Contacts of the helix formed by residues 1194 - 1223 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157B PRO* 4.8 13.9 - - + -
1158B TYR* 3.7 26.5 - - + -
1192B SER* 2.7 15.6 + - - +
1193B MET* 1.3 81.3 - - + +
1195B LYS* 1.3 64.9 + - - +
1196B GLY 3.0 4.9 + - - +
1197B THR* 3.3 24.1 + - + +
1198B ILE* 3.2 26.7 + - + +
1301B ERG 5.6 7.9 - - + -
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Residues in contact with LYS1195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188B TRP* 3.5 53.8 - - + +
1190B GLY 3.7 16.4 + - - -
1191B LYS* 3.8 6.5 - - - +
1192B SER* 3.0 38.4 + - - +
1193B MET 3.7 1.4 - - - -
1194B LEU* 1.3 76.1 - - - +
1196B GLY* 1.3 64.2 + - - +
1198B ILE* 3.3 0.7 + - - +
1199B GLU* 2.9 36.2 + - - +
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Residues in contact with GLY1196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194B LEU* 3.0 2.6 - - - +
1195B LYS* 1.3 81.8 - - - +
1197B THR* 1.3 62.7 + - - +
1199B GLU* 3.5 4.8 + - - +
1200B LYS* 3.3 22.7 + - - +
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Residues in contact with THR1197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194B LEU* 3.3 30.3 + - + +
1196B GLY* 1.3 72.3 - - - +
1198B ILE* 1.3 58.9 + - - +
1200B LYS* 3.1 8.3 + - - +
1201B GLY* 2.7 33.8 + - - -
1301B ERG 4.7 12.1 - - - +
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Residues in contact with ILE1198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1157B PRO* 3.7 24.2 - - + +
1158B TYR* 4.4 6.1 - - + -
1162B PHE* 3.7 36.6 - - + -
1186B VAL* 4.9 2.7 - - + -
1188B TRP* 3.8 23.6 - - + -
1194B LEU* 3.2 24.8 + - + +
1195B LYS 3.7 4.0 - - - +
1197B THR* 1.3 75.6 + - - +
1199B GLU* 1.3 59.0 + - - +
1201B GLY* 2.8 17.5 + - - +
1202B SER* 2.8 21.8 + - - +
1301B ERG 3.9 35.3 - - + +
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Residues in contact with GLU1199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B THR* 5.7 1.2 + - - -
1186B VAL* 3.7 30.7 + - + +
1188B TRP* 3.4 24.5 + - + +
1195B LYS* 2.9 26.5 + - - +
1196B GLY* 3.9 4.0 - - - +
1198B ILE* 1.3 76.0 - - - +
1200B LYS* 1.3 65.7 + - + +
1202B SER* 3.7 5.6 - - - -
1203B ILE* 3.1 35.3 + - + +
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Residues in contact with LYS1200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196B GLY 3.3 12.6 + - - +
1197B THR* 3.1 11.2 + - - +
1199B GLU* 1.3 81.5 - - + +
1201B GLY* 1.3 58.5 + - - +
1203B ILE* 4.1 7.9 - - + -
1204B ASP* 2.8 43.0 + - - +
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Residues in contact with GLY1201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197B THR 2.7 16.8 + - - -
1198B ILE* 2.8 6.6 + - - -
1200B LYS* 1.3 72.4 - - - +
1202B SER* 1.3 58.5 + - - -
1203B ILE 3.1 1.3 - - - -
1204B ASP* 3.3 3.5 + - - +
1205B GLY* 2.9 28.8 + - - -
1301B ERG 4.0 23.6 - - - +
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Residues in contact with SER1202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1164B VAL* 3.7 34.3 - - - -
1184B THR* 4.7 1.8 - - - +
1186B VAL* 3.6 18.2 - - - +
1198B ILE* 2.8 21.4 + - - +
1199B GLU 3.5 4.7 + - - -
1201B GLY* 1.3 72.1 - - - -
1203B ILE* 1.3 64.4 + - - +
1205B GLY 4.1 0.2 - - - -
1206B GLN* 3.3 27.7 + - - +
1301B ERG 4.1 24.7 - - - +
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Residues in contact with ILE1203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B THR* 3.9 35.2 - - + +
1063B ILE* 3.2 30.7 - - + +
1184B THR* 4.2 25.1 - - + +
1185B ASN* 5.4 0.9 - - - -
1186B VAL* 4.6 7.2 - - + -
1199B GLU* 3.1 34.6 + - + +
1200B LYS* 4.4 8.1 - - + +
1201B GLY 3.1 0.6 - - - -
1202B SER* 1.3 85.1 - - - +
1204B ASP* 1.3 75.4 + - - +
1205B GLY 3.4 0.2 + - - -
1207B ARG* 3.2 28.2 + - - +
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Residues in contact with ASP1204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200B LYS* 2.8 35.2 + - - +
1201B GLY* 3.3 4.2 + - - +
1203B ILE* 1.3 83.8 - - - +
