Contacts of the helix formed by residues 205 - 230 (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 GLY 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B THR* 3.7 4.5 - - - -
204B VAL* 1.3 77.5 - - - +
206B LEU* 1.3 66.6 + - - -
207B GLY* 3.0 5.9 + - - -
208B ILE* 3.6 4.7 + - - +
209B GLU* 3.2 19.8 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.3 36.1 - - - +
81B LEU* 4.4 16.4 - - + -
82B ASP* 3.4 32.3 - - - +
84B TYR* 5.0 8.1 - - + -
198B THR* 3.5 19.3 - - + +
205B GLY* 1.3 70.1 - - - -
207B GLY* 1.3 58.3 + - - +
209B GLU* 4.1 7.4 - - - +
210B THR* 2.6 38.3 + - - +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 6.4 2.0 - - - -
13B GLU* 4.5 13.5 - - - -
16B TRP* 3.6 14.9 - - - -
205B GLY 3.0 3.6 + - - -
206B LEU* 1.3 75.4 - - - +
208B ILE* 1.3 65.4 + - - -
210B THR* 3.0 16.5 + - - -
211B LEU 3.1 7.8 + - - -
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 5.5 6.7 - - + +
204B VAL* 3.6 23.3 - - + -
205B GLY 3.6 4.0 + - - +
207B GLY* 1.3 73.7 - - - +
209B GLU* 1.3 57.6 + - - +
211B LEU* 3.2 20.0 + - + +
212B ALA* 2.8 30.2 + - + +
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Residues in contact with GLU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 4.1 8.3 + - - -
193B LEU* 4.0 13.2 - - + -
194B TRP* 5.1 2.3 - - - +
197B GLY* 3.1 10.0 - - - -
198B THR* 2.7 47.3 + - - +
199B GLU* 4.6 4.6 + - - +
204B VAL* 3.4 10.2 - - + +
205B GLY 3.2 17.8 + - - +
206B LEU* 4.1 9.9 - - + +
207B GLY 3.1 0.4 + - - -
208B ILE* 1.3 76.1 - - - +
210B THR* 1.3 59.5 + - - +
212B ALA* 3.0 8.3 + - - +
213B PHE* 2.8 57.9 + - + -
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.7 26.1 - - + +
16B TRP* 3.9 18.2 - - + -
17B LEU* 4.0 22.4 - - + +
61B TYR* 5.2 1.1 + - + -
84B TYR* 5.2 3.8 - - + -
87B ARG* 4.3 19.9 + - - +
206B LEU* 2.6 24.0 + - - +
207B GLY 3.0 9.7 + - - -
209B GLU* 1.3 78.5 - - - +
211B LEU* 1.3 57.7 + - - +
213B PHE* 3.6 1.4 + - - +
214B MET* 3.1 27.6 + - + +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.4 59.2 - - + +
207B GLY 3.1 7.9 + - - +
208B ILE* 3.4 24.2 - - + +
209B GLU 3.1 0.6 - - - -
210B THR* 1.3 76.2 - - - +
212B ALA* 1.3 65.6 + - + +
214B MET* 3.4 11.0 + - + +
215B VAL* 3.0 50.2 + - + +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.6 23.6 - - + -
208B ILE* 2.8 20.8 + - + +
209B GLU* 3.0 6.5 + - - +
211B LEU* 1.3 81.6 - - + +
213B PHE* 1.3 60.1 + - - +
215B VAL* 3.3 5.9 + - - +
216B LEU* 2.9 34.9 + - + +
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Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 4.2 0.9 - - - +
87B ARG* 3.3 43.7 - - - +
91B TRP* 3.8 15.5 - + + -
190B TYR* 3.7 45.1 - + + -
193B LEU* 3.6 24.9 - - + -
194B TRP* 4.3 22.2 - + + -
209B GLU* 2.8 51.7 + - + +
210B THR 4.0 1.1 - - - +
212B ALA* 1.3 72.5 - - - +
214B MET* 1.3 54.0 + - - +
216B LEU* 3.1 4.5 + - + +
217B ASP* 2.6 46.7 + - - +
261B RET 5.0 0.4 - - + -
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Residues in contact with MET 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.9 21.5 - - + +
19B ILE* 3.9 32.1 - - + -
20B GLY* 3.7 22.0 - - - -
23B LEU* 4.2 19.7 - - + -
24B MET* 5.4 0.7 - - + +
61B TYR* 3.3 22.4 + - + +
210B THR* 3.1 20.2 + - + +
211B LEU* 3.6 26.5 - - + +
213B PHE* 1.3 77.2 - - - +
215B VAL* 1.3 64.7 + - + +
217B ASP* 3.6 0.9 - - - +
218B VAL* 2.9 34.8 + - - +
