Contacts of the helix formed by residues 1219 - 1255 (chain A) in PDB entry 6J8H
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 LYS1219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211A PHE* 4.1 25.1 + - - +
1213A ASP* 4.6 2.8 + - - -
1215A TYR* 3.6 30.2 + - - +
1216A ILE* 3.8 12.9 - - + +
1218A ARG* 1.3 93.8 - - + +
1220A LYS* 1.3 67.7 + - - +
1221A THR* 3.1 4.6 + - - +
1222A ILE* 3.3 43.2 + - + +
1223A LYS* 3.5 5.5 + - - +
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Residues in contact with LYS1220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A ILE 4.6 0.9 - - - -
1217A GLU* 3.4 24.5 - - - +
1218A ARG* 3.4 0.4 - - - -
1219A LYS* 1.3 74.9 - - - +
1221A THR* 1.3 63.5 + - - +
1223A LYS* 3.1 30.2 + - - +
1224A ILE* 3.2 12.0 + - - +
24B VAL* 4.3 8.3 - - - -
25B ASP* 3.6 25.5 + - - +
26B SER 4.5 0.4 + - - -
27B GLU* 2.5 47.1 + - - +
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Residues in contact with THR1221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219A LYS* 3.1 2.1 - - - +
1220A LYS* 1.3 79.9 - - - +
1222A ILE* 1.3 62.6 + - + +
1224A ILE* 2.9 29.8 - - - +
1225A ILE* 3.3 13.9 + - + +
153B ASP* 5.4 2.8 + - - -
155B ALA* 4.1 23.6 - - + +
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Residues in contact with ILE1222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211A PHE* 4.0 26.7 - - + -
1216A ILE* 5.2 2.5 - - + -
1219A LYS* 3.3 36.8 + - + +
1221A THR* 1.3 78.7 - - + +
1223A LYS* 1.3 64.5 + - - +
1225A ILE* 3.4 14.4 + - + +
1226A LEU* 3.0 46.8 + - + +
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Residues in contact with LYS1223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1216A ILE* 4.0 44.1 - - + +
1217A GLU* 4.7 18.7 + - - -
1219A LYS 3.5 5.1 + - - +
1220A LYS* 3.1 26.2 + - - +
1222A ILE* 1.3 81.0 - - - +
1224A ILE* 1.3 69.2 + - - +
1226A LEU* 3.8 4.8 - - - +
1227A GLU* 3.1 31.0 + - + +
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Residues in contact with ILE1224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1220A LYS 3.2 6.6 + - - +
1221A THR* 2.9 20.4 - - - +
1223A LYS* 1.3 87.3 - - - +
1225A ILE* 1.3 74.7 + - + +
1227A GLU* 3.3 19.2 + - - +
1228A TYR* 3.2 35.1 + - + -
155B ALA* 4.1 24.7 - - + +
156B SER* 4.2 30.1 - - - +
159B SER* 5.2 0.7 - - - +
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Residues in contact with ILE1225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221A THR* 3.3 21.7 + - + +
1222A ILE* 3.5 21.8 - - + +
1224A ILE* 1.3 82.0 - - + +
1226A LEU* 1.3 68.3 + - + +
1228A TYR* 3.3 1.7 + - - +
1229A ALA* 2.7 39.4 + - + +
155B ALA* 5.6 1.8 - - + +
159B SER* 3.9 21.9 + - - +
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Residues in contact with LEU1226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208A ALA* 3.9 31.9 - - + +
1211A PHE* 3.4 39.5 - - + -
1212A GLU* 5.2 2.7 - - + +
1216A ILE* 5.1 6.1 - - + -
1222A ILE* 3.0 27.8 + - + +
1223A LYS* 3.8 4.5 - - - +
1225A ILE* 1.3 93.7 - - + +
1227A GLU* 1.3 63.6 + - - +
1229A ALA* 3.6 9.1 - - + +
1230A ASP* 3.1 23.4 + - - +
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Residues in contact with GLU1227 (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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1223A LYS* 3.1 25.7 + - + +
1224A ILE* 3.7 19.1 - - - +
1226A LEU* 1.3 77.7 - - - +
1228A TYR* 1.3 77.6 + - + +
1230A ASP* 3.6 14.4 + - - +
1231A LYS* 3.9 15.8 + - - +
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Residues in contact with TYR1228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224A ILE* 3.2 31.2 + - + +
1225A ILE 3.8 3.1 - - - +
1227A GLU* 1.3 88.8 - - + +
1229A ALA* 1.3 65.7 + - - +
1231A LYS* 3.2 35.0 + - + +
1232A ILE* 3.5 4.0 + - - +
152B ARG* 5.0 2.3 + - - -
