Contacts of the helix formed by residues 1126 - 1160 (chain E) in PDB entry 6C3P
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 SER1126 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ILE* 4.3 19.7 - - - +
1122E ASN* 2.8 24.4 + - - -
1125E SER* 1.3 75.8 - - - +
1127E ASP* 1.3 64.7 + - - +
1128E CYS 3.5 1.6 - - - -
1129E ASN* 3.4 7.5 - - - +
1130E THR* 2.8 38.5 + - - -
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Residues in contact with ASP1127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122E ASN* 3.1 8.5 + - - +
1123E ARG* 3.2 51.8 + - - +
1126E SER* 1.3 78.1 + - - +
1128E CYS* 1.3 61.4 + - - +
1130E THR* 3.3 8.7 + - - -
1131E ILE* 2.9 31.2 + - - +
1310E ALA* 4.5 10.7 - - + +
1313E ARG* 4.2 20.7 + - - -
1314E ILE* 3.5 18.2 - - + -
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Residues in contact with CYS1128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495E ARG* 5.1 1.1 - - - +
526E ARG* 3.4 31.2 - - - -
1093E ALA* 5.2 2.5 - - - -
1096E LEU* 5.8 3.4 - - - -
1097E HIS* 3.7 25.4 - - + -
1100E LEU* 6.0 1.6 - - + -
1123E ARG 2.9 20.4 + - - +
1124E PHE* 3.7 17.0 + - + +
1127E ASP* 1.3 74.4 - - - +
1129E ASN* 1.3 58.1 - - - +
1131E ILE* 3.6 7.3 - - - +
1132E ASP* 2.8 38.4 + - - +
1314E ILE* 3.8 9.2 - - + +
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Residues in contact with ASN1129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E ILE* 4.5 27.9 - - - +
492E SER* 5.2 9.4 + - - +
495E ARG* 5.2 5.3 - - - +
1124E PHE 4.4 0.8 + - - -
1125E SER 3.6 19.4 + - - +
1126E SER* 3.4 10.6 + - - +
1128E CYS* 1.3 75.1 - - - +
1130E THR* 1.3 65.4 + - - +
1132E ASP* 2.6 22.7 - - - +
1133E GLN* 2.4 48.3 + - - +
1134E HIS* 5.5 1.5 - - - -
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Residues in contact with THR1130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126E SER* 2.8 28.0 + - - -
1127E ASP* 3.4 13.6 + - - +
1129E ASN* 1.3 71.1 - - - +
1131E ILE* 1.3 69.9 + - + +
1134E HIS* 2.9 38.5 + - + +
1135E ILE 3.6 1.4 + - - -
1306E LEU* 5.5 5.8 - - + -
1307E GLN* 4.4 28.5 - - + +
1310E ALA* 5.1 9.9 - - + -
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Residues in contact with ILE1131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003E TYR* 4.4 7.6 - - + +
1093E ALA* 4.6 9.2 - - + -
1096E LEU* 3.6 33.9 - - + -
1127E ASP 2.9 12.4 + - - +
1128E CYS* 3.6 11.2 - - + +
1129E ASN 3.2 0.2 - - - -
1130E THR* 1.3 81.8 - - + +
1132E ASP* 1.3 65.2 + - + +
1133E GLN 3.0 2.8 + - - -
1135E ILE* 3.0 42.9 + - + +
1136E PRO* 3.9 1.4 - - - +
1307E GLN 5.2 0.7 - - - +
1310E ALA* 5.2 2.0 - - + -
1311E VAL* 3.6 35.2 - - + +
1314E ILE* 3.5 31.6 - - + -
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Residues in contact with ASP1132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495E ARG* 5.6 0.9 + - - -
526E ARG* 3.3 31.4 + - - +
529E GLU* 4.6 4.0 - - - +
533E LEU* 3.2 40.8 - - + +
536E PHE* 5.9 0.3 - - - -
1089E GLY 5.7 0.4 - - - -
1093E ALA* 3.6 26.5 - - + -
1128E CYS* 2.8 20.7 + - - +
1129E ASN* 2.6 35.2 - - - +
