Contacts of the helix formed by residues 208 - 233 (chain B) in PDB entry 4QI1
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 208 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.7 8.7 - - - -
201B THR* 3.6 11.2 - - - -
207B THR* 1.3 80.6 + - - +
209B LEU* 1.3 66.8 + - - -
210B TYR 3.3 3.3 + - - -
211B GLY 3.3 3.0 + - - +
212B GLU* 3.1 21.5 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.9 13.7 - - + -
14B GLU* 3.2 17.2 + - + +
16B GLU* 3.7 32.8 - - - +
85B ASP* 3.8 42.4 - - + +
87B TYR* 4.1 15.3 - - + -
201B THR* 3.4 11.5 - - + +
208B GLY* 1.3 72.2 - - - -
210B TYR* 1.3 54.8 + - - +
212B GLU* 4.0 21.5 - - - +
213B THR* 2.7 48.6 + - - +
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 2.9 31.3 + - - +
15B GLY* 3.4 36.8 - - - -
16B GLU* 3.9 8.7 - - - -
18B ILE* 4.0 7.1 - - + +
19B TRP* 3.2 50.4 + + - -
209B LEU* 1.3 72.8 - - - +
211B GLY* 1.4 66.0 + - - +
213B THR 3.4 0.2 + - - -
214B LEU* 3.1 22.2 + - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 3.5 22.1 + - - -
208B GLY 3.3 4.6 + - - +
210B TYR* 1.4 79.4 - - - +
212B GLU* 1.3 59.6 + - - +
214B LEU* 3.3 12.0 + - - +
215B LEU* 2.9 29.3 + - - +
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Residues in contact with GLU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP 5.4 0.5 - - - +
90B ARG* 5.7 1.2 + - - -
196B ALA* 4.7 2.7 - - - +
197B TRP* 5.9 1.6 - - - -
199B VAL* 6.4 0.2 - - - -
200B GLY* 4.2 16.4 - - - -
201B THR* 2.5 44.5 + - - +
202B GLU* 4.0 19.2 - - - +
207B THR* 3.9 5.9 - - + +
208B GLY 3.1 13.2 + - - +
209B LEU* 3.8 15.8 - - - +
211B GLY* 1.3 75.4 - - - +
213B THR* 1.3 59.0 + - - +
215B LEU* 3.3 8.7 + - - +
216B PHE* 3.0 60.8 + - + -
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.6 30.8 - - + +
19B TRP* 4.0 8.3 - - + -
20B LEU* 3.8 22.0 - - + -
64B TYR* 5.7 0.2 - - + -
87B TYR* 4.7 3.4 - - + -
90B ARG* 3.5 25.8 + - - +
209B LEU* 2.7 35.2 + - - +
210B TYR 3.8 3.6 - - - -
212B GLU* 1.3 75.5 - - - +
214B LEU* 1.3 63.0 + - - +
216B PHE* 3.5 1.6 + - - +
217B MET* 3.0 24.2 + - + +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 3.6 55.7 - - + +
210B TYR* 3.1 16.8 + - + +
211B GLY* 3.5 13.5 - - - +
213B THR* 1.3 75.8 - - - +
215B LEU* 1.3 64.2 + - - +
217B MET* 3.3 6.5 + - + +
218B VAL* 3.1 38.2 + - + +
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Residues in contact with LEU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 4.6 12.1 - - + -
195B VAL* 6.1 1.3 - - + -
196B ALA* 3.4 38.1 - - + +
199B VAL* 4.8 10.5 - - + -
211B GLY 2.9 17.1 + - - +
212B GLU* 3.3 6.7 + - - +
214B LEU* 1.3 78.6 - - - +
216B PHE* 1.3 58.3 + - - +
218B VAL* 3.4 9.3 + - + +
219B LEU* 3.0 42.4 + - + +
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Residues in contact with PHE 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.6 1.8 - - - -
90B ARG* 3.7 37.9 - - - +
91B TYR* 6.0 0.4 - - - -
94B TRP* 3.8 17.9 - + - -
193B TYR* 3.7 39.0 - + - -
196B ALA* 3.9 26.5 - - + -
197B TRP* 4.1 20.6 - + + -
212B GLU* 3.0 54.2 + - + +
213B THR 4.1 0.9 - - - +
215B LEU* 1.3 72.3 - - - +
217B MET* 1.3 60.8 + - - +
219B LEU* 4.4 5.6 - - + -
