Contacts of the helix formed by residues 165 - 191 (chain B) in PDB entry 1BRR
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 PRO 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B MET 4.7 1.1 - - - +
164B ARG* 1.3 87.4 - - + +
166B GLU* 1.3 65.5 + - + +
168B ALA* 4.1 6.0 - - + +
169B SER* 2.9 30.5 + - - -
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ARG* 3.4 34.2 + - + +
165B PRO* 1.3 80.0 - - + +
167B VAL* 1.3 59.4 + - - +
169B SER* 2.7 8.5 + - - -
170B THR* 2.7 42.2 + - - +
227B ARG* 3.5 37.0 - - + +
229B ILE* 5.7 0.2 - - - -
230B PHE 5.3 3.1 + - - -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 3.3 36.2 - - + +
101B VAL* 5.0 1.6 - - - -
160B ALA* 4.7 1.8 - - - +
163B MET* 3.6 24.2 - - + -
164B ARG* 3.0 28.0 + - + +
166B GLU* 1.3 79.6 - - + +
168B ALA* 1.3 58.3 + - - +
170B THR* 3.1 3.8 + - - -
171B PHE* 2.8 35.1 + - + +
227B ARG 5.0 2.2 - - - +
229B ILE* 4.0 33.7 - - + +
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Residues in contact with ALA 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 3.1 35.2 + - - +
161B GLU* 4.0 14.1 - - + -
164B ARG 2.9 13.9 + - - +
165B PRO* 4.2 5.4 - - + +
167B VAL* 1.3 76.7 - - - +
169B SER* 1.3 60.8 + - - +
171B PHE* 4.4 0.7 - - - +
172B LYS* 3.3 34.5 + - - +
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PRO 2.9 17.3 + - - -
166B GLU* 2.7 22.5 + - - -
168B ALA* 1.3 77.6 - - - +
170B THR* 1.3 62.7 + - - +
172B LYS* 3.7 6.9 + - - +
173B VAL* 3.4 26.9 + - - +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.3 11.9 - - + -
166B GLU* 2.7 29.6 + - - +
167B VAL* 3.9 4.3 - - - -
169B SER* 1.3 74.2 + - - +
171B PHE* 1.3 66.2 + - - +
173B VAL* 3.2 7.9 + - - +
174B LEU* 3.2 37.7 + - + +
222B ILE* 4.5 10.3 - - + +
223B LEU* 4.4 4.7 - - + -
226B SER* 3.4 35.5 + - - +
227B ARG 4.9 4.1 + - - -
228B ALA* 6.5 0.2 - - - -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.4 20.9 - - + -
100B LEU* 4.0 18.0 - - + +
101B VAL* 3.4 22.7 - - + -
152B LEU* 3.1 26.7 - - + -
156B PHE* 3.2 35.7 - + + -
157B THR* 3.6 13.7 - - - -
160B ALA* 3.6 20.4 - - + -
167B VAL* 2.8 21.6 + - + +
168B ALA 4.4 0.9 - - - +
170B THR* 1.3 73.0 - - - +
172B LYS* 1.3 59.0 + - + +
174B LEU* 3.4 3.9 + - - +
175B ARG* 2.6 59.1 + - + +
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Residues in contact with LYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B THR* 4.1 9.9 - - - -
160B ALA* 6.0 0.7 - - + -
161B GLU* 3.0 39.9 + - - +
168B ALA* 3.3 22.9 + - - +
169B SER* 3.9 7.4 - - - +
170B THR 3.2 0.6 - - - -
171B PHE* 1.3 82.2 - - + +
173B VAL* 1.3 65.4 + - + +
175B ARG* 3.2 28.9 - - - +
176B ASN* 2.9 33.7 + - - +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER 3.4 13.2 + - - +
170B THR* 3.2 9.8 + - - +
172B LYS* 1.3 76.6 - - + +
174B LEU* 1.3 58.8 + - - +
176B ASN* 3.1 11.8 + - - +
177B VAL* 2.9 30.2 + - + +
222B ILE* 3.6 35.2 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.1 16.2 - - + -
100B LEU* 3.9 13.9 - - + -
170B THR* 3.2 18.1 + - + +
171B PHE* 3.5 6.3 - - - +
173B VAL* 1.3 74.6 - - - +
175B ARG* 1.3 58.0 + - - +
