Contacts of the helix formed by residues 1146 - 1171 (chain A) in PDB entry 2DGZ
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 SER1146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144A VAL* 3.8 3.2 + - - -
1145A ILE* 1.3 72.2 - - - +
1147A ALA* 1.3 64.4 + - - +
1148A GLN* 2.6 34.7 + - - +
1149A GLU* 2.8 12.3 + - - +
1150A GLN* 2.8 19.8 + - - -
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Residues in contact with ALA1147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145A ILE 3.3 3.8 + - - -
1146A SER* 1.3 70.3 - - - +
1148A GLN* 1.3 70.6 + - - +
1150A GLN* 3.7 15.6 + - - +
1151A GLU* 3.1 35.9 + - + +
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Residues in contact with GLN1148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146A SER* 2.6 33.3 + - - +
1147A ALA* 1.3 78.9 + - - +
1149A GLU* 1.3 59.7 + - + +
1151A GLU* 4.9 0.9 - - - +
1152A THR* 3.9 12.0 + - - -
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Residues in contact with GLU1149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145A ILE* 3.3 23.1 - - + +
1146A SER* 2.8 16.0 + - - +
1148A GLN* 1.3 74.5 - - + +
1150A GLN* 1.3 72.2 + - - +
1151A GLU 3.2 2.2 - - - -
1152A THR* 2.9 18.8 + - - -
1153A GLN* 3.0 28.8 + - - +
1191A ARG* 4.7 14.8 + - - +
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Residues in contact with GLN1150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1144A VAL* 4.7 8.7 - - - +
1145A ILE* 2.7 59.4 + - + +
1146A SER 2.8 14.7 + - - +
1147A ALA* 3.7 12.2 + - - +
1149A GLU* 1.3 73.4 - - - +
1151A GLU* 1.3 63.9 + - - +
1153A GLN* 2.9 10.9 + - + +
1154A ILE* 2.9 42.9 + - + +
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Residues in contact with GLU1151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147A ALA* 3.1 26.0 + - + +
1148A GLN 4.9 0.9 - - - +
1150A GLN* 1.3 77.5 - - - +
1152A THR* 1.3 65.9 + - - +
1154A ILE* 2.7 27.4 + - + +
1155A VAL* 2.9 29.0 + - + +
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Residues in contact with THR1152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147A ALA 4.6 0.2 + - - -
1148A GLN 3.9 10.9 + - - -
1149A GLU* 2.9 12.1 + - - -
1151A GLU* 1.3 77.4 - - - +
1153A GLN* 1.3 56.7 + - - +
1155A VAL* 4.8 2.9 - - - +
1156A LEU* 2.9 31.4 + - - +
1191A ARG* 3.6 28.3 - - - +
1222A PHE* 3.6 30.7 - - + -
1228A VAL* 3.7 20.4 - - + +
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Residues in contact with GLN1153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1145A ILE* 3.0 29.5 - - - +
1149A GLU* 3.0 52.2 + - - +
1150A GLN* 2.9 7.0 + - - +
1152A THR* 1.3 73.4 - - - +
1154A ILE* 1.3 59.1 + - + +
1156A LEU* 4.3 2.2 - - - -
1157A TYR* 2.8 37.5 + - - +
1188A ALA* 3.3 30.4 - - + +
1189A LYS* 3.8 19.8 - - - +
1191A ARG* 4.3 15.0 - - - +
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Residues in contact with ILE1154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A GLN* 2.9 44.3 + - + +
1151A GLU* 2.7 22.4 + - + +
1153A GLN* 1.3 74.8 - - + +
1155A VAL* 1.3 67.0 + - + +
1157A TYR* 3.8 6.6 - - - +
1158A GLY* 3.4 15.6 + - - -
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Residues in contact with VAL1155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151A GLU* 2.9 32.7 + - + +
