP* 3.5 22.5 + - - +
----------------------------------------------------------
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Residues in contact with SER1149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A THR* 4.9 6.2 - - - -
993A ASP* 4.0 19.3 - - - -
994A PHE* 3.8 21.8 - - - -
997A LEU* 4.5 0.6 - - - +
1145A TRP 2.8 18.9 + - - -
1146A ALA* 2.7 26.0 + - - -
1148A ASN* 1.3 72.2 + - - +
1150A SER* 1.3 53.4 + - - +
1152A ASP* 2.8 16.6 + - - +
1153A VAL* 2.8 36.5 + - - +
----------------------------------------------------------
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Residues in contact with SER1150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A TYR* 5.4 0.3 + - - -
994A PHE* 3.8 26.0 - - - -
1030A ARG* 3.6 29.5 + - - -
1146A ALA 3.4 3.2 + - - -
1147A VAL* 2.7 27.0 + - - -
1149A SER* 1.3 81.4 + - - +
1151A ILE* 1.3 51.4 + - - +
1153A VAL* 3.7 9.0 - - - +
1154A ASP* 2.8 36.3 + - - +
----------------------------------------------------------
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Residues in contact with ILE1151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A ARG* 4.5 9.2 - - + +
1033A PHE* 4.3 17.7 - - + -
1034A LEU* 4.1 25.4 - - + -
1037A SER* 6.1 3.4 - - - -
1038A GLN* 4.6 6.9 + - - +
1092A TYR* 5.5 6.5 - - - +
1099A PHE* 4.0 26.9 - - + -
1100A GLN* 6.0 0.7 - - - +
1147A VAL 3.8 17.5 - - - +
1148A ASN* 3.7 15.2 + - - +
1149A SER 3.2 0.6 - - - -
1150A SER* 1.3 79.1 + - - +
1152A ASP* 1.3 63.4 + - - +
1154A ASP* 3.5 6.3 + - - +
1155A SER* 2.9 29.5 + - - +
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Residues in contact with ASP1152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A THR* 5.0 13.2 - - + -
1148A ASN* 3.5 24.8 + - - +
1149A SER* 2.8 17.3 + - - +
1151A ILE* 1.3 74.8 - - - +
1153A VAL* 1.3 58.4 + - - +
1155A SER* 2.7 21.1 + - - -
1156A LEU* 3.0 25.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL1153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A TYR* 4.9 9.2 - - + +
987A LEU* 5.3 3.2 - - + +
990A THR* 3.7 41.1 - - - +
991A ILE* 4.5 12.6 - - + +
994A PHE* 4.3 13.9 - - + -
1149A SER 2.8 23.7 + - - +
1150A SER* 3.7 9.9 - - - +
1152A ASP* 1.3 73.4 - - - +
1154A ASP* 1.3 52.9 + - - +
1156A LEU* 3.4 8.2 + - - +
1157A MET* 2.8 54.7 + - + +
----------------------------------------------------------
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Residues in contact with ASP1154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A THR* 2.9 42.7 + - - +
849A TYR* 3.4 19.1 + - - +
1030A ARG* 5.2 5.4 - - - +
1034A LEU* 4.4 17.9 - - + +
1038A GLN* 4.3 16.3 + - - +
1150A SER 2.8 22.0 + - - +
1151A ILE* 3.7 6.3 - - - +
1153A VAL* 1.3 73.6 - - - +
1155A SER* 1.3 57.1 + - - +
1157A MET* 3.4 3.9 + - - +
1158A ARG* 2.9 27.5 + - - +
----------------------------------------------------------
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Residues in contact with SER1155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1038A GLN* 3.9 21.1 - - - +
1041A LYS* 4.8 16.6 + - - -
1151A ILE* 2.9 16.6 + - - -
1152A ASP* 2.7 27.0 + - - -
1154A ASP* 1.3 73.3 + - - +
1156A LEU* 1.3 65.4 + - - +
1158A ARG* 3.4 25.6 + - - +
