Contacts of the helix formed by residues 1108 - 1129 (chain K) in PDB entry 3F5P
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 SER1108 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1107K PRO* 1.3 73.6 - - - +
1109K LEU* 1.3 62.7 + - - +
1110K SER* 3.8 7.2 + - - -
1111K LYS* 3.2 28.7 + - - +
1112K MET* 3.0 30.3 + - - +
1238K PRO* 5.7 0.4 - - - -
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Residues in contact with LEU1109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108K SER* 1.3 72.9 - - - +
1110K SER* 1.3 61.2 + - - +
1112K MET* 3.2 9.5 + - + +
1113K ILE* 2.9 54.4 + - + +
1238K PRO* 3.8 35.7 - - + +
1240K MET* 4.2 18.2 - - + -
1241K LEU* 4.8 7.4 - - + -
1269K GLU* 6.4 1.8 - - + -
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Residues in contact with SER1110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108K SER* 3.3 7.7 + - - -
1109K LEU* 1.3 80.3 - - - +
1111K LYS* 1.3 66.2 + - - +
1112K MET 3.0 0.3 + - - -
1113K ILE* 3.1 8.5 + - - +
1114K GLN* 2.8 24.9 + - - +
1269K GLU* 4.3 16.0 + - - +
1271K GLU* 4.2 15.3 + - - +
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Residues in contact with LYS1111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107K PRO* 4.1 14.8 - - + -
1108K SER* 3.2 26.5 + - - +
1110K SER* 1.3 78.6 - - - +
1112K MET* 1.3 62.2 + - - +
1114K GLN* 3.4 10.5 - - + +
1115K MET* 3.2 33.6 + - + +
1271K GLU* 4.6 15.6 + - - +
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Residues in contact with MET1112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107K PRO* 3.6 23.1 - - + +
1108K SER 3.0 20.9 - - - +
1109K LEU* 3.2 9.6 + - + +
1110K SER 3.1 0.6 - - - -
1111K LYS* 1.3 73.2 - - - +
1113K ILE* 1.3 55.0 + - - +
1114K GLN 3.0 1.6 - - - -
1115K MET* 2.9 8.4 + - - +
1116K ALA* 2.7 35.8 + - - +
1202K LEU* 5.6 0.2 - - - +
1205K ILE* 3.5 26.1 - - + +
1206K ALA* 3.1 42.4 - - + +
1238K PRO* 4.8 12.3 - - + -
1241K LEU* 3.4 35.0 - - + -
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Residues in contact with ILE1113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109K LEU* 2.9 47.8 + - + +
1110K SER* 3.6 7.0 - - - +
1112K MET* 1.3 75.5 - - - +
1114K GLN* 1.3 59.5 + - - +
1116K ALA* 3.5 7.0 - - + +
1117K GLY* 2.9 26.3 + - - -
1240K MET* 3.3 27.1 - - + -
1241K LEU* 4.8 5.2 - - + -
1244K LEU* 6.5 0.2 - - + -
1266K ILE* 3.9 24.2 - - + +
1269K GLU* 3.8 42.2 - - + +
1270K MET* 3.8 14.8 - - - +
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Residues in contact with GLN1114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110K SER 2.8 12.6 + - - +
1111K LYS* 3.4 16.2 - - + +
1113K ILE* 1.3 79.3 - - - +
1115K MET* 1.3 62.4 + - + +
1118K GLU* 3.1 54.6 + - - +
1269K GLU 4.1 2.3 - - - +
1270K MET* 3.4 29.1 - - - +
1271K GLU* 3.0 56.9 + - + +
1274K PHE* 4.8 4.0 - - - +
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Residues in contact with MET1115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087K LEU* 4.0 19.7 - - - -
1090K TYR* 3.6 35.2 - - + +
1091K LEU* 4.8 4.0 - - + -
1094K LEU* 5.8 0.4 - - + -
1107K PRO* 5.5 7.4 - - + -
1111K LYS* 3.4 22.4 - - + +
1112K MET* 2.9 7.2 + - - +
1114K GLN* 1.3 75.0 - - + +
1116K ALA* 1.3 67.0 + - - +
1118K GLU* 3.3 8.1 + - - +
1119K ILE* 2.9 33.2 + - + +
1147K PHE* 5.0 9.6 - - + +