1131E ILE* 1.3 75.6 - - + +
1133E GLN* 1.3 59.6 + - - +
1136E PRO* 4.9 8.4 - - - +
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Residues in contact with GLN1133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E GLN* 4.7 5.3 - - - +
485E GLN* 4.5 13.0 + - - +
488E THR* 4.8 10.4 - - - +
533E LEU* 4.5 7.4 - - + +
536E PHE* 4.8 17.3 - - + -
598E ARG* 3.5 18.8 + - - +
602E LYS* 3.5 27.4 + - - +
1129E ASN* 2.4 46.6 + - - +
1132E ASP* 1.3 88.9 + - - +
1134E HIS* 1.3 79.2 + - + +
1136E PRO* 4.8 4.3 - - - -
1137E SER* 5.4 0.2 - - - -
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Residues in contact with HIS1134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E GLN* 5.9 0.9 - - + -
430E TRP* 3.3 38.4 - + - -
598E ARG* 5.6 1.6 - - - -
602E LYS* 3.4 29.4 + - - -
1129E ASN* 4.8 2.2 - - - -
1130E THR* 2.9 26.2 + - + +
1133E GLN* 1.3 105.1 + - + +
1135E ILE* 1.3 68.8 + - - +
1136E PRO* 3.5 2.4 - - - +
1137E SER* 3.5 12.9 + - - -
1138E THR* 3.2 22.0 + - - -
1307E GLN* 3.9 15.9 - - - +
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Residues in contact with ILE1135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003E TYR* 3.0 35.7 - - + +
1130E THR* 4.8 1.3 - - + +
1131E ILE* 3.0 46.2 + - + +
1134E HIS* 1.3 75.7 - - - +
1136E PRO* 1.3 68.7 - - + +
1138E THR* 3.0 3.6 + - - -
1139E LEU* 2.8 30.8 + - + +
1304E MET* 5.9 2.5 - - + -
1307E GLN* 3.2 38.8 - - + +
1308E LEU* 4.6 9.6 - - + -
1311E VAL* 4.3 15.0 - - + -
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Residues in contact with PRO1136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E ALA* 6.5 1.3 - - + -
540E THR* 6.2 4.5 - - + -
544E ILE* 6.1 1.6 - - + -
1085E VAL* 4.2 22.1 - - + +
1086E GLU* 5.1 6.5 - - - +
1089E GLY* 4.1 25.1 - - - -
1090E LEU 5.3 0.4 - - - +
1131E ILE 3.9 6.1 - - - +
1132E ASP 4.9 6.7 - - - +
1133E GLN* 4.8 2.9 - - - -
1134E HIS 3.6 6.5 - - - +
1135E ILE* 1.3 94.3 - - + +
1137E SER* 1.3 63.7 + - - +
1139E LEU* 3.9 8.0 - - + +
1140E GLU* 2.9 28.6 + - - +
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Residues in contact with SER1137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ILE* 5.9 2.0 - - - -
595E SER* 5.7 6.7 - - - -
598E ARG* 2.4 41.2 + - - -
1134E HIS* 3.5 16.2 + - - -
1135E ILE 3.2 0.6 - - - -
1136E PRO* 1.3 79.3 - - - +
1138E THR* 1.3 64.2 + - - +
1140E GLU* 2.8 28.9 - - - +
1141E CYS* 2.9 16.9 + - - -
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Residues in contact with THR1138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134E HIS* 3.2 2.8 + - - +
1135E ILE 3.0 2.6 + - - -
1137E SER* 1.3 78.2 - - - +
1139E LEU* 1.3 58.2 + - - +
1141E CYS* 3.3 6.8 + - - +
1142E LEU* 2.9 28.6 + - - +
1300E ASN* 4.0 11.8 - - + +
1303E ASP* 4.2 8.6 - - + +
1304E MET* 3.5 41.3 - - + +
1307E GLN* 2.6 37.2 + - - +
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Residues in contact with LEU1139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000E CYS* 5.9 1.1 - - - -
1003E TYR* 5.0 17.9 - - + -
1015E LEU* 4.5 24.0 - - + -
1085E VAL* 5.4 7.2 - - + -
