Contacts of the helix formed by residues 280 - 309 (chain V) in PDB entry 5GJQ
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 280 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251V LEU* 3.6 17.0 - - + +
254V ASN* 3.0 30.7 - - + +
255V TYR* 2.7 45.1 - - + +
258V ALA* 4.4 10.8 - - + -
278V GLN 3.4 2.0 - - - +
279V ASP* 1.3 86.5 - - + +
281V LYS* 1.3 65.4 + - + +
282V ARG 3.6 0.2 - - - -
283V HIS* 3.4 9.5 + - + +
284V LEU* 3.2 28.3 + - - +
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Residues in contact with LYS 281 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270U VAL* 3.5 29.3 - - + +
273U HIS* 4.5 8.1 - - + +
274U ASN* 3.5 33.8 - - - +
255V TYR* 4.1 28.3 - - + -
279V ASP* 3.2 16.9 - - + +
280V PRO* 1.3 75.2 - - + +
282V ARG* 1.3 65.5 + - + +
283V HIS 2.9 7.8 + - - -
284V LEU* 3.2 5.6 + - - +
285V GLU* 3.2 39.0 + - - +
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Residues in contact with ARG 282 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K ASP* 4.7 18.3 + - - +
121K ARG 5.6 2.1 - - - +
122K GLU* 3.3 30.9 - - - +
279V ASP* 3.9 18.0 + - - +
281V LYS* 1.3 85.0 - - + +
283V HIS* 1.3 63.2 + - + +
285V GLU* 4.6 6.3 - - - -
286V GLU* 2.8 40.1 + - - +
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Residues in contact with HIS 283 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122K GLU* 2.5 44.1 + - - -
247V GLU* 5.0 7.5 + - - -
251V LEU* 2.8 39.5 - - + +
278V GLN* 3.8 24.7 - - + -
279V ASP 4.0 7.2 - - - -
280V PRO 3.4 7.3 + - - +
281V LYS 2.9 1.0 - - - -
282V ARG* 1.3 84.7 - - + +
284V LEU* 1.3 53.7 + - - +
286V GLU* 4.1 13.3 + - - +
287V HIS* 2.7 44.3 + + + +
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Residues in contact with LEU 284 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403Q THR* 5.3 1.1 - - - +
407Q MET* 4.1 6.1 - - + -
266U ILE* 2.9 35.7 - - + -
270U VAL* 4.6 6.7 - - + -
248V MET* 3.0 48.4 - - + +
251V LEU* 4.5 5.4 - - + -
252V ALA* 4.0 18.2 - - + +
255V TYR* 3.7 31.6 - - + -
280V PRO 3.2 16.3 + - - +
281V LYS* 3.2 4.1 + - - +
283V HIS* 1.3 78.0 - - - +
285V GLU* 1.3 56.4 + - - +
288V VAL* 2.7 40.7 + - - +
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Residues in contact with GLU 285 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267U ARG* 4.6 19.8 - - + +
270U VAL* 3.3 42.0 - - + +
271U ALA* 4.9 3.8 + - - +
274U ASN* 4.3 5.9 + - - -
281V LYS* 3.2 27.7 + - - +
282V ARG* 4.6 4.0 - - - -
284V LEU* 1.3 77.5 - - - +
286V GLU* 1.3 60.9 + - - +
288V VAL* 3.6 7.0 + - - +
289V ASP* 3.2 31.1 + - - +
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Residues in contact with GLU 286 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282V ARG* 2.8 32.9 + - + +
283V HIS* 4.1 17.8 + - - -
285V GLU* 1.3 77.0 - - - +
287V HIS* 1.3 75.8 + - - +
289V ASP* 3.1 29.4 - - - +
290V VAL* 3.7 9.6 + - + +
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Residues in contact with HIS 287 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244V VAL* 3.6 30.0 - - + +
247V GLU* 2.5 39.3 + - + +
248V MET* 3.5 36.1 - - + -
251V LEU* 4.7 8.3 - - + -
283V HIS* 2.7 27.4 + + + +
286V GLU* 1.3 84.1 + - - +
288V VAL* 1.3 64.7 + - - +
289V ASP 3.2 0.7 + - - -
290V VAL* 3.4 20.1 + - + +
291V LEU* 3.5 13.9 + - - +
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Residues in contact with VAL 288 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263U ALA* 2.9 38.7 - - + +
266U ILE* 3.1 32.8 - - + -
267U ARG* 3.4 22.2 - - + +
248V MET* 3.2 8.7 - - + -
284V LEU 2.7 27.4 + - - +
285V GLU 3.6 5.8 - - - +
287V HIS* 1.3 74.4 - - - +
289V ASP* 1.3 63.0 + - - +
291V LEU* 3.9 1.6 - - - -
292V MET* 2.9 44.3 + - + +
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Residues in contact with ASP 289 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267U ARG* 5.4 3.8 - - - +
285V GLU* 3.2 24.5 - - - +
286V GLU* 3.1 17.4 - - - +
287V HIS 3.1 0.6 - - - -
288V VAL* 1.3 82.4 - - - +
290V VAL* 1.3 66.4 + - + +
292V MET* 3.6 4.3 - - - +
293V THR* 3.1 27.6 + - - -
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Residues in contact with VAL 290 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240V HIS* 4.8 22.2 - - + +
244V VAL* 5.5 6.7 - - + -
286V GLU* 4.2 12.6 - - + +
287V HIS* 3.4 14.5 + - + +
289V ASP* 1.3 76.6 - - + +
291V LEU* 1.3 57.8 + - + +
293V THR* 4.6 3.6 - - - -
294V SER* 2.8 50.9 + - - +