1205B GLY* 1.3 65.1 + - - +
1207B ARG* 3.2 14.9 + - - +
1208B SER* 3.1 22.3 + - - -
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Residues in contact with GLY1205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201B GLY 2.9 12.6 + - - -
1204B ASP* 1.3 77.3 - - - +
1206B GLN* 1.3 56.3 + - - +
1208B SER* 3.4 9.5 + - - -
1209B SER* 2.9 24.3 + - - -
1301B ERG 3.5 30.5 - - - -
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Residues in contact with GLN1206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063B ILE* 3.4 16.8 - - + -
1149B GLN* 3.9 5.9 + - - -
1164B VAL* 3.9 8.0 - - - +
1166B THR* 2.4 49.3 + - + +
1168B PHE* 3.9 7.5 - - - -
1184B THR* 3.8 10.0 - - - +
1202B SER 3.3 17.5 + - - +
1204B ASP 3.3 0.6 - - - -
1205B GLY* 1.3 73.3 - - - +
1207B ARG* 1.3 55.7 + - - +
1208B SER 3.3 0.2 - - - -
1209B SER* 3.5 7.6 - - - -
1210B THR* 2.7 47.1 + - + +
1301B ERG 2.9 42.1 + - + +
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Residues in contact with ARG1207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B THR* 5.5 2.8 - - - +
1062B VAL 4.6 6.3 + - - -
1063B ILE* 2.8 45.7 + - + +
1064B ASP* 4.0 9.8 + - - +
1203B ILE* 3.2 33.5 + - - +
1204B ASP* 3.2 18.2 + - - +
1206B GLN* 1.3 73.9 - - - +
1208B SER* 1.3 68.8 + - - +
1210B THR* 3.6 9.0 + - - +
1211B LYS* 3.4 25.4 + - - +
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Residues in contact with SER1208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204B ASP 3.1 13.0 + - - -
1205B GLY* 3.5 10.8 - - - -
1207B ARG* 1.3 75.8 - - - +
1209B SER* 1.3 61.8 + - - +
1211B LYS* 3.4 17.0 + - - +
1212B GLN* 3.0 35.7 + - - +
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Residues in contact with SER1209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1095B GLN* 2.8 33.1 + - - +
1117B LYS* 4.2 5.5 + - - -
1205B GLY 2.9 14.3 + - - -
1206B GLN* 3.2 15.5 + - - -
1208B SER* 1.3 71.1 - - - +
1210B THR* 1.3 59.7 + - - +
1211B LYS 3.0 5.0 + - - -
1212B GLN* 3.2 10.6 + - - +
1213B LEU* 2.9 24.7 + - - +
1301B ERG 3.3 26.5 - - - +
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Residues in contact with THR1210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063B ILE* 4.2 7.6 - - + +
1064B ASP* 4.6 11.4 + - - +
1067B ILE* 5.1 4.4 - - - +
1168B PHE* 4.1 13.0 - - + -
1180B MET* 5.6 0.4 - - - -
1182B VAL* 3.9 38.6 - - + -
1206B GLN* 2.7 32.5 + - + +
1207B ARG* 3.6 11.3 + - - +
1209B SER* 1.3 72.3 - - - +
1211B LYS* 1.3 58.3 + - - +
1213B LEU* 3.9 13.0 - - + +
1214B VAL* 3.0 33.9 + - - +
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Residues in contact with LYS1211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ILE* 6.3 0.2 - - - -
1207B ARG* 3.4 21.5 + - - +
1208B SER* 3.7 15.4 + - - +
1209B SER 3.0 1.6 + - - -
1210B THR* 1.3 76.9 - - - +
1212B GLN* 1.3 59.0 + - + +
1214B VAL* 3.0 10.6 - - + +
1215B ASP* 2.7 47.7 + - - +
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Residues in contact with GLN1212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B ASN* 2.9 26.3 + - - +
1095B GLN* 3.7 30.7 - - + +
1096B ASN* 4.6 8.3 + - - +
1117B LYS* 5.7 1.2 - - - +
1208B SER* 3.0 25.9 + - - +
1209B SER* 3.5 9.4 + - - +
1211B LYS* 1.3 72.2 - - + +
1213B LEU* 1.3 59.8 + - - +
1215B ASP* 4.0 8.5 - - + -
1216B ASP* 2.8 48.0 + - - +
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Residues in contact with LEU1213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080B LEU* 4.1 24.7 - - + -
1081B TYR* 5.7 0.4 - - - +
1088B ILE* 5.1 3.6 - - + -
1091B ILE* 3.6 26.8 - - + +
1095B GLN* 3.8 13.4 - - - +
1168B PHE* 4.0 20.0 - - + -
1170B TYR* 4.4 4.7 - - - +
1180B MET* 3.6 31.0 - - + -
1209B SER 2.9 17.4 + - - +
1210B THR* 3.9 9.6 - - - +
1212B GLN* 1.3 77.0 - - - +
1214B VAL* 1.3 56.4 + - - +
1216B ASP* 4.1 1.0 - - - +
1217B LEU* 3.0 31.9 + - + +
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Residues in contact with VAL1214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ILE* 4.0 39.7 - - + -