1088E THR* 5.3 8.1 - - + -
1135E ILE* 2.8 26.4 + - + +
1136E PRO* 3.9 7.6 - - + +
1138E THR* 1.3 75.0 - - - +
1140E GLU* 1.3 58.2 + - - +
1142E LEU* 3.4 5.4 + - + +
1143E SER* 2.8 37.3 + - - -
1304E MET* 3.6 36.5 - - + +
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Residues in contact with GLU1140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ILE* 4.1 24.0 - - + +
591E PHE 5.7 1.0 - - - +
594E SER* 5.8 0.3 + - - -
1019E GLN* 5.7 2.9 + - - +
1085E VAL* 4.1 22.2 - - + +
1136E PRO 2.9 26.8 + - - +
1137E SER* 2.8 20.5 - - - +
1139E LEU* 1.3 74.6 - - - +
1141E CYS* 1.3 90.2 + - - +
1143E SER* 4.2 5.6 - - - -
1144E ARG* 2.9 69.4 + - - +
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Residues in contact with CYS1141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591E PHE 5.8 3.6 - - - -
592E LEU* 6.5 0.9 - - - -
595E SER* 6.3 3.4 - - - -
1137E SER* 2.9 21.1 + - - +
1138E THR* 3.5 7.0 - - - +
1140E GLU* 1.3 103.3 - - - +
1142E LEU* 1.3 59.9 + - - +
1144E ARG* 3.2 6.9 - - - +
1145E SER* 2.6 32.1 + - - -
1300E ASN* 3.5 26.7 - - - +
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Residues in contact with LEU1142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138E THR 2.9 20.1 + - - +
1139E LEU* 3.8 7.6 - - + +
1141E CYS* 1.3 72.4 - - - +
1143E SER* 1.3 60.7 + - - +
1145E SER* 3.7 2.2 - - - -
1146E THR* 2.9 49.0 + - + +
1297E MET* 5.0 4.7 - - + +
1300E ASN* 3.5 19.4 - - + +
1301E LEU* 3.5 44.9 - - + +
1304E MET* 3.5 28.7 - - + -
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Residues in contact with SER1143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015E LEU* 5.1 4.9 - - - +
1019E GLN* 3.0 38.4 + - - +
1139E LEU* 2.8 29.2 + - - -
1140E GLU* 3.8 5.8 - - - -
1141E CYS 3.2 0.2 - - - -
1142E LEU* 1.3 76.9 - - - +
1144E ARG* 1.3 65.1 + - - +
1146E THR* 3.3 7.6 - - - +
1147E LEU* 2.9 27.7 + - - +
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Residues in contact with ARG1144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544E ILE* 3.3 33.1 + - - +
547E ASN* 4.8 4.2 + - - +
548E THR* 3.5 22.3 + - - +
591E PHE* 3.6 33.7 + - - +
1019E GLN* 4.2 3.4 + - - +
1023E HIS* 4.0 21.8 - - + -
1140E GLU* 2.9 45.0 + - - +
1141E CYS* 3.2 9.6 - - - +
1143E SER* 1.3 75.7 - - - +
1145E SER* 1.3 70.2 + - - +
1148E LEU* 2.9 35.6 + - + +
1293E TYR* 6.3 5.6 - - + -
1296E TRP* 6.4 2.9 - - - -
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Residues in contact with SER1145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141E CYS* 2.6 23.0 + - - +
1142E LEU 3.7 2.2 - - - -
1144E ARG* 1.3 80.0 - - - +
1146E THR* 1.3 58.7 + - - +
1148E LEU* 3.8 3.4 - - - +
1149E CYS* 2.9 30.3 + - - +
1293E TYR* 4.1 17.2 - - - +
1296E TRP* 3.9 14.2 - - - +
1297E MET* 3.7 29.5 - - - +
1300E ASN* 3.4 13.9 + - - -
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Residues in contact with THR1146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142E LEU* 2.9 36.3 + - + +
1143E SER* 3.3 11.2 - - - +
1145E SER* 1.3 73.4 - - - +
1147E LEU* 1.3 67.1 + - + +
