Contacts of the helix formed by residues 169 - 197 (chain B) in PDB entry 1VGO
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 SER 169 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 3.9 17.8 + - - -
232A ARG* 3.2 13.5 + - - -
168B ARG* 1.3 77.5 - - - +
170B GLU* 1.3 61.1 + - - +
171B GLU 3.9 0.9 + - - -
172B VAL* 3.3 13.3 + - - +
173B ARG* 2.9 31.8 + - - +
401B SO4 3.0 31.7 + - - -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU* 3.5 38.4 - - - +
171A GLU* 5.3 4.1 + - - +
169B SER* 1.3 72.1 - - - +
171B GLU* 1.3 69.2 + - - +
173B ARG* 3.5 37.6 - - - +
174B SER* 2.8 42.2 + - - -
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 3.9 6.2 + - - -
170A GLU* 5.1 0.7 + - - +
171A GLU* 3.2 29.0 + - - +
232A ARG* 3.2 26.4 + - - +
169B SER* 4.1 8.2 - - - +
170B GLU* 1.3 89.4 + - - +
172B VAL* 1.3 61.7 + - + +
174B SER* 3.7 4.5 + - - -
175B THR* 3.3 23.0 + - - -
232B ARG* 2.8 54.0 + - + -
233B ALA* 3.7 7.3 - - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.9 15.5 - - - +
105B LEU* 3.4 44.7 - - + +
165B ALA* 6.1 0.4 - - + -
168B ARG* 3.6 25.1 - - + +
169B SER* 3.3 12.2 + - - +
170B GLU 3.3 0.2 - - - -
171B GLU* 1.3 75.2 - - - +
173B ARG* 1.3 60.0 + - - +
175B THR* 3.1 4.7 + - - -
176B PHE* 3.0 26.3 + - + +
233B ALA* 3.6 13.2 - - - +
401B SO4 3.2 25.4 - - - +
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 3.4 25.1 + - + +
166B ALA* 3.9 24.9 + - - +
168B ARG 4.4 2.2 + - - -
169B SER 2.9 22.2 + - - +
170B GLU* 3.5 39.6 + - - +
172B VAL* 1.3 74.2 - - - +
174B SER* 1.3 67.3 + - - +
176B PHE* 4.1 7.6 - - - -
177B ASN* 3.1 41.1 + - - +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B GLU* 2.8 26.5 + - - -
171B GLU* 3.8 7.4 - - - -
173B ARG* 1.3 81.9 - - - +
175B THR* 1.3 53.5 + - - +
177B ASN* 3.9 4.8 - - - +
178B THR* 2.7 37.4 + - - -
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.4 5.2 - - + -
171B GLU 3.3 11.1 + - - -
172B VAL 3.1 8.1 + - - -
174B SER* 1.3 76.7 - - - +
176B PHE* 1.3 59.6 + - - +
178B THR* 3.6 5.3 - - - -
179B LEU* 2.8 51.3 + - + +
227B VAL* 4.6 10.5 - - + +
228B LEU* 4.7 2.9 - - + -
231B SER* 3.5 28.2 + - - +
233B ALA* 3.6 16.7 - - + +
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.7 36.1 - - + -
105B LEU* 4.0 20.8 - - + +
106B ALA* 3.9 4.9 - - + -
157B LEU* 3.7 8.3 - - + -
161B LEU* 3.4 32.5 - - + -
162B ARG* 3.3 29.2 - - + -
165B ALA* 3.6 18.6 - - + -
172B VAL 3.0 16.8 + - - +
173B ARG* 3.8 8.3 - - - +
175B THR* 1.3 77.4 - - - +
177B ASN* 1.3 66.5 + - - +
179B LEU* 3.2 2.1 + - - +
180B THR* 2.7 61.4 + - + -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ARG* 3.7 38.6 + - - +
165B ALA* 5.6 0.2 - - - +
173B ARG* 3.1 28.8 + - - +
174B SER* 3.9 5.6 - - - +
176B PHE* 1.3 96.2 - - - +
178B THR* 1.3 59.8 + - - +
180B THR* 3.2 4.1 + - - -
181B ALA* 2.8 33.1 + - - +
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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
----------------------------------------------------------
174B SER* 2.7 24.0 + - - -
175B THR* 3.6 8.0 - - - -
176B PHE 3.3 0.2 - - - -
177B ASN* 1.3 79.0 - - - +
179B LEU* 1.3 58.1 + - + +
181B ALA* 3.2 5.7 + - - +
182B LEU* 3.0 28.1 + - + +
227B VAL* 4.5 20.0 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.9 13.0 - - + -