220B ASP* 2.8 37.4 + - - +
301B RET 4.7 2.5 - - + -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 3.4 44.4 - - + +
22B LEU* 4.0 14.8 - - + -
23B GLY* 3.8 23.3 - - - -
64B TYR* 3.4 14.7 + - + +
213B THR 3.0 18.6 + - - +
214B LEU* 3.5 15.7 - - + +
215B LEU 3.2 0.2 - - - -
216B PHE* 1.3 76.3 - - - +
218B VAL* 1.3 77.8 + - + +
220B ASP* 3.8 1.4 - - - +
221B LEU* 3.0 53.9 + - + +
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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
----------------------------------------------------------
214B LEU* 3.1 24.0 + - + +
215B LEU* 3.7 11.9 - - + +
217B MET* 1.3 90.3 - - + +
219B LEU* 1.3 70.7 + - + +
221B LEU* 3.3 6.0 + - - +
222B VAL* 3.0 35.0 + - + +
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 3.8 26.5 - - + +
192B ILE* 3.9 36.8 - - + -
193B TYR* 3.3 46.2 - - + +
196B ALA* 4.4 4.7 - - + -
215B LEU* 3.0 37.0 + - + +
216B PHE* 3.9 4.0 - - + +
218B VAL* 1.3 79.1 - - + +
220B ASP* 1.3 58.1 + - - +
222B VAL* 3.3 7.3 + - + +
223B ALA* 2.8 32.1 + - - +
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.5 16.9 - - + +
64B TYR* 2.6 32.8 + - + +
90B ARG* 3.8 7.6 + - - -
93B ASP* 4.9 1.1 - - - +
94B TRP* 3.4 18.1 + - - -
193B TYR* 2.7 36.2 + - - -
216B PHE* 2.8 23.2 + - - +
217B MET 3.8 3.4 - - - +
219B LEU* 1.3 75.2 - - - +
221B LEU* 1.3 55.9 + - - +
223B ALA* 4.5 0.9 - - - -
224B LYS* 2.9 47.7 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU 5.0 3.4 - - - +
23B GLY* 4.1 8.3 - - - +
26B GLY* 3.8 12.6 - - - -
27B MET* 3.8 41.3 - - + +
217B MET* 3.0 50.6 + - + +
218B VAL* 3.8 5.4 - - - +
220B ASP* 1.3 74.6 - - - +
222B VAL* 1.3 60.1 + - + +
225B VAL* 2.9 36.0 + - + +
226B GLY 3.1 6.6 + - - -
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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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185B ILE* 4.2 10.9 - - + +
189B THR* 3.6 25.6 - - + -
218B VAL* 3.0 28.9 + - + +
219B LEU* 3.7 5.4 - - + +
221B LEU* 1.3 77.3 - - + +
223B ALA* 1.3 56.3 + - - +
224B LYS 3.2 0.2 + - - -
226B GLY* 3.3 8.7 + - - +
227B PHE* 3.0 28.1 + - - +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.4 15.9 - - - +
185B ILE* 4.7 3.6 - - - -
189B THR* 3.9 19.3 - - - +
190B TRP* 4.2 4.7 + - - +
193B TYR* 3.9 6.3 - - - +
219B LEU 2.8 20.2 + - - +
220B ASP 4.0 2.2 - - - +
222B VAL* 1.3 73.5 - - - +
224B LYS* 1.3 60.7 + - + +
227B PHE* 3.2 20.1 - - - +
301B RET 3.8 27.6 - - + -
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.9 14.4 - - + -
34B PHE* 4.5 3.5 - - - -
53B THR* 5.1 2.1 - - - +
56B ILE* 3.7 29.7 - - + +
57B PRO* 5.2 3.6 - - - +
60B ALA* 3.8 22.0 - - + -
93B ASP* 3.9 11.9 - - - -
94B TRP* 4.1 1.0 - - - -
97B THR* 3.4 19.7 - - - -
101B LEU* 4.3 2.4 - - + +
220B ASP* 2.9 26.3 + - - +
223B ALA* 1.3 82.2 - - - +
225B VAL* 1.3 61.7 + - + +
226B GLY 3.5 0.2 - - - -
227B PHE* 4.0 1.6 - - - +
228B GLY* 2.9 25.6 + - - -
301B RET 1.1 75.7 - - + +
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Residues in contact with VAL 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 4.0 16.6 - - - +
27B MET* 4.0 26.7 - - - -
30B GLY* 3.9 25.4 - - - +