1149E CYS* 3.3 1.2 - - - +
1150E VAL* 2.9 36.6 + - - +
1297E MET* 3.4 31.8 - - - +
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Residues in contact with LEU1147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019E GLN* 4.2 20.0 - - + +
1020E LEU* 3.9 30.3 - - + +
1023E HIS* 3.5 37.9 - - + +
1024E MET* 5.0 4.0 - - + +
1143E SER* 2.9 19.3 + - - +
1146E THR* 1.3 82.3 - - + +
1148E LEU* 1.3 65.5 + - - +
1150E VAL* 4.1 8.0 - - + -
1151E SER* 2.9 33.0 + - - +
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Residues in contact with LEU1148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584E HIS* 6.2 1.6 - - + -
1023E HIS* 3.2 41.7 - - + +
1026E LEU* 5.6 8.7 - - + -
1027E VAL* 6.2 2.0 - - + -
1144E ARG* 2.9 34.3 + - + +
1145E SER* 3.9 3.6 - - - +
1147E LEU* 1.3 75.5 - - - +
1149E CYS* 1.3 63.9 + - - +
1151E SER* 2.6 22.8 + - - +
1152E ALA* 2.9 12.8 + - - +
1289E MET* 3.6 36.4 - - + +
1293E TYR* 5.2 9.4 - - + -
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Residues in contact with CYS1149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145E SER 2.9 19.3 + - - +
1146E THR 3.3 6.7 - - - +
1147E LEU 3.1 0.2 - - - -
1148E LEU* 1.3 75.7 - - - +
1150E VAL* 1.3 70.4 + - - +
1152E ALA* 2.9 7.3 + - - +
1153E LEU* 2.9 43.7 + - - +
1290E VAL* 4.9 7.0 - - + +
1293E TYR* 5.5 2.9 - - - +
1294E LEU* 3.6 37.0 - - + +
1297E MET* 3.8 17.0 - - + -
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Residues in contact with VAL1150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146E THR* 2.9 31.1 + - - +
1147E LEU* 4.3 9.6 - - + +
1149E CYS* 1.3 77.9 - - + +
1151E SER* 1.3 64.0 + - - +
1153E LEU* 3.3 10.3 + - + +
1154E ALA* 2.9 24.4 + - + +
1297E MET* 5.6 1.1 - - - -
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Residues in contact with SER1151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023E HIS* 5.1 4.6 - - - +
1024E MET* 6.1 3.4 - - - -
1027E VAL* 3.9 23.4 - - - +
1147E LEU* 2.9 26.0 + - - +
1148E LEU* 2.6 33.3 + - - +
1150E VAL* 1.3 76.9 - - - +
1152E ALA* 1.3 57.8 + - - +
1154E ALA* 3.1 7.4 + - - +
1155E VAL* 2.9 33.5 + - - +
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Residues in contact with ALA1152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027E VAL* 5.9 0.7 - - - -
1148E LEU 3.4 12.1 - - - +
1149E CYS 2.9 4.2 + - - -
1151E SER* 1.3 79.5 + - - +
1153E LEU* 1.3 58.6 + - - +
1155E VAL* 3.8 7.1 - - - +
1156E ILE* 2.9 36.7 + - - +
1286E TYR* 3.9 23.3 - - + +
1289E MET* 4.5 10.5 - - + -
1290E VAL* 3.6 22.9 - - + -
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Residues in contact with LEU1153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1149E CYS* 2.9 48.6 + - - +
1150E VAL* 3.4 14.1 - - + +
1152E ALA* 1.3 76.3 - - - +
1154E ALA* 1.3 63.5 + - - +
1156E ILE* 3.1 18.5 - - + +
1157E SER* 2.9 23.6 + - - -
1163E PHE* 5.3 0.3 - - - -
1167E LEU* 3.6 38.7 - - + +
1258E VAL* 5.9 2.0 - - + -
1290E VAL* 3.7 22.2 - - + -
1294E LEU* 5.6 0.4 - - + -