105B LEU* 4.0 8.5 - - + -
175B THR* 2.8 35.2 + - + +
176B PHE 3.7 2.7 - - - +
178B THR* 1.3 71.7 - - + +
180B THR* 1.3 60.3 + - - +
182B LEU* 3.5 11.6 - - + +
183B VAL* 3.0 35.0 + - - +
224B PHE* 3.8 41.8 - - + +
227B VAL* 3.9 24.2 - - + -
228B LEU* 3.6 35.4 - - + +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.3 8.4 - - - +
157B LEU* 4.3 27.0 - - + +
158B LEU* 3.9 27.5 - - + +
162B ARG* 6.1 1.3 - - + -
176B PHE* 2.7 51.5 + - + -
177B ASN* 3.7 6.7 - - - -
179B LEU* 1.3 73.0 - - - +
181B ALA* 1.3 60.6 + - - +
183B VAL* 3.8 6.4 - - - +
184B ALA* 3.0 27.6 + - + +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 6.4 0.2 - - - -
177B ASN 2.8 17.7 + - - +
178B THR* 3.5 6.3 - - - +
180B THR* 1.3 74.0 - - - +
182B LEU* 1.3 66.8 + - - +
184B ALA* 3.3 7.1 + - - +
185B VAL* 3.1 27.3 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.0 16.1 + - + +
179B LEU* 3.5 15.0 - - + +
181B ALA* 1.3 77.3 - - - +
183B VAL* 1.3 57.3 + - - +
185B VAL* 3.0 11.3 - - + +
186B LEU* 2.8 59.6 + - + +
219B THR* 4.9 7.6 - - + +
223B GLY 5.0 2.0 - - - +
224B PHE* 4.0 42.0 - - + +
227B VAL* 5.5 6.1 - - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 6.3 0.2 - - + -
102B LEU* 4.1 13.9 - - + -
154B LEU* 4.7 4.0 - - + -
157B LEU* 4.1 21.1 - - + -
179B LEU 3.0 28.5 + - - +
180B THR* 3.8 6.3 - - - +
182B LEU* 1.3 76.6 - - - +
184B ALA* 1.3 57.8 + - - +
186B LEU* 4.7 0.7 - - - -
187B TRP* 2.9 84.5 + - + +
224B PHE* 3.9 23.1 - - + -
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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
----------------------------------------------------------
150B PHE* 4.7 0.9 - - - -
154B LEU* 4.4 24.2 - - + +
158B LEU* 5.5 12.3 - - + -
180B THR 3.0 18.8 + - - +
181B ALA* 3.3 8.3 + - - +
183B VAL* 1.3 78.5 - - - +
185B VAL* 1.3 57.1 + - - +
188B THR* 2.4 31.9 + - - -
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ALA 3.1 15.1 + - - +
182B LEU* 3.0 21.8 - - + +
184B ALA* 1.3 75.4 - - - +
186B LEU* 1.3 76.2 + - + +
188B THR* 3.2 17.7 + - - -
189B ALA* 3.7 5.4 + - - +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 2.8 40.3 + - + +
185B VAL* 1.3 77.5 - - + +
187B TRP* 1.3 67.0 + - + +
189B ALA* 3.1 21.8 + - - +
190B TYR* 3.6 9.7 - - + -
216B LEU* 4.1 23.9 - - + +
219B THR* 3.8 25.6 - - + +
220B ALA* 3.3 48.0 - - + +
224B PHE* 6.5 0.2 - - + -
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Residues in contact with TRP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR* 3.8 23.3 - - + -
98B LEU* 4.0 21.6 - - + +
99B LEU* 3.6 26.9 - - + -
120B ASP* 3.7 19.3 - - - -
123B MET* 4.4 2.7 - - + -
150B PHE* 3.6 26.8 - + + -
153B VAL* 4.5 6.7 - - + -
183B VAL* 2.9 53.9 + - + +
186B LEU* 1.3 83.3 - - + +
188B THR* 1.3 60.3 + - - +
189B ALA 3.1 0.4 - - - -
190B TYR* 3.2 22.4 + + - +
191B PRO* 3.2 10.0 - - - +
220B ALA* 4.4 9.3 + - + +
224B PHE* 5.9 2.2 - - - -
261B RET 3.6 51.7 - - + +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 3.8 19.4 - - + -
154B LEU* 4.4 4.3 - - - +
184B ALA 2.4 25.6 + - - -
185B VAL* 3.2 8.4 + - - -
186B LEU 3.1 1.2 - - - -
187B TRP* 1.3 79.0 - - - +
189B ALA* 1.3 57.5 + - - +
191B PRO* 3.1 21.9 - - + +
192B ILE* 3.4 24.8 - - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B VAL 3.7 4.7 + - - +
