Contacts of the helix formed by residues 1194 - 1219 (chain C) in PDB entry 5YS0
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 LEU1194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1075B THR* 3.9 24.0 - - + -
1078B SER* 4.7 10.3 - - - -
1079B LEU* 3.6 41.3 - - + +
1087B TYR* 3.1 20.3 + - + -
1221B ILE* 6.1 2.0 - - + -
1157C PRO* 5.2 4.0 - - + -
1158C TYR* 4.6 21.3 - - + -
1192C SER* 6.1 0.7 - - - -
1193C MET* 1.3 79.7 - - + +
1195C LYS* 1.3 64.6 + - - +
1196C GLY 3.2 3.4 + - - -
1197C THR* 3.3 5.9 + - - -
1198C ILE* 3.1 41.3 + - + +
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Residues in contact with LYS1195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087B TYR* 3.9 1.2 + - - -
1188C TRP* 3.6 42.0 - - + +
1191C LYS* 5.8 10.3 - - + +
1192C SER 4.3 11.0 - - - +
1193C MET* 2.9 7.5 + - - +
1194C LEU* 1.3 78.0 - - - +
1196C GLY* 1.3 67.8 + - - +
1197C THR 3.1 1.2 + - - -
1199C GLU* 3.4 47.1 + - - +
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Residues in contact with GLY1196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1084B ASP* 4.2 12.1 + - - -
1087B TYR* 4.4 4.4 + - - -
1194C LEU 3.2 1.2 + - - -
1195C LYS* 1.3 83.7 - - - +
1197C THR* 1.3 58.9 + - - +
1199C GLU* 4.2 3.3 + - - +
1200C LYS* 3.3 29.0 + - - +
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Residues in contact with THR1197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B SER* 5.3 9.2 - - - +
1082B GLY* 6.3 0.7 - - - -
1083B ASP* 5.2 9.2 - - + +
1084B ASP* 3.1 34.5 + - + +
1087B TYR* 5.3 1.2 + - - -
1194C LEU* 3.3 5.6 + - - -
1196C GLY* 1.3 74.1 - - - +
1198C ILE* 1.3 60.4 + - - +
1199C GLU 2.9 10.8 + - - -
1200C LYS* 2.9 38.0 + - + +
1201C GLY* 3.3 8.3 + - - -
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Residues in contact with ILE1198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157C PRO* 3.7 26.2 - - + -
1158C TYR* 5.4 3.1 - - + +
1162C PHE* 3.4 38.3 - - + -
1186C VAL* 5.1 0.3 - - - +
1188C TRP* 3.2 42.8 - - + -
1194C LEU* 3.1 26.2 + - + +
1195C LYS 3.9 4.0 - - - +
1197C THR* 1.3 75.6 - - - +
1199C GLU* 1.3 62.0 + - + +
1201C GLY* 4.1 2.8 - - - +
1202C SER* 3.5 21.7 + - - -
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Residues in contact with GLU1199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186C VAL* 3.8 28.9 - - + +
1188C TRP* 3.4 21.6 + - + -
1195C LYS* 3.4 37.7 + - - +
1196C GLY* 4.5 3.6 - - - +
1197C THR 2.9 0.8 - - - -
1198C ILE* 1.3 83.9 - - + +
1200C LYS* 1.3 65.1 + - - +
1201C GLY 3.0 1.6 - - - -
1202C SER* 4.3 4.7 - - - +
1203C ILE* 3.0 43.3 + - + +
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Residues in contact with LYS1200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B ASP* 4.3 14.9 + - + +
1084B ASP* 4.3 12.7 - - - +
1196C GLY 3.3 25.4 - - - +
1197C THR* 2.9 33.2 + - + +
1199C GLU* 1.3 76.5 - - - +
1201C GLY* 1.3 58.0 + - - +
1203C ILE* 4.2 7.3 - - - +
1204C ASP* 3.2 27.2 + - - +
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Residues in contact with GLY1201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197C THR 3.3 8.6 + - - -
1198C ILE* 4.1 2.4 + - - -
1199C GLU 3.0 0.8 - - - -
1200C LYS* 1.3 77.4 - - - +
1202C SER* 1.3 54.5 + - - +
1203C ILE 3.2 1.3 - - - -
1204C ASP* 2.9 4.7 + - - +
1205C GLY* 2.5 36.2 + - - -
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Residues in contact with SER1202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162C PHE* 4.8 6.4 - - - -
1164C VAL* 3.3 37.0 - - - +
1184C THR* 5.0 2.8 - - - +
1186C VAL* 4.1 12.8 - - - +
1198C ILE 3.5 18.3 + - - -