1159A SER* 4.2 2.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU1156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982A ILE* 3.6 31.6 - - + +
986A LEU* 4.6 13.7 - - + +
987A LEU* 4.1 28.9 - - + +
990A THR* 3.9 29.2 - - + +
1152A ASP* 3.0 22.3 + - + +
1153A VAL* 3.7 4.0 - - - +
1155A SER* 1.3 82.6 + - - +
1157A MET* 1.3 58.4 + - - +
1159A SER* 2.8 33.5 + - - +
1160A VAL* 4.1 1.0 + - - +
----------------------------------------------------------
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Residues in contact with MET1157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A THR* 5.8 2.5 - - - +
848A THR* 4.9 10.5 - - + +
849A TYR* 3.5 56.3 - - + +
852A TYR* 4.2 28.9 - - + -
987A LEU* 4.3 16.1 - - + +
991A ILE* 4.8 6.3 - - + -
1153A VAL* 2.8 36.2 + - + +
1154A ASP* 3.9 6.7 - - - +
1156A LEU* 1.3 68.6 - - - +
1158A ARG* 1.3 65.4 + - - +
1159A SER 3.1 0.2 - - - -
1160A VAL* 3.1 30.6 + - + +
1161A SER* 4.1 2.9 + - - -
----------------------------------------------------------
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Residues in contact with ARG1158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A THR* 4.7 22.9 - - - +
1038A GLN* 3.6 32.3 + - - +
1041A LYS* 6.0 4.2 - - - +
1042A GLN* 5.5 9.7 - - - +
1154A ASP 2.9 13.4 + - - +
1155A SER* 3.4 17.7 + - - +
1156A LEU 3.2 0.2 - - - -
1157A MET* 1.3 76.3 - - - +
1159A SER* 1.3 57.1 + - - +
1161A SER* 2.7 28.9 + - - +
1162A ARG* 4.2 26.7 + - - +
----------------------------------------------------------
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Residues in contact with SER1159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A ASP* 2.7 50.2 + - - +
982A ILE* 5.8 1.4 - - - +
983A LEU* 5.1 4.8 - - - +
987A LEU* 5.8 0.3 - - - +
1155A SER 5.1 2.0 - - - -
1156A LEU* 2.8 22.5 + - - +
1158A ARG* 1.3 76.9 - - - +
1160A VAL* 1.3 60.2 + - - +
1162A ARG* 3.2 33.8 - - - +
1163A VAL* 3.7 4.7 - - - +
----------------------------------------------------------
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Residues in contact with VAL1160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A THR* 3.9 11.7 - - + -
852A TYR* 4.0 22.9 - - + -
948A LEU* 4.8 2.7 - - + -
983A LEU* 3.8 27.4 - - + -
987A LEU* 4.3 10.8 - - + -
1156A LEU 4.5 0.7 - - - +
1157A MET* 3.1 33.3 + - + +
1159A SER* 1.3 76.6 - - - +
1161A SER* 1.3 65.7 + - - +
1163A VAL* 3.1 15.5 + - + +
1164A PHE* 3.1 37.7 + - + -
----------------------------------------------------------
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Residues in contact with SER1161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A THR* 5.1 4.9 - - - -
848A THR* 4.2 22.7 - - - +
1157A MET 4.1 2.3 + - - -
1158A ARG* 2.7 24.3 + - - +
1160A VAL* 1.3 78.7 - - - +
1162A ARG* 1.3 54.8 + - - +
1164A PHE* 2.9 11.5 + - - +
1165A LYS* 2.8 38.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG1162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A ARG* 3.4 60.6 + - + +
979A ASP* 4.1 9.8 - - - +
1158A ARG* 4.2 29.3 + - - +
1159A SER* 3.2 35.7 - - - +
1161A SER* 1.3 82.9 + - - +
1163A VAL* 1.3 60.3 + - - +
1165A LYS* 3.5 15.2 - - + +
1166A PHE* 3.5 16.5 + - - -
----------------------------------------------------------