177B VAL* 2.8 7.5 + - - +
178B THR* 2.8 37.0 + - - +
219B PHE* 3.6 39.0 - - + +
222B ILE* 3.6 34.3 - - + -
223B LEU* 3.6 31.0 - - + +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 5.6 2.2 - - - +
152B LEU* 3.7 14.8 - - + +
153B PHE* 3.1 44.0 - - + +
157B THR* 3.1 31.3 + - - +
171B PHE* 2.6 45.5 + - + +
172B LYS* 3.2 37.8 + - - +
173B VAL 3.4 0.2 - - - -
174B LEU* 1.3 72.2 - - - +
176B ASN* 1.3 88.3 + - - +
178B THR* 3.2 8.6 + - - -
179B VAL* 3.1 29.2 + - + +
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Residues in contact with ASN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PHE* 5.0 1.1 - - - -
172B LYS* 2.9 23.9 + - - +
173B VAL* 3.3 10.0 - - - +
175B ARG* 1.3 109.0 + - - +
177B VAL* 1.3 64.5 + - + +
179B VAL* 4.1 2.1 - - - +
180B VAL* 3.1 33.7 + - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 2.9 18.4 + - + +
174B LEU* 2.8 13.2 + - + +
176B ASN* 1.3 73.3 - - + +
178B THR* 1.3 58.4 + - + +
180B VAL* 4.2 2.6 - - - +
181B LEU* 3.0 48.9 + - + +
214B SER 4.5 7.9 - - - +
215B ALA* 5.4 0.9 - - - -
219B PHE* 5.1 10.8 - - + +
222B ILE* 3.7 28.0 - - + -
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 6.2 1.8 - - + -
97B LEU* 4.4 10.3 - - + +
149B LEU* 4.1 1.6 - - - +
152B LEU* 4.2 17.4 - - - +
174B LEU 2.8 21.1 + - - +
175B ARG* 3.2 14.7 + - - -
177B VAL* 1.3 73.3 - - + +
179B VAL* 1.3 63.5 + - - +
180B VAL 3.2 1.8 - - - -
181B LEU* 4.8 0.2 - - - -
182B TRP* 3.0 56.4 + - + +
215B ALA* 5.9 0.9 - - + +
219B PHE* 3.5 35.9 - - + -
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 3.8 43.8 - - + +
152B LEU* 5.1 3.1 - - + -
153B PHE* 4.7 17.3 - - + -
175B ARG* 3.1 31.1 + - + +
176B ASN* 4.2 3.1 - - - +
178B THR* 1.3 79.6 + - - +
180B VAL* 1.3 56.8 + - + +
183B SER* 2.7 35.0 + - - -
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 3.1 20.6 + - + +
177B VAL* 4.2 3.6 - - - +
178B THR 3.2 0.2 - - - -
179B VAL* 1.3 82.1 - - + +
181B LEU* 1.3 71.7 + - + +
183B SER* 2.9 18.8 + - - -
184B ALA* 3.5 10.0 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.0 33.8 + - + +
178B THR* 4.8 0.2 - - - -
180B VAL* 1.3 83.2 - - + +
182B TRP* 1.3 62.4 + - + +
184B ALA* 3.4 13.8 + - + +
185B TYR* 3.0 23.7 - - + -
211B LEU* 4.1 21.6 - - + +
214B SER* 3.3 36.3 - - - +
215B ALA* 3.5 34.8 - - + +
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Residues in contact with TRP 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 3.9 22.2 - - + -
93B LEU* 4.3 11.3 - - + +
94B LEU* 3.2 35.4 - - + -
115B ASP* 3.6 22.0 - - - -
118B MET* 4.2 9.0 - - + -
145B MET* 3.2 21.5 - - + +
148B ILE* 4.0 15.0 - - + -
149B LEU* 4.2 20.4 - - + -
152B LEU* 5.5 1.1 - - + -
178B THR* 3.0 45.5 + - + +
181B LEU* 1.3 79.5 - - + +
183B SER* 1.3 64.6 + - - +
185B TYR* 3.3 15.1 + + - +
186B PRO* 3.3 9.0 - - - +
215B ALA* 4.9 6.8 + - + +
999B RET 3.4 43.9 - - + +
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Residues in contact with SER 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B MET* 3.8 15.4 - - - +
149B LEU* 4.3 9.4 - - - +
179B VAL* 2.7 25.5 + - - -
180B VAL* 2.9 14.3 + - - -