156B SER* 4.0 28.6 + - - -
159B SER* 3.8 26.0 - - - +
160B GLU* 4.1 26.7 + - + +
163B MET* 4.1 37.0 - - + +
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Residues in contact with ALA1229 (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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1225A ILE* 2.7 22.5 + - + +
1226A LEU* 3.6 15.7 - - + +
1228A TYR* 1.3 73.9 - - - +
1230A ASP* 1.3 59.0 + - - +
1232A ILE* 2.7 34.3 - - + +
1233A PHE* 3.2 20.4 + - + -
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Residues in contact with ASP1230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1226A LEU 3.1 12.7 + - - +
1227A GLU* 3.8 11.5 - - - +
1228A TYR 3.2 0.4 - - - -
1229A ALA* 1.3 77.4 - - - +
1231A LYS* 1.3 55.2 + - - +
1233A PHE* 3.0 15.0 + - - +
1234A THR* 2.8 45.2 + - - -
1269A SER* 6.0 1.4 - - - -
1273A LEU* 6.1 0.9 - - - +
1293A ARG* 4.7 7.5 + - - -
1296A ARG* 2.8 35.3 + - - +
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Residues in contact with LYS1231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227A GLU* 3.9 13.4 + - - +
1228A TYR* 3.2 34.3 + - + +
1230A ASP* 1.3 82.7 + - - +
1232A ILE* 1.3 63.0 + - - +
1234A THR* 3.2 7.0 + - - +
1235A TYR* 3.0 23.7 + - - +
1273A LEU* 3.2 38.7 - - + +
1276A ASN* 5.6 5.5 - - - +
1277A THR* 5.1 9.6 - - - +
163B MET* 4.7 12.8 - - - -
167B ILE* 5.3 3.1 - - + +
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Residues in contact with ILE1232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1228A TYR 3.5 4.7 + - - +
1229A ALA* 2.7 30.5 + - + +
1231A LYS* 1.3 79.0 - - - +
1233A PHE* 1.3 77.0 + - + +
1235A TYR* 3.3 6.4 + - + +
1236A ILE* 3.0 37.3 + - + +
163B MET* 4.8 10.7 - - + +
166B LEU* 3.4 38.6 - - + -
167B ILE* 4.2 22.7 - - + +
170B LEU* 4.7 11.0 - - + -
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Residues in contact with PHE1233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201A MET* 3.8 39.0 - - + -
1204A LEU* 4.2 24.2 - - + -
1205A SER* 4.0 36.3 - - - +
1208A ALA* 4.9 10.1 - - + -
1229A ALA* 3.3 28.5 - - + -
1230A ASP* 3.0 18.0 + - - +
1232A ILE* 1.3 89.5 - - + +
1234A THR* 1.3 66.0 + - - +
1236A ILE* 3.2 6.9 + - + +
1237A PHE* 3.0 39.9 + + + -
1296A ARG* 5.2 6.1 - - - +
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Residues in contact with THR1234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1230A ASP* 2.8 34.4 + - - -
1231A LYS* 3.2 6.3 + - - -
1233A PHE* 1.3 72.8 - - - +
1235A TYR* 1.3 63.4 + - - +
1237A PHE* 3.5 5.1 + - - +
1238A ILE* 3.1 38.6 + - + +
1269A SER* 4.0 29.4 + - - +
1270A LEU* 4.4 2.7 - - + -
1273A LEU* 3.7 32.2 - - + +
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Residues in contact with TYR1235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231A LYS 3.0 15.7 + - - +
1232A ILE* 3.7 6.1 - - + +
1233A PHE 3.2 0.2 - - - -
1234A THR* 1.3 79.9 - - - +
1236A ILE* 1.3 70.5 + - + +
1238A ILE* 3.5 5.9 + - + +
1239A LEU* 2.9 56.8 + - + +
1273A LEU* 5.8 0.2 - - - +
167B ILE* 4.4 40.4 - - + -
170B LEU* 5.1 8.1 - - + -
171B THR* 2.4 33.3 + - - +
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Residues in contact with ILE1236 (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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1197A PHE* 4.3 19.7 - - + -
1198A ILE* 4.6 11.4 - - + -
1201A MET* 4.0 33.0 - - + -
1232A ILE* 3.0 27.7 + - + +
1233A PHE* 3.2 8.0 + - + +
1235A TYR* 1.3 85.0 - - + +
1237A PHE* 1.3 61.6 + - + +
1239A LEU* 3.3 7.7 + - + +
1240A GLU* 2.9 26.9 + - + +
170B LEU* 3.4 33.4 - - + -
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Residues in contact with PHE1237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1198A ILE* 4.6 12.8 - - + -
1201A MET* 4.0 28.0 - - + -
1202A ILE* 4.1 29.6 - - + -