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Residues in contact with VAL 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.0 39.2 + - + +
212B ALA* 3.7 6.7 - - - +
214B MET* 1.3 82.1 - - + +
216B LEU* 1.3 59.8 + - + +
218B VAL* 2.9 17.5 - - + +
219B THR* 2.6 35.5 + - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.1 26.1 - - + +
189B ALA* 3.9 36.8 - - + +
190B TYR* 3.1 28.3 + - + +
193B LEU* 4.2 20.9 - - + -
212B ALA* 2.9 20.0 + - + +
213B PHE* 3.5 9.4 - - + +
215B VAL* 1.3 79.2 - - + +
217B ASP* 1.3 59.5 + - - +
219B THR* 3.3 4.1 + - - -
220B ALA* 2.9 28.8 + - - +
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Residues in contact with ASP 217 (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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24B MET* 3.9 14.1 - - + -
61B TYR* 2.7 34.7 + - - +
87B ARG* 5.5 2.8 + - - +
90B ASP* 4.7 0.7 - - - +
91B TRP* 3.2 31.8 + - - -
190B TYR* 2.9 23.9 + - - -
213B PHE* 2.6 22.6 + - - +
214B MET 3.6 2.0 - - - +
216B LEU* 1.3 72.7 - - - +
218B VAL* 1.3 56.6 + - - +
220B ALA 3.3 1.0 + - - -
221B LYS* 3.0 42.5 + - - +
261B RET 3.6 2.0 - - - +
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Residues in contact with VAL 218 (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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23B LEU* 4.7 25.6 - - + +
24B MET* 4.1 15.8 - - + +
214B MET* 2.9 33.7 + - + +
215B VAL* 2.9 25.4 - - + +
217B ASP* 1.3 74.4 - - - +
219B THR* 1.3 63.3 + - - +
222B VAL* 2.8 45.9 + - + -
223B GLY 3.2 3.6 + - - -
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Residues in contact with THR 219 (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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182B LEU* 4.9 8.9 - - + +
186B LEU* 3.8 27.0 - - + +
215B VAL* 2.6 32.3 + - - +
216B LEU* 3.8 4.0 - - - +
218B VAL* 1.3 79.9 - - - +
220B ALA* 1.3 56.2 + - - +
223B GLY* 3.3 9.5 - - - +
224B PHE* 3.1 25.1 + - - +
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Residues in contact with ALA 220 (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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98B LEU* 3.7 18.4 - - - +
186B LEU* 3.3 21.5 - - + +
187B TRP* 4.4 6.7 + - + +
190B TYR* 3.9 4.0 - - + +
216B LEU 2.9 18.7 + - - +
217B ASP 3.8 3.6 - - - +
219B THR* 1.3 77.3 - - - +
221B LYS* 1.3 57.3 + - - +
224B PHE* 3.4 18.9 - - - +
261B RET 3.8 26.2 - - + -
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Residues in contact with LYS 221 (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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24B MET* 3.3 31.2 - - + -
31B PHE* 4.1 5.0 - - - -
50B THR* 4.9 1.7 - - - +
53B VAL* 3.5 23.9 - - + +
54B PRO* 4.7 8.9 - - + +
57B ALA* 3.6 23.6 - - + -
90B ASP* 3.8 4.6 + - - -
91B TRP* 3.9 7.3 - - - -
94B THR* 3.1 19.4 - - - +
98B LEU* 4.8 1.4 - - - +
217B ASP* 3.0 20.2 + - - +
220B ALA* 1.3 79.7 - - - +
222B VAL* 1.3 61.5 + - - +
223B GLY 3.5 0.7 - - - -
224B PHE* 4.2 1.3 - - - +
225B GLY* 3.0 25.6 + - - -
261B RET 1.4 71.3 - - + +
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Residues in contact with VAL 222 (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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23B LEU 4.0 13.0 - - - +
24B MET* 4.2 18.4 - - - -
27B GLY* 3.9 30.7 - - - -
30B TYR* 6.2 1.1 - - + -
31B PHE* 3.4 13.2 - - + -
54B PRO* 4.3 7.2 - - + -
218B VAL* 2.8 27.8 + - + +