1152A THR* 4.1 4.5 - - - +
1154A ILE* 1.3 79.9 - - + +
1156A LEU* 1.3 64.6 + - - +
1158A GLY* 3.6 2.6 + - - -
1159A LYS* 3.4 25.8 + - + +
1222A PHE* 4.1 19.7 - - + -
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Residues in contact with LEU1156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152A THR 2.9 19.5 + - - +
1153A GLN* 3.8 3.1 - - - +
1155A VAL* 1.3 75.1 - - - +
1157A TYR* 1.3 59.3 + - - +
1159A LYS* 2.6 38.9 + - + +
1160A LEU* 3.1 20.1 + - + -
1188A ALA* 4.1 13.9 - - - +
1191A ARG* 3.2 39.5 - - + -
1218A VAL* 5.0 0.9 - - + +
1219A ILE* 4.0 29.2 - - + +
1222A PHE* 3.6 36.5 - - + -
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Residues in contact with TYR1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1153A GLN 2.8 22.3 + - - +
1154A ILE* 3.8 6.1 - - - +
1156A LEU* 1.3 72.1 - - - +
1158A GLY* 1.3 67.7 + - - +
1160A LEU* 3.0 8.4 + - + +
1161A VAL* 3.0 45.7 + - + +
1181A ASN* 2.5 32.1 + - - +
1184A LEU* 3.6 40.1 - - + +
1185A VAL* 4.1 17.6 - - + +
1188A ALA* 4.1 13.0 - - + +
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Residues in contact with GLY1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A ILE 3.4 9.6 + - - -
1155A VAL 4.0 3.8 - - - -
1156A LEU 2.9 1.2 + - - -
1157A TYR* 1.3 82.3 - - - +
1159A LYS* 1.3 62.1 + - - +
1161A VAL* 3.5 8.6 + - - +
1162A GLU* 3.2 28.0 + - - +
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Residues in contact with LYS1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A VAL* 3.4 22.6 + - - +
1156A LEU* 2.6 16.5 + - + +
1158A GLY* 1.3 70.9 - - - -
1160A LEU* 1.3 61.0 + - - +
1162A GLU* 3.3 9.9 + - - +
1163A ALA* 3.2 20.1 + - - +
1218A VAL* 4.0 24.4 - - + +
1222A PHE* 3.8 42.8 - - + +
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Residues in contact with LEU1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156A LEU* 3.1 17.7 + - + +
1157A TYR* 3.0 9.1 + - - +
1159A LYS* 1.3 75.5 - - + +
1161A VAL* 1.3 66.0 + - - +
1163A ALA* 2.9 17.8 + - - +
1164A ARG* 2.9 13.9 + - - +
1184A LEU* 3.9 38.4 - - + +
1187A MET* 4.2 7.2 - - + -
1188A ALA* 4.0 24.9 - - + +
1215A LEU* 3.2 41.9 - - + +
1218A VAL* 5.1 2.2 - - + -
1219A ILE* 3.7 25.6 - - + -
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Residues in contact with VAL1161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157A TYR* 3.0 53.4 + - + +
1158A GLY* 3.7 8.5 - - - +
1160A LEU* 1.3 76.0 - - - +
1162A GLU* 1.3 67.5 + - + +
1164A ARG* 3.3 21.5 + - - +
1165A GLN* 3.1 22.5 + - + +
1184A LEU* 4.1 14.4 - - + -
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Residues in contact with GLU1162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A GLY 3.2 15.6 + - - +
1159A LYS* 3.4 10.1 - - - +
1160A LEU 3.1 0.4 - - - -
1161A VAL* 1.3 80.9 - - + +
1163A ALA* 1.3 64.2 + - - +
1165A GLN* 3.3 19.6 + - - +
1166A LYS* 3.2 23.2 + - - +
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Residues in contact with ALA1163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159A LYS 3.2 7.9 + - - +
1160A LEU* 2.9 11.6 + - - +
1162A GLU* 1.3 76.0 - - - +
1164A ARG* 1.3 66.2 - - - +
1166A LYS* 3.0 17.3 - - + +
1167A HIS* 2.9 25.2 + - - +
1214A PRO* 4.1 27.1 - - + +
1215A LEU* 4.7 5.4 - - - -
1218A VAL* 4.4 11.7 - - + -
