Contacts of the helix formed by residues 1201 - 1227 (chain A) in PDB entry 4N78
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 LEU1201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A SER* 3.2 29.6 - - - +
970A PRO* 3.8 18.2 - - + -
973A LEU* 3.8 24.0 - - + -
1183A LEU* 3.8 26.2 - - + -
1187A GLN* 3.9 8.5 - - + -
1192A LYS 3.4 19.7 - - - +
1193A ASP* 4.1 1.3 - - - +
1194A GLU* 2.8 25.8 + - + +
1196A ILE* 5.6 0.7 - - + -
1199A VAL 2.9 6.1 + - - -
1200A PRO* 1.3 70.3 - - - +
1202A LYS* 1.3 62.5 + - - +
1204A MET* 3.2 6.7 + - + +
1205A VAL* 2.9 35.1 + - + +
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Residues in contact with LYS1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1187A GLN* 4.1 28.0 + - - +
1193A ASP* 3.2 32.3 + - + +
1200A PRO* 3.1 2.1 + - + -
1201A LEU* 1.3 78.7 - - - +
1203A LYS* 1.3 64.4 + - + +
1205A VAL* 3.0 12.2 - - + +
1206A GLU* 3.0 51.3 + - - +
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Residues in contact with LYS1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A PRO* 4.0 20.9 - - + -
1200A PRO* 3.2 24.5 + - + +
1202A LYS* 1.3 79.5 - - + +
1204A MET* 1.3 63.9 + - - +
1206A GLU* 3.2 21.1 + - - +
1207A ARG* 3.0 30.6 + - + +
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Residues in contact with MET1204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A LEU* 4.4 7.6 - - + -
1136A PHE* 3.7 48.7 - - + +
1139A CYS* 3.5 31.0 - - + +
1140A ILE* 3.8 11.9 - - + -
1141A PRO* 3.9 9.5 - - - +
1180A CYS* 4.3 0.7 - - - -
1183A LEU* 4.1 18.2 - - + -
1199A VAL* 3.8 18.2 - - + -
1200A PRO 2.9 12.9 + - - +
1201A LEU* 3.3 12.1 - - - +
1202A LYS 3.2 0.2 - - - -
1203A LYS* 1.3 78.1 - - - +
1205A VAL* 1.3 57.9 + - - +
1207A ARG* 3.4 3.3 + - - +
1208A ILE* 3.1 41.1 + - + +
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Residues in contact with VAL1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183A LEU* 4.1 15.5 - - + -
1184A LEU* 3.6 27.3 - - + +
1187A GLN* 3.7 42.6 - - + +
1201A LEU* 2.9 29.0 + - + +
1202A LYS* 3.0 27.1 - - + +
1204A MET* 1.3 74.4 - - - +
1206A GLU* 1.3 61.2 + - + +
1208A ILE* 3.7 8.4 - - + +
1209A ARG* 3.1 26.9 + - - +
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Residues in contact with GLU1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202A LYS* 3.0 54.1 + - + +
1203A LYS* 3.2 26.6 + - - +
1205A VAL* 1.3 78.9 - - + +
1207A ARG* 1.3 62.0 + - + +
1209A ARG* 3.6 8.0 + - - +
1210A LYS* 3.3 29.1 + - - +
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Residues in contact with ARG1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A TYR 3.0 20.8 + - - -
1139A CYS* 3.1 30.3 + - - +
1140A ILE 4.3 5.0 + - - -
1141A PRO* 4.1 23.5 - - - +
1142A VAL 6.0 0.2 - - - -
1148A THR* 4.2 15.5 - - - +
1149A VAL* 4.3 2.6 - - - +
1150A GLU* 3.2 39.0 + - - -
1203A LYS* 3.0 16.4 + - + +
1204A MET 3.7 0.9 - - - +
1206A GLU* 1.3 77.1 - - + +
1208A ILE* 1.3 64.8 + - - +
1210A LYS* 3.0 18.3 + - + +
1211A PHE* 3.0 36.4 + - + -
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Residues in contact with ILE1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A GLN* 5.9 0.4 - - - -
1139A CYS* 3.8 22.4 - - + -
1180A CYS* 3.5 60.3 - - + +
1181A TYR* 4.1 11.1 - - + -
1183A LEU* 4.1 11.0 - - + -
1184A LEU* 4.1 12.3 - - + +
1204A MET* 3.1 32.3 + - + +
1205A VAL* 3.7 14.6 - - + +
1206A GLU 3.4 0.2 - - - -
1207A ARG* 1.3 74.1 - - - +
1209A ARG* 1.3 58.9 + - - +
1211A PHE* 3.3 2.4 + - - +
1212A GLN* 2.8 28.1 + - - +
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Residues in contact with ARG1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184A LEU* 4.0 17.5 - - + -
1188A LYS* 6.5 0.4 - - - -
1205A VAL 3.1 18.0 + - - +