186B LEU* 3.1 15.7 + - - +
188B THR* 1.3 77.7 - - - +
190B TYR* 1.3 59.2 + - - +
192B ILE* 3.7 10.6 - - + +
193B LEU* 3.0 31.9 + - - +
216B LEU* 3.9 25.1 - - + +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TRP* 3.7 13.0 - + - -
186B LEU* 3.6 17.0 - - + -
187B TRP* 3.6 16.2 - - - +
189B ALA* 1.3 76.4 - - - +
191B PRO* 1.3 74.6 - - + +
193B LEU* 3.5 1.2 + - - +
194B TRP* 2.9 25.3 + - - +
213B PHE* 3.7 28.7 - + - -
216B LEU* 3.1 38.1 + - + -
217B ASP* 2.9 30.4 + - - -
220B ALA* 3.9 4.5 - - + +
261B RET 3.4 63.1 - - + +
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Residues in contact with PRO 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 3.1 30.7 + - + +
147B THR* 4.0 10.3 - - + +
150B PHE* 4.9 7.2 - - + -
187B TRP 3.2 11.7 - - - +
188B THR* 3.1 24.0 - - + +
190B TYR* 1.3 93.0 - - + +
192B ILE* 1.3 62.5 + - + +
194B TRP* 3.5 0.3 - - - +
195B ILE* 3.0 20.5 + - - +
261B RET 3.6 39.5 - - + -
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP* 5.7 1.8 - - + -
188B THR* 3.4 32.5 - - + +
189B ALA* 3.7 10.8 - - - +
190B TYR 3.1 0.4 - - - -
191B PRO* 1.3 77.9 - - + +
193B LEU* 1.3 68.0 + - - +
195B ILE* 3.1 12.7 - - + +
196B VAL* 3.0 37.6 + - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 3.0 19.0 + - - +
190B TYR 4.0 2.5 - - - +
192B ILE* 1.3 77.2 - - - +
194B TRP* 1.3 54.8 + - - +
196B VAL* 3.6 13.7 - - + -
197B GLY* 2.7 34.8 + - - -
204B VAL* 5.0 9.9 - - + -
209B GLU* 4.0 17.5 - - + +
212B ALA* 3.6 32.5 - - + -
213B PHE* 3.6 44.6 - - + +
216B LEU* 4.2 7.4 - - + -
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Residues in contact with TRP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B TYR* 3.2 26.1 + - - -
91B TRP* 5.8 0.4 - + - -
127B GLY* 4.2 4.6 + - - -
130B GLY* 4.0 2.5 - - - -
131B ALA* 3.6 26.2 - - - -
139B ARG* 3.7 35.0 - - + -
143B TRP* 3.4 29.4 - + + -
190B TYR 2.9 18.5 + - - +
191B PRO* 3.5 6.5 - - + +
193B LEU* 1.3 80.1 - - - +
195B ILE* 1.3 64.0 + - - +
197B GLY* 3.4 6.3 + - - -
199B GLU* 3.5 49.4 + - + +
200B GLY 3.7 0.7 + - - -
209B GLU* 5.1 2.4 - - - +
213B PHE* 4.5 15.0 - + + -
261B RET 3.8 30.2 - - + +
312B BNG 4.4 12.8 - - + -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B TYR* 4.8 3.6 - - + -
143B TRP* 3.8 39.5 - - + +
191B PRO 3.0 15.9 + - - +
192B ILE* 3.1 22.2 - - + +
194B TRP* 1.3 83.8 - - - +
196B VAL* 1.3 66.9 + - + +
197B GLY 3.4 0.2 - - - -
200B GLY* 3.0 6.6 - - - -
201B ALA* 2.8 24.1 + - - +
312B BNG 3.6 40.1 - - + +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 3.0 31.5 + - + +
193B LEU* 3.5 18.8 - - + +
195B ILE* 1.3 85.5 - - + +
197B GLY* 1.3 70.1 + - - +
201B ALA* 3.9 10.3 - - + -
202B GLY 3.0 10.3 + - - -
203B VAL* 3.0 39.8 + - + +
204B VAL* 5.1 3.6 - - + -
----------------------------------------------------------
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 2.7 18.3 + - - -
194B TRP 3.4 1.7 + - - -
195B ILE 3.4 1.4 - - - -
196B VAL* 1.3 79.4 - - - +
198B THR* 1.3 61.4 + - - -
199B GLU 3.1 7.6 + - - -
200B GLY 3.2 4.2 + - - -
202B GLY 2.9 22.7 + - - -
204B VAL* 3.9 17.7 - - - -
209B GLU* 3.1 13.5 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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