1199C GLU 3.4 2.4 + - - -
1201C GLY* 1.3 73.8 - - - +
1203C ILE* 1.3 58.6 + - - +
1204C ASP 2.9 5.5 + - - -
1205C GLY* 4.3 1.6 - - - +
1206C GLN* 3.1 31.2 + - - +
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Residues in contact with ILE1203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061C THR* 3.5 44.6 - - + +
1063C ILE* 3.7 17.3 - - + +
1184C THR* 4.7 7.2 - - + -
1185C ASN* 6.5 0.2 - - - -
1186C VAL* 5.7 3.4 - - + -
1199C GLU* 3.0 34.3 + - + +
1200C LYS* 4.2 7.9 - - - +
1202C SER* 1.3 75.4 - - - +
1204C ASP* 1.3 63.8 + - - +
1207C ARG* 3.1 25.7 - - - +
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Residues in contact with ASP1204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200C LYS 3.2 15.5 - - - +
1201C GLY* 2.9 7.1 + - - +
1203C ILE* 1.3 90.7 - - - +
1205C GLY* 1.3 56.8 + - - +
1207C ARG* 3.3 19.2 + - + +
1208C SER* 2.5 35.5 + - - -
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Residues in contact with GLY1205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117C LYS* 4.9 13.1 + - - -
1201C GLY 2.5 20.6 + - - -
1202C SER* 4.0 2.2 - - - -
1204C ASP* 1.3 69.8 - - - +
1206C GLN* 1.3 61.2 + - - +
1208C SER* 3.0 10.1 + - - -
1209C SER* 2.8 27.7 + - - -
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Residues in contact with GLN1206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C ILE* 4.5 4.8 - - + +
1117C LYS* 5.5 4.6 - - - +
1149C GLN* 3.6 17.3 - - - +
1151C VAL* 4.6 14.6 - - - +
1164C VAL* 4.4 8.7 - - + -
1166C THR* 3.5 30.8 + - + +
1168C PHE* 4.5 5.5 - - - -
1184C THR* 4.3 21.5 - - + +
1202C SER* 3.1 19.2 + - - +
1205C GLY* 1.3 77.0 - - - +
1207C ARG* 1.3 60.9 + - - +
1209C SER* 4.2 14.4 + - - -
1210C THR* 3.0 35.1 + - + +
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Residues in contact with ARG1207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C THR* 6.2 1.4 - - - +
1062C VAL 3.9 8.3 + - - -
1063C ILE* 3.2 51.8 + - + +
1064C ASP* 5.7 3.3 + - - -
1203C ILE* 3.1 27.6 + - - +
1204C ASP* 3.1 23.9 + - - +
1206C GLN* 1.3 78.3 - - - +
1208C SER* 1.3 58.2 + - - +
1210C THR* 4.3 0.7 + - - -
1211C LYS* 3.1 33.0 + - + +
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Residues in contact with SER1208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C LYS* 5.5 3.3 + - - -
1204C ASP 2.5 20.5 + - - -
1205C GLY* 3.4 6.8 + - - -
1207C ARG* 1.3 73.6 - - - +
1209C SER* 1.3 70.9 + - - +
1211C LYS* 3.4 14.8 + - - +
1212C GLN* 3.4 16.5 + - - +
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Residues in contact with SER1209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C LYS* 5.5 6.5 - - - -
1168C PHE* 6.1 0.3 - - - -
1205C GLY 2.8 15.4 + - - -
1206C GLN* 3.4 19.4 + - - -
1208C SER* 1.3 81.4 + - - +
1210C THR* 1.3 67.7 + - - +
1212C GLN* 3.2 4.9 + - - +
1213C LEU* 3.0 25.4 + - - +
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Residues in contact with THR1210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C ILE* 4.0 15.8 - - + +
1064C ASP* 5.4 4.0 - - - +
1067C ILE* 5.6 3.8 - - - +
1168C PHE* 3.7 33.9 - - + -
1180C MET* 5.7 0.4 - - - -
1182C VAL* 4.2 19.6 - - + +
1206C GLN* 3.0 24.6 + - + +
1207C ARG 4.3 0.7 + - - -
1209C SER* 1.3 79.4 - - - +
1211C LYS* 1.3 60.8 + - - +
1213C LEU* 2.7 32.2 + - + +
1214C VAL* 3.2 18.0 + - - +
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Residues in contact with LYS1211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1064C ASP* 5.6 6.5 - - - +
1067C ILE* 6.0 3.4 - - - -
1207C ARG* 3.1 25.7 + - + +
1208C SER* 3.4 7.8 + - - +
1209C SER 3.2 0.8 - - - -