1149K VAL* 3.6 23.8 - - + -
1205K ILE* 4.4 28.9 - - + -
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Residues in contact with ALA1116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112K MET 2.7 19.4 + - - +
1113K ILE* 3.5 11.9 - - + +
1115K MET* 1.3 73.0 - - - +
1117K GLY* 1.3 58.0 + - - +
1119K ILE* 4.7 2.5 - - - -
1120K ALA* 2.9 30.6 + - - +
1198K PHE* 3.5 13.0 - - + -
1202K LEU* 3.5 32.1 - - + -
1205K ILE* 5.0 0.8 - - - +
1241K LEU* 5.1 5.2 - - + -
1244K LEU* 5.3 4.0 - - + -
1266K ILE* 4.4 8.5 - - + -
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Residues in contact with GLY1117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113K ILE 2.9 13.0 + - - -
1116K ALA* 1.3 76.1 - - - +
1118K GLU* 1.3 60.4 + - - +
1120K ALA* 3.7 4.1 - - - +
1121K ASP* 2.8 31.0 + - - +
1263K ILE* 4.3 5.2 - - - +
1266K ILE* 3.7 19.7 - - - +
1270K MET* 3.9 15.0 - - - -
1274K PHE* 4.1 4.1 - - - -
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Residues in contact with GLU1118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061K HIS* 3.4 40.3 + - + +
1114K GLN* 3.1 49.8 + - - +
1115K MET* 3.9 5.7 - - - +
1117K GLY* 1.3 75.2 - - - +
1119K ILE* 1.3 65.0 + - - +
1121K ASP* 3.3 1.2 + - - -
1122K GLY* 3.2 17.8 + - - -
1147K PHE 4.5 1.2 - - - +
1148K THR* 3.2 29.9 + - - +
1149K VAL* 3.3 31.5 + - - +
1270K MET* 4.1 4.2 - - + +
1274K PHE* 4.5 1.6 - - + -
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Residues in contact with ILE1119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087K LEU* 4.1 21.3 - - + -
1115K MET* 2.9 21.8 + - + +
1116K ALA* 3.9 3.8 - - - +
1118K GLU* 1.3 76.7 - - - +
1120K ALA* 1.3 63.8 + - - +
1122K GLY 3.3 0.5 + - - -
1123K MET* 3.0 27.7 + - + +
1136K LEU* 4.4 11.4 - - + -
1141K CYS* 4.2 8.1 - - - -
1149K VAL* 3.8 21.1 - - + -
1151K ILE* 3.6 23.1 - - + +
1198K PHE* 3.7 21.8 - - + -
1201K VAL* 3.9 23.6 - - + -
1205K ILE* 4.2 10.5 - - + -
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Residues in contact with ALA1120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116K ALA 2.9 20.5 + - - +
1117K GLY* 3.7 6.1 - - - +
1119K ILE* 1.3 78.1 - - - +
1121K ASP* 1.3 55.7 + - - +
1123K MET* 3.2 3.1 + - - +
1124K ALA* 2.8 29.6 + - - +
1198K PHE* 3.8 19.5 - - + -
1259K PHE* 3.8 18.7 - - + +
1262K ILE* 4.7 7.6 - - + -
1263K ILE* 3.7 17.7 - - + -
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Residues in contact with ASP1121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059K CYS* 4.0 2.6 - - - -
1061K HIS* 3.0 25.7 + - - +
1117K GLY 2.8 23.7 + - - +
1118K GLU 3.7 0.7 - - - +
1119K ILE 3.3 0.2 - - - -
1120K ALA* 1.3 70.9 - - - +
1122K GLY* 1.3 59.9 + - - +
1124K ALA* 3.3 3.1 + - - +
1125K TYR* 3.0 24.8 + - - +
1263K ILE* 3.4 12.6 - - + +
1274K PHE* 3.9 4.8 - - + -
1278K SER* 3.5 6.8 - - - -
1279K PHE* 2.7 26.8 + - - +
1280K TYR* 2.8 37.6 + - - +
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Residues in contact with GLY1122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059K CYS* 4.3 1.1 - - - -
1061K HIS* 3.9 25.4 - - - +
1062K VAL* 4.1 15.6 - - - +
1118K GLU 3.2 8.9 + - - -
1119K ILE 3.8 3.1 - - - -
1121K ASP* 1.3 74.5 - - - +
1123K MET* 1.3 61.1 + - - +
1125K TYR* 3.2 7.3 + - - +
1126K LEU* 2.8 27.3 + - - +