182B TRP* 1.3 79.3 - - - +
184B ALA* 1.3 57.1 - - - +
186B PRO* 3.1 15.6 - - - +
187B VAL* 3.8 12.6 - - - +
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Residues in contact with ALA 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL 3.5 7.5 + - - +
181B LEU* 3.4 8.2 + - + +
182B TRP 3.2 0.8 - - - -
183B SER* 1.3 79.9 + - - +
185B TYR* 1.3 65.1 - - - +
187B VAL* 3.0 12.9 + - + +
188B VAL* 3.0 27.4 + - + +
211B LEU* 3.6 24.0 - - + -
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 3.7 10.5 - + - -
181B LEU* 3.0 33.7 - - + -
182B TRP* 3.5 11.4 - + - +
184B ALA* 1.3 77.3 - - - +
186B PRO* 1.3 67.8 - - + +
188B VAL* 3.3 2.1 + - - +
189B TRP* 3.0 25.8 + - - +
208B PHE* 3.3 38.9 - + - -
211B LEU* 3.4 36.8 + - + -
212B ASP* 2.6 26.7 + - - -
215B ALA* 4.2 1.6 - - + +
999B RET 3.4 61.0 - - + +
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Residues in contact with PRO 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 2.9 44.0 + - + +
142B THR* 4.1 7.4 - - + +
145B MET* 3.7 17.5 - - + -
182B TRP 3.3 10.8 - - - +
183B SER 3.1 21.1 - - - +
185B TYR* 1.3 87.4 - - + +
187B VAL* 1.3 57.2 + - + +
189B TRP* 4.4 0.9 - - + -
190B LEU* 3.1 18.0 + - - +
999B RET 3.5 35.0 - - + -
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 5.6 0.9 - - + -
183B SER 3.8 16.4 - - - +
184B ALA* 3.0 11.1 + - - +
186B PRO* 1.3 78.4 - - + +
188B VAL* 1.3 67.1 + - + +
190B LEU* 3.4 7.4 + - + +
191B ILE* 3.1 39.4 + - + +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA* 3.0 17.9 + - + +
185B TYR 3.3 3.3 + - - +
187B VAL* 1.3 73.6 - - + +
189B TRP* 1.3 66.4 + - - +
191B ILE* 3.2 10.8 + - + +
192B GLY* 2.9 23.4 + - - -
204B GLU* 3.9 20.7 - - + +
207B LEU* 3.8 45.1 - - + -
208B PHE* 4.1 16.2 - - + -
211B LEU* 4.2 17.3 - - + -
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Residues in contact with TRP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.9 16.9 + - - -
86B TRP* 5.6 0.4 - + - -
122B GLY* 4.6 3.3 + - - -
125B GLY* 4.0 2.9 - - - -
126B ALA* 3.9 24.1 - - - +
134B ARG* 3.8 28.0 - - + -
135B PHE* 4.6 9.6 - + - -
138B TRP* 3.2 36.6 - + + -
185B TYR 3.0 17.0 + - - +
186B PRO 3.9 3.8 - - - +
188B VAL* 1.3 77.9 - - - +
190B LEU* 1.3 65.9 + - - +
192B GLY* 3.3 8.8 + - - +
194B GLU* 2.9 54.9 + - + -
195B GLY* 3.7 17.5 + - - -
204B GLU* 4.4 5.2 - - - -
208B PHE* 4.1 11.6 - + + -
999B RET 3.9 33.0 - - + +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 3.5 34.3 - - + -
138B TRP* 3.8 34.8 - - + +
186B PRO 3.1 15.2 + - - +
187B VAL* 3.6 7.4 - - + +
188B VAL 3.2 0.2 - - - -
189B TRP* 1.3 86.7 - - + +
191B ILE* 1.3 63.3 + - + +
192B GLY 3.3 0.4 - - - -
195B GLY* 4.9 0.7 - - - -
196B ALA* 3.1 30.6 + - + +
198B ILE* 5.1 0.8 - - + +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 3.1 33.0 + - + +
188B VAL* 3.2 13.0 + - + +
190B LEU* 1.3 83.0 - - + +
192B GLY* 1.3 60.7 + - - +
196B ALA 3.4 8.3 - - - +
198B ILE* 3.4 32.6 + - + -
199B VAL* 2.8 52.5 + - + -
207B LEU* 4.9 11.4 - - + -
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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