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Residues in contact with ARG1164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160A LEU 2.9 10.7 + - - +
1161A VAL* 3.6 23.2 + - - +
1163A ALA* 1.3 75.2 - - - +
1165A GLN* 1.3 60.9 + - - +
1167A HIS* 3.2 1.3 + - - -
1168A ALA* 2.6 32.4 + - - +
1175A PRO* 2.7 49.2 + - - +
1176A ALA* 4.3 4.4 - - - +
1178A LEU* 2.9 32.6 - - + +
1179A ALA* 3.2 28.2 + - + +
1180A THR* 5.2 0.2 - - - +
1181A ASN* 4.4 14.3 - - - +
1184A LEU* 3.9 29.9 - - + +
1215A LEU* 4.5 9.5 - - + +
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Residues in contact with GLN1165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1161A VAL* 3.1 9.8 + - + +
1162A GLU* 3.4 23.1 + - - +
1163A ALA 3.1 0.6 - - - -
1164A ARG* 1.3 84.6 - - - +
1166A LYS* 1.3 61.8 + - - +
1167A HIS 2.7 5.9 + - - -
1168A ALA* 2.5 34.7 + - - +
1169A ASN* 3.2 18.0 + - - +
1175A PRO* 5.2 10.8 - - + -
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Residues in contact with LYS1166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162A GLU 3.2 10.1 + - - +
1163A ALA* 3.0 27.6 - - + +
1165A GLN* 1.3 85.7 - - - +
1167A HIS* 1.3 61.6 + - + +
1169A ASN* 4.2 6.1 + - - +
1170A LYS* 3.7 16.8 + - - +
1214A PRO* 6.2 3.8 - - + -
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Residues in contact with HIS1167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1163A ALA 2.9 18.2 + - - +
1164A ARG* 3.4 4.5 - - - +
1165A GLN 2.7 5.1 + - - -
1166A LYS* 1.3 80.6 - - + +
1168A ALA* 1.3 64.5 + - - +
1169A ASN 3.3 0.4 - - - -
1170A LYS* 3.3 29.5 + - + +
1171A MET* 3.2 39.2 + - + +
1178A LEU* 3.7 17.8 - - + +
1211A MET* 2.8 29.1 + - + -
1212A LEU* 4.9 0.2 - - - -
1214A PRO* 3.7 29.9 - - + +
1215A LEU* 4.2 8.1 - - + -
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Residues in contact with ALA1168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1164A ARG 2.6 13.7 + - - +
1165A GLN* 2.5 17.7 + - - +
1167A HIS* 1.3 73.3 - - - +
1169A ASN* 1.3 61.0 + - - +
1171A MET 3.4 0.7 + - - -
1172A ASP 3.0 3.5 + - - -
1173A VAL* 2.8 49.5 + - - +
1174A PRO 4.2 1.8 - - - +
1175A PRO* 3.7 27.1 - - + -
1178A LEU* 3.6 10.7 - - + +
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Residues in contact with ASN1169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165A GLN* 3.2 21.6 + - - +
1166A LYS* 4.4 6.3 - - - +
1168A ALA* 1.3 80.1 - - - +
1170A LYS* 1.3 60.5 + - - +
1172A ASP* 2.6 31.3 + - - +
1173A VAL 4.7 1.5 + - - -
1175A PRO* 5.3 7.9 - - - +
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Residues in contact with LYS1170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166A LYS 3.7 13.9 + - - +
1167A HIS* 3.3 28.4 + - - +
1169A ASN* 1.3 79.3 - - - +
1171A MET* 1.3 74.8 + - + +
1172A ASP* 2.9 14.9 - - - +
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Residues in contact with MET1171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167A HIS* 3.2 29.5 + - + +
1170A LYS* 1.3 90.9 - - + +
1172A ASP* 1.3 77.8 + - - +
1173A VAL* 3.5 25.5 + - + +
1178A LEU* 3.1 31.4 - - + -
1211A MET* 3.6 37.7 - - + +
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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
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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