1210C THR* 1.3 82.1 + - - +
1212C GLN* 1.3 60.6 + - + +
1214C VAL* 4.0 7.2 + - - +
1215C ASP* 3.8 20.5 + - - +
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Residues in contact with GLN1212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094C ASN* 4.2 18.3 - - - +
1208C SER 3.4 9.6 + - - +
1209C SER* 3.2 8.0 + - - +
1210C THR 3.1 0.4 - - - -
1211C LYS* 1.3 78.8 - - + +
1213C LEU* 1.3 60.1 + - - +
1214C VAL 3.1 5.6 - - - -
1215C ASP* 3.5 23.1 + - - +
1216C ASP* 3.2 31.4 + - - +
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Residues in contact with LEU1213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080C LEU* 5.0 10.1 - - + -
1081C TYR* 6.2 0.4 - - - +
1088C ILE* 6.0 2.9 - - + -
1091C ILE* 4.2 26.5 - - + +
1149C GLN* 6.3 0.4 - - - +
1168C PHE* 4.5 20.6 - - + -
1170C TYR* 4.8 2.9 - - - +
1180C MET* 3.5 34.8 - - + -
1209C SER* 3.0 13.6 + - - +
1210C THR* 2.7 28.7 + - - +
1212C GLN* 1.3 72.7 - - - +
1214C VAL* 1.3 54.7 + - + -
1216C ASP* 4.1 7.3 - - - +
1217C LEU* 3.4 28.1 + - + +
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Residues in contact with VAL1214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067C ILE* 3.7 43.5 - - + -
1069C ILE* 4.9 6.1 - - + -
1180C MET* 4.1 16.8 - - - -
1210C THR* 3.2 13.6 + - - +
1211C LYS* 4.3 4.9 - - - +
1212C GLN 3.1 0.6 - - - -
1213C LEU* 1.3 80.5 - - + +
1215C ASP* 1.3 65.7 + - - +
1216C ASP 3.2 0.7 - - - -
1217C LEU* 2.9 5.9 + - + +
1218C LYS* 2.9 58.9 + - + +
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Residues in contact with ASP1215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211C LYS* 3.8 14.3 - - - +
1212C GLN* 3.5 24.4 + - - +
1214C VAL* 1.3 80.5 - - - +
1216C ASP* 1.3 59.0 + - - +
1217C LEU 3.0 5.0 + - - -
1218C LYS* 3.5 11.7 + - - +
1219C LYS* 3.0 49.0 - - - +
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Residues in contact with ASP1216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087C TYR* 2.8 20.8 + - - -
1090C LYS* 3.2 30.7 - - - -
1091C ILE* 3.3 25.3 - - + +
1094C ASN* 2.7 35.2 + - - +
1212C GLN* 3.2 20.6 + - - +
1213C LEU* 4.1 6.7 - - - +
1215C ASP* 1.3 78.0 - - - +
1217C LEU* 1.3 56.2 + - - +
1219C LYS* 4.7 7.5 + - - +
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Residues in contact with LEU1217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069C ILE* 3.8 41.4 - - + +
1071C VAL* 6.2 0.2 - - + -
1076C VAL* 4.4 11.0 - - + -
1079C LEU* 5.3 3.1 - - + -
1080C LEU* 3.9 31.0 - - + -
1087C TYR* 3.8 27.4 - - + +
1091C ILE* 5.4 0.9 - - + -
1180C MET* 4.9 2.9 - - - -
1213C LEU* 3.4 23.1 + - + +
1214C VAL* 3.2 12.0 - - - +
1215C ASP 2.9 0.8 - - - -
1216C ASP* 1.3 78.1 - - - +
1218C LYS* 1.3 53.4 + - - +
1219C LYS 2.6 18.2 + - - -
1220C ILE* 3.1 30.8 - - + +
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Residues in contact with LYS1218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067C ILE* 5.2 0.8 - - - +
1068C ASN 3.2 25.9 + - - +
1069C ILE* 4.6 6.3 - - + -
1070C PRO* 4.0 30.1 - - + +
1071C VAL* 5.9 0.9 - - - -
1214C VAL* 2.9 41.0 + - + +
1215C ASP* 3.5 11.1 + - - +
1217C LEU* 1.3 68.9 - - - +
1219C LYS* 1.3 60.9 + - + +
1220C ILE* 3.5 7.0 + - - +
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Residues in contact with LYS1219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1087C TYR* 4.9 1.0 + - - -
1215C ASP* 3.0 38.5 - - - +
1216C ASP* 5.1 6.1 - - - +
1217C LEU 2.6 8.6 + - - -
1218C LYS* 1.3 78.3 - - + +
1220C ILE* 1.3 66.2 + - - +
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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