1069B ILE* 5.0 7.4 - - + -
1180B MET* 4.1 21.1 - - + -
1210B THR* 3.0 18.7 + - - +
1211B LYS* 3.0 26.7 - - + +
1212B GLN 3.1 0.6 - - - -
1213B LEU* 1.3 78.0 - - + +
1215B ASP* 1.3 68.5 + - - +
1217B LEU* 4.1 4.9 - - + -
1218B LYS* 3.0 37.1 + - + +
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Residues in contact with ASP1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211B LYS* 2.7 46.7 + - - +
1212B GLN* 3.7 7.5 - - - +
1214B VAL* 1.3 75.4 - - - +
1216B ASP* 1.3 64.1 + - - +
1218B LYS* 3.7 13.9 + - - +
1219B LYS* 2.9 31.4 + - - +
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Residues in contact with ASP1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1090B LYS 4.9 0.2 - - - +
1091B ILE* 3.6 26.2 - - + +
1094B ASN* 2.7 42.2 + - - +
1095B GLN* 5.9 0.2 - - - +
1212B GLN* 2.8 27.7 + - - +
1215B ASP* 1.3 79.7 - - - +
1217B LEU* 1.3 52.2 + - - +
1219B LYS* 3.6 25.4 + - - +
1220B ILE* 2.7 41.9 + - + +
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Residues in contact with LEU1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B ILE* 3.4 30.5 - - + -
1076B VAL* 4.4 5.8 - - + -
1079B LEU* 4.1 24.0 - - + -
1080B LEU* 3.6 46.7 - - + -
1091B ILE* 5.0 1.8 - - + -
1180B MET* 5.0 9.9 - - - -
1213B LEU* 3.0 26.3 + - + +
1214B VAL* 3.1 7.9 + - - +
1216B ASP* 1.3 75.8 - - - +
1218B LYS* 1.3 64.0 + - - +
1220B ILE* 3.5 11.3 + - + +
1221B ILE* 3.1 24.4 + - - +
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Residues in contact with LYS1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1068B ASN 4.5 5.2 - - - +
1069B ILE* 3.9 26.9 - - + -
1070B PRO* 3.9 26.6 - - + +
1214B VAL* 3.0 26.3 + - + +
1215B ASP* 3.7 16.8 + - - +
1217B LEU* 1.3 72.4 - - - +
1219B LYS* 1.3 61.8 + - - +
1221B ILE* 2.8 26.3 + - - +
1222B SER* 2.9 15.0 + - - -
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Residues in contact with LYS1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094B ASN* 4.7 4.8 - - - +
1215B ASP 2.9 16.7 + - - +
1216B ASP* 3.6 37.1 + - - +
1218B LYS* 1.3 77.1 - - - +
1220B ILE* 1.3 70.2 + - + +
1221B ILE 3.4 0.3 + - - -
1222B SER* 3.6 15.0 + - - -
1223B ASN* 3.8 12.0 + - - +
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Residues in contact with ILE1220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079B LEU* 4.1 29.8 - - + -
1080B LEU* 6.3 0.2 - - + -
1087B TYR* 4.6 26.7 - - + +
1090B LYS* 6.0 3.6 - - + -
1091B ILE* 4.0 23.1 - - + -
1216B ASP* 2.7 29.0 + - + +
1217B LEU* 3.8 12.6 - - + +
1218B LYS 3.1 0.6 - - - -
1219B LYS* 1.3 83.2 - - + +
1221B ILE* 1.3 57.9 + - + +
1223B ASN 3.2 17.0 - - - +
1193C MET* 4.8 16.4 - - + +
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Residues in contact with ILE1221 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B PRO* 3.9 23.3 - - + +
1071B VAL* 3.4 33.2 - - + -
1075B THR* 5.0 1.8 - - + -
1079B LEU* 3.5 31.6 - - + -
1217B LEU 3.1 17.0 - - - +
1218B LYS* 2.8 10.4 + - - +
1220B ILE* 1.3 81.1 - - + +
1222B SER* 1.3 63.7 + - - +
1223B ASN* 3.1 7.5 + - - +
1158C TYR* 4.4 31.9 + - + -
1194C LEU* 6.1 2.0 - - + -
----------------------------------------------------------
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Residues in contact with SER1222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1218B LYS 2.9 13.3 + - - -
1219B LYS* 3.6 11.0 + - - -
1220B ILE 3.6 0.6 - - - -
1221B ILE* 1.3 77.4 - - - +
1223B ASN* 1.3 69.0 + - - +
1158C TYR* 5.1 4.6 + - - -
----------------------------------------------------------
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Residues in contact with ASN1223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219A LYS* 5.5 5.0 + - - -
1219B LYS 3.8 9.4 + - - +
1220B ILE 3.2 19.6 - - - +
1221B ILE 3.8 3.7 - - - +
1222B SER* 1.3 86.8 + - - +
1158C TYR* 5.7 3.7 - - - -
1192C SER* 5.9 4.0 - - - -
1193C MET* 5.4 8.4 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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