1206A GLU* 3.7 9.0 - - - +
1207A ARG 3.2 0.2 - - - -
1208A ILE* 1.3 77.4 - - - +
1210A LYS* 1.3 65.6 + - + +
1212A GLN* 2.8 40.7 + - - +
1213A ILE* 3.0 64.4 + - + +
1216A ASP* 5.0 3.8 + - - -
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Residues in contact with LYS1210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206A GLU* 3.3 18.4 + - - +
1207A ARG* 3.0 12.6 + - + +
1209A ARG* 1.3 80.6 - - + +
1211A PHE* 1.3 62.1 + - + +
1213A ILE* 3.3 18.8 + - + +
1214A LEU* 3.0 26.2 + - - +
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Residues in contact with PHE1211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A GLN* 4.1 14.6 - - - +
1138A TYR* 3.5 21.1 - + + -
1139A CYS* 3.8 15.5 - - - -
1149A VAL* 4.0 3.8 - - + -
1150A GLU* 3.7 17.7 - - + -
1158A HIS* 3.3 43.1 - + - -
1207A ARG* 3.0 65.5 + - + +
1208A ILE 3.9 3.8 - - - +
1210A LYS* 1.3 76.7 - - + +
1212A GLN* 1.3 56.9 + - - +
1214A LEU* 3.7 11.8 - - + +
1215A ASN* 2.8 43.4 + - - +
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Residues in contact with GLN1212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181A TYR* 3.5 54.1 + - + +
1184A LEU* 3.6 16.2 - - - +
1208A ILE 2.8 18.0 + - - +
1209A ARG* 2.8 37.8 + - - +
1210A LYS 3.2 0.2 - - - -
1211A PHE* 1.3 74.5 - - - +
1213A ILE* 1.3 59.3 + - - +
1215A ASN* 3.4 0.9 + - - +
1216A ASP* 2.9 47.9 + - - +
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Residues in contact with ILE1213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1209A ARG* 3.0 55.5 + - + +
1210A LYS* 3.3 20.8 + - + +
1212A GLN* 1.3 75.8 - - - +
1214A LEU* 1.3 62.3 + - - +
1216A ASP* 3.6 6.6 + - - +
1217A GLU* 3.2 25.8 + - + +
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Residues in contact with LEU1214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A ASP* 4.2 26.7 - - + +
1158A HIS* 3.6 37.7 - - + +
1159A TRP* 5.5 1.3 - - - +
1210A LYS 3.0 13.9 + - - +
1211A PHE* 3.7 17.3 - - + +
1213A ILE* 1.3 75.2 - - - +
1215A ASN* 1.3 67.1 + - - +
1217A GLU* 3.2 19.2 + - - +
1218A ILE* 3.0 45.0 + - + +
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Residues in contact with ASN1215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1131A TRP* 4.9 2.6 + - - +
1135A GLN* 2.5 32.5 + - - +
1138A TYR* 4.1 3.6 + - - -
1158A HIS* 4.2 19.1 + - - +
1162A CYS* 3.5 26.7 - - - -
1174A PHE* 4.4 9.2 - - + -
1181A TYR* 3.0 21.4 + - - +
1211A PHE* 2.8 26.0 + - - +
1212A GLN 3.8 0.2 - - - +
1214A LEU* 1.3 73.6 - - - +
1216A ASP* 1.3 60.5 + - - +
1218A ILE* 3.4 1.3 + - - +
1219A ILE* 2.8 42.8 + - + +
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Residues in contact with ASP1216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A ALA* 6.0 2.3 - - - +
1181A TYR* 5.0 6.2 + - - -
1209A ARG* 5.0 3.5 + - - -
1212A GLN* 2.9 36.4 + - - +
1213A ILE* 3.8 7.0 - - - +
1215A ASN* 1.3 75.8 - - - +
1217A GLU* 1.3 56.0 + - - +
1219A ILE* 4.0 8.7 - - - +
1220A THR* 2.6 41.2 + - - +
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Residues in contact with GLU1217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A GLY* 5.6 3.5 - - - +
1159A TRP* 6.1 1.2 - - - -
1213A ILE* 3.2 15.6 + - + +
1214A LEU* 3.2 21.9 + - - +
1216A ASP* 1.3 79.9 - - - +
1218A ILE* 1.3 65.9 + - + +
1220A THR* 3.4 5.0 + - - -
1221A ILE* 3.0 47.2 + - + +
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Residues in contact with ILE1218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1155A ASP 4.7 0.2 - - - +
1158A HIS* 3.8 18.2 - - + +
1159A TRP* 3.6 70.2 - - + +
1162A CYS* 3.8 21.5 - - + -
1214A LEU* 3.0 32.8 + - + +
1215A ASN 3.8 2.9 - - - +
1217A GLU* 1.3 78.2 - - + +
1219A ILE* 1.3 57.8 + - - +