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Residues in contact with VAL1163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A LEU* 4.8 17.5 - - + +
952A MET* 3.7 37.9 - - + -
975A ARG* 5.2 5.4 - - + +
979A ASP* 3.8 12.1 - - + +
980A ILE* 5.5 10.1 - - + -
983A LEU* 5.0 9.4 - - + -
1159A SER 3.7 15.7 - - - +
1160A VAL* 3.1 10.8 + - - +
1162A ARG* 1.3 78.4 - - + +
1164A PHE* 1.3 59.7 + - + +
1166A PHE* 3.0 6.9 + - - +
1167A ILE* 2.9 40.5 + - + +
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Residues in contact with PHE1164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A THR* 4.5 9.9 - - + -
851A ARG* 3.8 35.4 - - + -
852A TYR* 4.5 10.1 - - - -
855A VAL* 5.0 8.3 - - + -
948A LEU* 4.3 26.0 - - + -
951A LYS* 6.5 1.3 - - - -
1160A VAL* 3.1 44.0 + - + -
1161A SER* 2.9 12.8 + - - +
1163A VAL* 1.3 74.7 - - + +
1165A LYS* 1.3 57.8 + - - +
1167A ILE* 4.0 21.8 - - + -
1168A ASP* 2.8 51.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS1165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A ARG* 4.6 15.2 - - - +
1161A SER* 2.8 20.5 + - - +
1162A ARG* 3.5 23.8 - - + +
1163A VAL 3.2 0.2 - - - -
1164A PHE* 1.3 72.4 - - - +
1166A PHE* 1.3 61.7 + - + +
1168A ASP* 3.4 6.0 + - - +
1169A MET* 3.4 23.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE1166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A MET* 4.0 23.8 - - + -
955A SER* 2.9 20.8 + - - +
956A VAL* 3.8 23.1 - - + -
964A LEU* 5.4 2.2 - - + -
967A LEU* 3.5 26.0 - - + -
971A GLY 5.2 0.2 - - - -
972A ILE* 3.7 39.3 - - + -
975A ARG* 3.4 39.3 - - + -
976A PHE* 6.4 0.4 - + + -
1162A ARG 3.5 17.8 + - - -
1163A VAL 3.0 9.9 + - - +
1165A LYS* 1.3 76.0 - - + +
1167A ILE* 1.3 62.2 + - - +
1169A MET* 3.5 37.4 - - + +
----------------------------------------------------------
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Residues in contact with ILE1167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A LEU* 4.5 20.0 - - + +
951A LYS* 5.0 21.5 - - + -
952A MET* 4.0 21.3 - - + +
955A SER* 2.8 24.5 + - - +
1163A VAL* 2.9 32.9 + - + +
1164A PHE* 3.7 33.0 - - + +
1165A LYS 3.3 0.2 - - - -
1166A PHE* 1.3 76.1 - - - +
1168A ASP* 1.3 67.8 + - - +
1169A MET 3.8 2.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP1168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164A PHE* 2.8 35.5 + - - +
1165A LYS* 3.4 6.3 + - - +
1166A PHE 3.4 0.6 - - - -
1167A ILE* 1.3 79.5 - - - +
1169A MET* 1.3 64.1 + - - +
1170A PRO* 3.8 1.0 - - - +
----------------------------------------------------------
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Residues in contact with MET1169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A SER* 3.9 17.9 + - - +
956A VAL* 5.0 1.6 - - - +
959A ALA* 4.1 18.6 - - + -
963A THR* 5.2 9.2 - - - +
964A LEU* 4.4 17.0 - - + -
967A LEU* 5.3 5.2 - - + -
1165A LYS 3.4 10.0 + - - +
1166A PHE* 3.5 55.4 - - + +
1167A ILE 3.3 6.3 - - - +
1168A ASP* 1.3 80.3 - - - +
1170A PRO* 1.4 78.9 - - + +
1171A THR* 4.3 5.9 - - - +
----------------------------------------------------------
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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