34B PHE* 3.5 12.5 - - + -
57B PRO* 4.7 6.1 - - + -
221B LEU* 2.9 21.2 + - + +
224B LYS* 1.3 72.3 - - - +
226B GLY* 1.3 61.1 + - - +
229B PHE* 2.9 31.1 + - + +
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Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ILE* 4.6 4.5 - - - -
221B LEU 3.1 10.6 + - - -
222B VAL* 3.3 12.5 + - - -
225B VAL* 1.3 72.7 - - - +
227B PHE* 1.3 65.7 + - - +
229B PHE* 3.3 6.6 + - - +
230B ILE* 3.1 29.7 + - - +
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Residues in contact with PHE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B THR* 5.7 0.9 - - + -
101B LEU* 3.5 41.1 - - + -
104B ASP* 4.0 22.9 - - + -
105B ILE* 4.2 13.2 - - + -
182B LEU* 3.6 44.3 - - + +
185B ILE* 4.2 21.0 - - + +
186B ILE* 3.8 28.3 - - + -
190B TRP* 6.2 0.2 - - - -
222B VAL 3.0 7.9 + - - +
223B ALA 3.2 25.6 - - - +
224B LYS 4.0 0.9 - - - +
226B GLY* 1.3 76.0 - - - +
228B GLY* 1.3 68.0 + - - +
230B ILE 3.2 0.5 + - - -
231B LEU* 3.0 26.6 + - + +
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Residues in contact with GLY 228 (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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34B PHE* 3.7 8.3 - - - -
53B THR* 3.5 26.2 - - - -
224B LYS 2.9 18.3 + - - -
225B VAL 3.7 0.9 - - - -
226B GLY 3.3 0.2 - - - -
227B PHE* 1.3 81.8 - - - +
229B PHE* 1.3 54.6 + - - +
231B LEU* 3.4 2.0 + - - +
232B LEU* 2.9 36.6 + - - +
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 4.0 36.1 - + - -
34B PHE* 3.4 11.2 - + + -
225B VAL* 2.9 23.0 + - + +
226B GLY* 3.6 6.1 - - - +
228B GLY* 1.3 71.5 - - - +
230B ILE* 1.3 77.6 + - + +
232B LEU* 4.5 1.1 - - - +
233B ARG* 3.1 59.3 + - + +
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Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 4.5 5.1 - - + +
181B ALA* 4.1 22.0 - - + -
182B LEU* 3.7 20.0 - - + -
185B ILE* 4.1 13.2 - - + -
226B GLY 3.1 15.8 + - - +
227B PHE 3.7 5.8 - - - +
229B PHE* 1.3 95.6 - - + +
231B LEU* 1.3 64.0 + - - +
233B ARG* 3.5 23.2 + - + +
234B SER* 3.5 11.1 + - - -
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 4.0 12.6 - - + -
53B THR* 3.5 13.2 - - + +
104B ASP* 3.4 40.6 - - + +
108B LEU* 4.2 13.9 - - + -
178B THR* 4.7 1.3 - - + -
182B LEU* 3.7 28.6 - - + +
227B PHE* 3.0 22.5 + - + +
228B GLY* 3.7 3.6 - - - +
230B ILE* 1.3 77.7 - - - +
232B LEU* 1.3 68.1 + - + +
234B SER* 2.9 26.4 + - - +
237B ILE* 3.8 25.1 - - + +
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 3.6 42.4 - - + -
37B ASP* 4.4 7.2 - - + +
46B GLN* 5.7 0.3 + - - -
49B PHE* 3.8 32.1 - - + +
50B TYR* 3.7 41.1 + - + +
53B THR* 3.8 21.5 - - + +
228B GLY 2.9 17.8 + - - +
229B PHE* 4.5 1.6 - - - +
231B LEU* 1.3 75.8 - - + +
233B ARG* 1.3 60.4 + - - +
234B SER 3.3 1.8 + - - +
237B ILE* 3.8 24.7 - - + +
238B MET* 5.5 4.0 - - - +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 5.7 1.1 - - - -
229B PHE* 3.1 59.9 + - + +
230B ILE* 3.5 21.5 + - - +
232B LEU* 1.3 79.2 - - - +
234B SER* 1.3 63.9 + - - +
235B ARG* 3.8 4.9 + - - +
238B MET* 4.0 9.4 - - - +
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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