1221A ILE* 3.1 9.3 + - - +
1222A LEU* 2.9 36.3 + - + +
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Residues in contact with ILE1219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162A CYS* 4.0 23.8 - - + -
1165A ILE* 5.2 4.7 - - + -
1166A VAL* 3.8 23.9 - - + +
1171A GLN* 3.8 27.8 - - + +
1174A PHE* 4.6 19.7 - - + -
1215A ASN* 2.8 30.9 + - + +
1216A ASP* 4.0 8.5 - - - +
1218A ILE* 1.3 71.4 - - - +
1220A THR* 1.3 59.0 + - - +
1222A LEU* 3.8 1.4 - - - +
1223A ASP* 2.9 37.7 + - - +
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Residues in contact with THR1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A ASP* 2.6 27.0 + - - +
1217A GLU* 3.7 5.4 - - - -
1219A ILE* 1.3 77.6 - - - +
1221A ILE* 1.3 57.4 + - + +
1223A ASP* 3.8 5.8 - - - +
1224A LYS* 2.9 30.4 + - + +
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Residues in contact with ILE1221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A LEU* 5.2 3.8 - - + -
1093A PHE* 5.3 1.1 - - + -
1159A TRP* 4.0 35.2 - - + -
1217A GLU* 3.0 40.1 + - + +
1218A ILE 3.5 6.1 - - - +
1220A THR* 1.3 75.9 - - + +
1222A LEU* 1.3 66.2 + - - +
1224A LYS* 3.2 7.2 + - - +
1225A TYR* 3.1 45.8 + - + -
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Residues in contact with LEU1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004A ILE* 5.3 1.1 - - + -
1093A PHE* 4.2 8.5 - - + -
1097A LEU* 4.1 35.6 - - + +
1159A TRP* 4.1 21.1 - - + +
1162A CYS* 3.8 6.7 - - + +
1163A MET* 3.4 40.2 - - + +
1166A VAL* 4.1 17.7 - - + -
1218A ILE* 2.9 33.6 + - + +
1219A ILE 3.8 3.1 - - - +
1221A ILE* 1.3 76.8 - - - +
1223A ASP* 1.3 58.3 + - - +
1224A LYS 3.3 0.2 + - - -
1225A TYR* 3.4 4.2 + - - +
1226A LEU* 2.9 30.9 + - - +
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Residues in contact with ASP1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166A VAL* 4.1 8.4 - - - +
1171A GLN* 3.2 36.8 + - - +
1172A ARG* 5.0 2.0 + - - -
1219A ILE* 2.9 23.4 + - - +
1220A THR* 3.8 6.5 - - - +
1222A LEU* 1.3 77.0 - - - +
1224A LYS* 1.3 62.9 + - - +
1226A LEU* 3.2 10.5 + - - +
1227A LYS* 2.9 20.8 + - - -
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Residues in contact with LYS1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220A THR* 2.9 21.3 + - + +
1221A ILE* 3.2 8.9 + - - +
1223A ASP* 1.3 76.5 - - - +
1225A TYR* 1.3 89.9 + - + +
1227A LYS* 3.2 26.6 + - - +
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Residues in contact with TYR1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008A LEU* 3.9 21.9 - - + +
1011A GLU* 6.4 0.9 - - - -
1012A GLN* 4.8 4.3 + - - +
1091A SER* 6.2 3.6 - - - -
1093A PHE* 3.7 39.3 - + + -
1094A GLU* 3.1 43.6 - - + +
1097A LEU* 4.5 5.2 - - + -
1221A ILE* 3.1 44.4 + - + +
1222A LEU 3.9 3.1 - - - +
1224A LYS* 1.3 98.0 + - + +
1226A LEU* 1.3 61.7 + - - +
1227A LYS* 3.0 14.4 + - - +
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Residues in contact with LEU1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A GLU* 4.6 4.3 - - + +
1097A LEU* 3.8 32.5 - - + -
1098A THR* 4.6 12.8 - - - +
1101A ARG* 3.9 21.3 - - - +
1166A VAL* 3.8 29.8 - - + +
1167A LEU* 3.9 19.1 - - + -
1222A LEU 2.9 16.0 + - - +
1223A ASP* 3.2 10.7 + - - +
1225A TYR* 1.3 76.0 - - - +
1227A LYS* 1.3 67.5 + - - +
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Residues in contact with LYS1227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094A GLU* 3.1 27.4 + - - +
1223A ASP 2.9 11.2 + - - -
1224A LYS* 3.2 16.8 - - + +
1225A TYR* 3.0 9.6 - - - +
1226A LEU* 1.3 89.8 - - - +
----------------------------------------------------------
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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