1205A SER* 4.1 18.6 - - - -
1233A PHE* 3.0 33.3 + - + +
1234A THR* 4.2 4.3 - - - +
1236A ILE* 1.3 78.6 - - + +
1238A ILE* 1.3 65.5 + - - +
1240A GLU* 3.2 19.7 + - - +
1241A MET* 3.0 23.7 + - - +
1266A VAL* 4.4 11.0 - - + +
1296A ARG* 5.5 1.8 - - - -
1299A ARG* 3.7 44.9 - - - +
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Residues in contact with ILE1238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1234A THR* 3.1 26.2 + - + +
1235A TYR* 3.9 6.1 - - + +
1237A PHE* 1.3 74.8 - - - +
1239A LEU* 1.3 64.2 + - - +
1241A MET* 3.3 18.4 + - + +
1242A LEU* 3.2 31.0 + - + +
1266A VAL* 3.4 21.8 - - + -
1270A LEU* 2.4 45.3 - - + -
1273A LEU* 5.7 0.2 - - + -
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Residues in contact with LEU1239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235A TYR* 2.9 50.9 + - + +
1236A ILE* 3.5 7.6 - - + +
1237A PHE 3.2 0.2 - - - -
1238A ILE* 1.3 79.9 - - - +
1240A GLU* 1.3 61.5 + - - +
1242A LEU* 3.3 20.8 + - + +
1243A LEU* 3.3 18.4 + - + +
170B LEU* 5.9 3.4 - - + +
171B THR* 5.2 4.5 - - + +
174B LEU* 4.6 31.4 - - + -
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Residues in contact with GLU1240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1194A PHE* 3.4 28.1 - - + -
1198A ILE* 3.6 25.4 - - + +
1236A ILE* 2.9 17.2 + - + +
1237A PHE* 3.2 20.2 + - - +
1239A LEU* 1.3 74.0 - - - +
1241A MET* 1.3 67.0 + - - +
1243A LEU* 3.2 10.4 + - - +
1244A LYS* 2.7 46.0 + - - +
1262A ASP* 4.2 10.8 - - - +
1303A ARG* 2.8 24.7 + - - -
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Residues in contact with MET1241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1237A PHE 3.0 15.9 + - - +
1238A ILE* 3.6 17.5 - - + +
1239A LEU 3.3 0.2 - - - -
1240A GLU* 1.3 79.8 + - - +
1242A LEU* 1.3 83.4 + - + +
1244A LYS* 2.9 20.4 + - - +
1245A TRP* 3.1 39.4 + - + +
1253A TYR* 4.0 11.0 - - - +
1262A ASP* 6.5 0.9 - - - -
1263A PHE* 3.8 23.1 - - + -
1266A VAL* 3.6 31.9 - - + -
1267A ASP* 5.6 1.8 - - - +
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Residues in contact with LEU1242 (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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1238A ILE* 3.2 17.7 + - + +
1239A LEU* 3.7 18.6 - - + +
1240A GLU 3.3 0.4 - - - -
1241A MET* 1.3 100.8 - - + +
1243A LEU* 1.3 67.7 + - + +
1245A TRP* 3.1 32.1 + - + +
1246A ILE* 3.1 25.9 + - + +
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Residues in contact with LEU1243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185A CYS* 3.6 29.7 - - + +
1188A ILE* 3.9 32.8 - - + -
1189A VAL* 4.3 11.0 - - + -
1194A PHE* 4.2 15.9 - - + -
1239A LEU* 3.3 14.6 + - + +
1240A GLU* 3.2 12.4 + - - +
1242A LEU* 1.3 79.6 - - + +
1244A LYS* 1.3 64.0 + - - +
1246A ILE* 3.4 4.7 + - + +
1247A ALA* 3.0 26.7 + - - +
174B LEU* 4.4 26.2 - - + -
178B MET* 5.0 5.4 - - + -
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Residues in contact with LYS1244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1189A VAL* 3.5 26.2 - - + +
1194A PHE* 4.6 4.0 - - - -
1240A GLU* 2.7 48.0 + - - +
1241A MET* 2.9 16.3 + - - +
1243A LEU* 1.3 78.0 - - - +
1245A TRP* 1.3 55.2 + - - +
1247A ALA* 4.7 1.3 - - - -
1248A TYR* 2.9 61.7 + - + +
1253A TYR* 3.4 27.1 - - + +
1259A CYS* 6.2 1.1 - - - -
1262A ASP* 5.0 5.3 + - - +
1303A ARG* 4.0 9.2 - - - +
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Residues in contact with TRP1245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A ARG* 4.5 1.0 + - - -
1241A MET* 3.1 40.6 + - + +
1242A LEU* 3.1 27.1 + - + +
1244A LYS* 1.3 77.2 - - - +
1246A ILE* 1.3 62.7 + - + +
1249A GLY* 2.6 36.9 + - - +
1250A TYR* 3.7 45.1 - + + -
1253A TYR* 3.7 42.9 - + + -
1254A PHE* 4.7 9.8 - + - -
1263A PHE* 4.3 16.2 - + - -