1151K ILE* 4.9 4.3 - - - -
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Residues in contact with MET1123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119K ILE* 3.0 19.7 + - + +
1120K ALA 3.5 7.6 - - - +
1122K GLY* 1.3 75.4 - - - +
1124K ALA* 1.3 60.0 + - - +
1126K LEU* 3.2 11.4 + - + +
1127K ASN* 2.9 33.0 + - - +
1133K HIS* 3.7 20.2 - - + +
1136K LEU* 4.0 25.8 - - + -
1151K ILE* 3.8 22.2 - - + -
1194K ASP* 3.3 35.4 - - + +
1259K PHE* 3.5 37.5 - - + -
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Residues in contact with ALA1124 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120K ALA 2.8 16.7 + - - +
1121K ASP 3.5 6.1 - - - +
1122K GLY 3.2 0.2 - - - -
1123K MET* 1.3 74.3 - - - +
1125K TYR* 1.3 58.8 + - - +
1127K ASN* 3.3 4.1 + - - +
1128K ALA* 2.9 31.0 + - - +
1259K PHE* 3.7 20.2 - - + +
1260K LEU* 4.3 15.6 - - + +
1263K ILE* 4.2 12.1 - - + -
1279K PHE* 3.8 16.0 - - + -
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Residues in contact with TYR1125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056K GLU* 4.0 3.8 + - - +
1057K PHE* 3.5 33.6 - + + -
1058K ASN* 2.8 30.3 + - - +
1059K CYS* 3.6 27.8 - - + -
1062K VAL* 4.2 8.5 - - + -
1121K ASP 3.0 13.8 + - - +
1122K GLY 3.2 8.7 - - - +
1124K ALA* 1.3 74.2 - - - +
1126K LEU* 1.3 70.0 + - + +
1128K ALA 3.3 0.7 + - - -
1129K ASN* 2.8 46.1 + - - -
1279K PHE* 3.5 33.3 - + + -
1284K GLU* 3.6 26.9 + - - -
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Residues in contact with LEU1126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057K PHE* 4.0 36.8 - - + -
1062K VAL* 4.7 4.0 - - + -
1122K GLY 2.8 17.6 + - - +
1123K MET* 3.2 21.7 + - + +
1125K TYR* 1.3 78.2 - - + +
1127K ASN* 1.3 63.0 + - - +
1129K ASN* 3.1 13.5 + - - +
1130K LYS 3.4 0.2 + - - -
1131K PHE* 3.2 52.3 + - + +
1132K VAL 4.7 0.2 - - - -
1133K HIS* 4.5 18.4 - - + +
1151K ILE* 5.2 1.1 - - + -
1154K PHE* 4.0 30.1 - - + -
1157K THR* 4.8 2.0 - - - -
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Residues in contact with ASN1127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123K MET* 2.9 20.9 + - - +
1124K ALA* 3.9 5.2 - - - +
1126K LEU* 1.3 70.7 - - - +
1128K ALA* 1.3 58.5 + - - +
1129K ASN 3.0 5.2 - - - -
1130K LYS* 2.8 28.1 + - - +
1131K PHE 2.9 23.2 + - - +
1160K ILE* 5.9 0.4 - - - +
1191K THR* 2.8 44.4 + - + +
1194K ASP* 3.8 14.1 + - - -
1259K PHE* 3.4 22.6 - - + -
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Residues in contact with ALA1128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124K ALA 2.9 17.6 + - - +
1125K TYR 3.7 4.3 - - - +
1126K LEU 3.2 0.4 - - - -
1127K ASN* 1.3 77.0 - - - +
1129K ASN* 1.3 64.8 + - - +
1130K LYS* 3.3 6.9 + - - +
1260K LEU* 6.3 2.5 - - + -
1279K PHE* 3.5 26.2 - - + -
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Residues in contact with ASN1129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056K GLU* 4.8 14.8 - - - +
1057K PHE* 4.9 8.1 - - + -
1125K TYR* 2.8 51.9 + - - +
1126K LEU 3.1 6.8 + - - +
1127K ASN 3.0 1.0 - - - -
1128K ALA* 1.3 85.8 - - - +
1130K LYS* 1.3 70.2 + - - +
1131K PHE* 3.3 25.5 - - + -
1159K ASP* 4.9 0.7 - - - +
1279K PHE* 5.3 1.0 - - - -
1284K GLU* 5.0 4.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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