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Residues in contact with ALA1154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150E VAL* 2.9 15.4 + - + +
1151E SER* 3.5 9.6 - - - +
1153E LEU* 1.3 75.5 - - - +
1155E VAL* 1.3 59.9 + - + +
1157E SER* 2.2 27.2 + - - -
1158E TYR* 2.9 14.6 + - - +
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Residues in contact with VAL1155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027E VAL* 3.5 32.3 - - + -
1031E TYR* 4.7 7.2 - - + -
1151E SER* 2.9 25.1 + - - +
1152E ALA* 3.8 4.3 - - - +
1154E ALA* 1.3 77.2 - - + +
1156E ILE* 1.3 61.9 + - - +
1158E TYR* 2.9 8.2 + - + +
1159E VAL* 2.9 31.6 + - + +
1282E LEU* 3.8 15.0 - - + -
1286E TYR* 3.4 32.3 - - + -
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Residues in contact with ILE1156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152E ALA 2.9 18.6 + - - +
1153E LEU* 3.1 28.7 - - + +
1155E VAL* 1.3 73.0 - - - +
1157E SER* 1.3 64.8 + - - +
1159E VAL* 3.7 8.1 - - + -
1160E THR* 3.1 30.8 + - + +
1163E PHE* 3.4 38.5 - - + +
1258E VAL* 4.4 12.6 - - + -
1262E ALA* 5.2 7.4 - - + -
1283E GLY* 3.3 28.5 - - - +
1286E TYR* 3.5 17.0 - - + -
1287E ALA* 4.0 8.3 - - + +
1290E VAL* 4.9 6.5 - - + -
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Residues in contact with SER1157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1153E LEU 2.9 12.9 + - - -
1154E ALA* 2.2 34.5 + - - -
1156E ILE* 1.3 78.4 - - - +
1158E TYR* 1.3 56.1 + - - +
1160E THR 2.8 25.9 - - - +
1161E PRO* 3.2 9.0 - - - +
1163E PHE* 4.6 8.3 - - - -
1164E LEU* 3.4 33.3 - - - +
1167E LEU* 6.4 2.0 - - - -
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Residues in contact with TYR1158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031E TYR* 3.1 41.7 + + - -
1154E ALA 2.9 10.6 + - - +
1155E VAL* 2.9 10.9 + - + +
1157E SER* 1.3 84.1 + - - +
1159E VAL* 1.3 64.5 + - + +
1160E THR 3.3 0.7 + - - -
1161E PRO* 3.7 11.1 - - - +
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Residues in contact with VAL1159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031E TYR* 3.8 19.1 - - + -
1155E VAL* 2.9 24.2 + - + +
1156E ILE* 3.5 15.7 - - - +
1158E TYR* 1.3 79.4 - - + +
1160E THR* 1.3 66.7 + - + +
1161E PRO* 4.0 4.0 - - - +
1266E SER* 5.2 2.9 - - - +
1269E ASN* 5.5 0.7 + - - -
1275E LEU* 4.6 18.5 - - - +
1279E LEU* 4.1 24.0 - - + +
1280E VAL* 6.1 0.2 - - - -
1282E LEU* 3.6 28.0 - - + -
1283E GLY* 3.8 19.3 - - - +
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Residues in contact with THR1160 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156E ILE* 3.1 16.5 + - + +
1157E SER 2.8 10.5 - - - +
1159E VAL* 1.3 81.7 - - + +
1161E PRO* 1.3 61.1 - - - +
1162E VAL* 2.9 10.1 + - - +
1163E PHE* 2.8 36.8 + - + +
1262E ALA* 5.0 4.7 - - + +
1265E THR* 3.2 29.3 - - + +
1266E SER* 3.9 24.7 - - - +
1269E ASN* 4.9 6.9 + - - +
1275E LEU* 6.4 0.4 - - - -
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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) + - + + + + + -
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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