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Residues in contact with ILE1246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A TRP* 3.9 26.5 - - + -
1181A ILE* 4.8 6.5 - - + -
1182A ARG* 3.4 55.4 - - + +
1185A CYS* 4.2 20.4 - - - -
1242A LEU* 3.1 23.1 + - + +
1243A LEU* 4.0 7.6 - - + +
1245A TRP* 1.3 82.5 - - + +
1247A ALA* 1.3 63.6 + - - +
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Residues in contact with ALA1247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A ARG* 4.1 11.7 + - - +
1185A CYS* 4.0 2.4 - - - +
1186A TYR* 3.5 38.7 - - - +
1189A VAL* 3.5 30.3 - - + -
1243A LEU 3.0 17.7 + - - +
1244A LYS* 4.0 1.3 - - - +
1246A ILE* 1.3 79.7 - - - +
1248A TYR* 1.3 67.3 + - + +
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Residues in contact with TYR1248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A ARG* 3.6 9.4 + - - -
1186A TYR* 4.1 11.0 - + - -
1189A VAL* 4.5 5.6 - - + +
1190A GLU* 4.0 29.5 + - - -
1244A LYS* 2.9 43.4 + - + +
1247A ALA* 1.3 90.7 - - + +
1249A GLY* 1.3 69.3 + - - +
1252A THR* 3.4 39.1 + - + -
1253A TYR* 4.3 19.5 - + + +
1256A ASN* 6.1 2.5 - - - -
1259A CYS* 5.3 10.3 - - - -
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Residues in contact with GLY1249 (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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1182A ARG* 3.7 20.8 - - - +
1245A TRP* 2.6 26.3 + - - -
1247A ALA 3.8 0.4 - - - -
1248A TYR* 1.3 78.7 - - - +
1250A TYR* 1.3 67.5 + - - -
1251A LYS 3.4 2.0 - - - -
1252A THR 4.3 0.2 - - - -
1253A TYR* 3.2 20.6 + - - +
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Residues in contact with TYR1250 (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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1245A TRP* 3.7 47.5 - + + -
1249A GLY* 1.3 71.4 - - - -
1251A LYS* 1.3 66.4 + - - +
1253A TYR* 4.3 4.9 - - - -
1254A PHE* 3.0 51.1 + + + +
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Residues in contact with LYS1251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A GLY 3.4 0.6 - - - -
1250A TYR* 1.3 79.2 - - - +
1252A THR* 1.3 67.5 + - - +
1254A PHE* 4.5 0.6 - - - -
1255A THR* 2.4 45.8 + - + +
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Residues in contact with THR1252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248A TYR* 3.4 40.0 + - + -
1249A GLY 3.7 1.4 + - - -
1250A TYR 3.4 0.2 - - - -
1251A LYS* 1.3 90.3 + - - +
1253A TYR* 1.3 63.9 + - - +
1255A THR* 3.3 19.5 + - - +
1256A ASN* 3.9 11.5 + - - +
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Residues in contact with TYR1253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1241A MET* 4.0 15.1 - - + +
1244A LYS* 3.4 38.6 - - + +
1245A TRP* 3.7 31.6 - + + -
1248A TYR* 4.3 11.4 - + + +
1249A GLY 3.2 19.8 + - - +
1250A TYR* 3.8 5.4 - - - +
1252A THR* 1.3 81.7 - - - +
1254A PHE* 1.3 78.8 + + + +
1255A THR 3.6 0.3 + - - -
1256A ASN* 3.7 4.2 + - - +
1259A CYS* 3.2 52.1 + - + +
1262A ASP* 4.9 6.8 + - - +
1263A PHE* 3.9 31.4 + + + +
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Residues in contact with PHE1254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1245A TRP* 4.7 9.6 - + - -
1250A TYR* 3.0 52.6 + + + +
1251A LYS* 4.9 1.1 - - - +
1253A TYR* 1.3 96.9 - + - +
1255A THR* 1.3 58.9 + - + +
1256A ASN 3.1 5.4 - - - -
1260A TRP* 2.9 67.4 + + + +
1263A PHE* 3.9 33.7 - + + -
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Residues in contact with THR1255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251A LYS* 2.4 43.0 + - + +
1252A THR* 3.3 14.4 + - - +
1253A TYR 3.4 0.6 - - - -
1254A PHE* 1.3 75.9 - - + +
1256A ASN* 1.3 58.6 + - - +
1257A ALA 4.0 1.6 + - - -
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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