221B LYS* 1.3 72.1 - - - +
223B GLY* 1.3 59.2 + - - +
226B PHE* 2.9 32.6 + - + +
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Residues in contact with GLY 223 (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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182B LEU* 5.0 2.9 - - - -
218B VAL* 3.2 10.1 + - - +
219B THR* 3.3 15.9 + - - +
222B VAL* 1.3 76.0 - - - +
224B PHE* 1.3 64.4 + - - +
226B PHE* 3.3 6.4 + - - +
227B VAL* 3.1 28.3 + - - +
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Residues in contact with PHE 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B THR* 5.2 0.4 - - + -
98B LEU* 3.6 43.5 - - + -
101B ASP* 3.9 18.8 - - + -
102B LEU* 4.1 14.8 - - + -
179B LEU* 3.8 27.4 - - + +
182B LEU* 4.0 22.6 - - + +
183B VAL* 3.9 26.9 - - + -
187B TRP* 5.9 2.0 - - - -
219B THR 3.1 7.7 + - - +
220B ALA* 3.4 26.5 - - - +
222B VAL 3.4 0.2 - - - -
223B GLY* 1.3 74.8 - - - +
225B GLY* 1.3 69.2 + - - +
227B VAL* 3.2 5.5 + - - +
228B LEU* 3.0 33.0 + - + +
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Residues in contact with GLY 225 (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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31B PHE* 3.6 10.1 - - - -
50B THR* 3.7 24.5 - - - -
221B LYS 3.0 20.6 + - - -
224B PHE* 1.3 82.0 - - - +
226B PHE* 1.3 55.2 - - - +
228B LEU* 3.9 1.5 - - - +
229B LEU* 3.0 36.4 + - - +
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Residues in contact with PHE 226 (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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30B TYR* 3.8 35.4 - + - -
31B PHE* 3.6 9.1 - - + -
34B ARG* 5.7 2.7 - - - -
222B VAL* 2.9 21.7 + - + +
223B GLY* 3.6 6.5 - - - +
224B PHE 3.2 0.2 - - - -
225B GLY* 1.3 76.2 - - - +
227B VAL* 1.3 68.5 + - + +
229B LEU* 5.2 0.7 - - - -
230B ARG* 2.8 73.3 + - + +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B THR* 4.6 4.9 - - + +
178B THR* 4.5 18.2 - - + -
179B LEU* 3.9 22.0 - - + -
182B LEU* 5.5 5.6 - - + -
223B GLY 3.1 15.1 + - - +
224B PHE* 3.7 7.2 - - - +
226B PHE* 1.3 85.8 - - + +
228B LEU* 1.3 62.0 + - - +
230B ARG* 4.2 9.5 - - - +
231B SER* 3.5 18.9 + - - -
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Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR* 4.4 7.9 - - + -
50B THR* 3.6 13.9 - - + +
101B ASP* 3.5 38.6 - - + +
105B LEU* 3.9 18.6 - - + -
175B THR* 4.7 3.6 - - + -
179B LEU* 3.6 28.0 - - + -
224B PHE* 3.0 23.4 + - + +
225B GLY 3.9 1.3 - - - +
227B VAL* 1.3 74.4 - - - +
229B LEU* 1.3 68.3 + - + +
230B ARG 3.1 4.7 - - - -
231B SER* 2.9 21.2 + - - -
234B ILE* 3.4 31.4 - - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.1 20.9 - - + -
34B ARG* 3.3 19.1 + - - +
46B TYR* 3.9 21.3 - - + -
47B TYR* 3.5 40.4 + - + +
50B THR* 3.6 31.2 - - + +
225B GLY 3.0 21.2 + - - +
226B PHE* 4.7 1.3 - - - +
228B LEU* 1.3 99.2 - - + +
230B ARG* 1.3 57.3 + - - +
231B SER 3.4 1.3 + - - +
234B ILE* 3.9 17.5 - - + +
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Residues in contact with ARG 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 4.2 23.5 + - - +
226B PHE* 2.8 59.8 + - + +
227B VAL* 4.2 9.5 - - - +
228B LEU 3.1 0.6 - - - -
229B LEU* 1.3 78.6 - - - +
231B SER* 1.3 58.3 + - - +
232B ARG* 6.0 0.2 - - - +
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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