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Residues in contact with LEU 291 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259U VAL* 3.3 30.1 - - + +
262U LEU* 5.4 2.5 - - + -
263U ALA* 3.7 20.0 - - + +
240V HIS* 4.1 0.4 - - + +
241V ASN* 3.7 21.1 - - - +
244V VAL* 3.5 39.0 - - + -
245V VAL* 3.8 20.6 - - + -
248V MET* 4.2 21.1 - - - -
287V HIS 3.5 4.6 + - - +
288V VAL* 3.8 1.8 - - - +
289V ASP 3.4 0.4 - - - -
290V VAL* 1.3 76.8 - - + +
292V MET* 1.3 68.1 + - - +
294V SER* 4.8 1.8 - - - -
295V ASN* 2.8 26.3 + - - +
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Residues in contact with MET 292 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346T LEU* 3.3 34.3 - - + -
187U LEU* 6.1 2.0 - - + -
260U VAL* 4.0 17.0 - - + +
263U ALA* 3.2 11.0 - - + -
264U SER* 2.9 43.7 - - - -
267U ARG* 6.3 1.1 - - - -
288V VAL* 2.9 40.9 + - + +
289V ASP* 3.6 5.2 - - - +
291V LEU* 1.3 78.6 - - - +
293V THR* 1.3 60.2 + - - +
295V ASN* 3.6 1.0 - - - +
296V ILE* 2.9 37.8 + - + +
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Residues in contact with THR 293 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186U THR* 4.8 10.2 - - - +
187U LEU* 3.3 49.6 + - - +
289V ASP 3.1 13.6 + - - -
290V VAL* 4.0 3.1 + - - -
292V MET* 1.3 79.2 - - - +
294V SER* 1.3 61.9 + - - +
296V ILE* 3.1 4.1 + - - +
297V VAL* 2.8 36.0 + - - +
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Residues in contact with SER 294 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237V HIS* 5.3 2.5 + - - -
240V HIS* 5.0 9.9 - - - +
241V ASN* 5.6 4.2 + - - -
290V VAL* 2.8 40.2 + - - +
291V LEU* 4.8 1.1 - - - -
293V THR* 1.3 76.0 + - - +
295V ASN* 1.3 56.9 + - - +
297V VAL* 2.7 26.2 - - - +
298V GLN* 3.2 12.0 + - - +
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Residues in contact with ASN 295 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256U GLN* 2.7 83.6 + - - +
259U VAL* 2.9 29.2 - - - +
260U VAL* 4.4 9.6 - - + -
237V HIS* 4.0 5.3 - - - -
241V ASN* 3.2 18.4 + - - +
291V LEU 2.8 19.4 + - - +
292V MET 3.6 1.6 - - - +
294V SER* 1.3 75.9 - - - +
296V ILE* 1.3 60.6 + - - +
298V GLN* 4.5 1.6 - - - -
299V CYS* 2.8 11.3 + - - +
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Residues in contact with ILE 296 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339T VAL* 5.6 5.1 - - + +
343T ALA* 4.9 12.8 - - + -
346T LEU* 2.5 49.4 - - + -
187U LEU* 4.6 17.0 - - + -
191U ILE* 5.3 6.1 - - + -
260U VAL* 4.6 16.4 - - + -
292V MET* 2.9 29.9 + - + +
293V THR* 3.1 6.3 + - - +
295V ASN* 1.3 75.1 - - - +
297V VAL* 1.3 55.8 + - - +
299V CYS* 3.6 8.0 - - + +
300V LEU* 2.7 42.3 + - + +
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Residues in contact with VAL 297 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187U LEU* 4.0 16.8 - - + -
190U ARG* 3.7 33.4 - - + -
191U ILE* 4.5 8.7 - - + +
194U GLN* 5.0 5.4 + - - +
293V THR 2.8 22.7 + - - +
294V SER* 2.7 35.4 - - - +
296V ILE* 1.3 72.8 - - - +
298V GLN* 1.3 55.1 + - + +
300V LEU* 3.7 7.1 - - - +
301V ALA* 2.7 36.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 298 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252U LYS* 5.5 0.7 - - - +
256U GLN* 3.2 21.2 + - - +
231V LEU* 3.9 13.0 - - + +
232V GLN* 5.1 7.6 - - + +
234V TYR* 2.6 63.3 + - + -
237V HIS* 2.0 48.2 + - + +
294V SER 3.2 15.6 + - - +
297V VAL* 1.3 81.6 - - + +
299V CYS* 1.3 62.1 + - - +
301V ALA* 3.5 2.5 + - - +
302V ALA 3.3 16.6 + - - -
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Residues in contact with CYS 299 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339T VAL* 6.0 4.9 - - + -
249U PHE* 5.9 0.2 - - - -
253U THR* 4.4 9.9 - - - -
256U GLN* 2.7 50.2 - - - +
257U MET* 4.3 18.2 - - - -
260U VAL* 5.8 2.5 - - - -
295V ASN* 2.8 13.4 + - - +
296V ILE* 3.6 8.7 - - + +
298V GLN* 1.3 72.5 - - - +
300V LEU* 1.3 62.0 + - - +
302V ALA* 3.6 3.0 + - - +
303V MET* 3.1 39.7 + - + +
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Residues in contact with LEU 300 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367O VAL* 5.5 6.5 - - + -
336T ALA* 6.1 3.1 - - + -
339T VAL* 4.1 25.8 - - + -
340T ILE* 5.9 4.5 - - + -
191U ILE* 4.2 30.3 - - + -
194U GLN* 3.7 23.8 - - - +
296V ILE* 2.7 26.5 + - + +
297V VAL* 3.8 4.5 - - - +
299V CYS* 1.3 70.4 - - - +
301V ALA* 1.3 67.2 + - - +
303V MET* 3.1 19.1 + - + +
304V LEU* 3.1 30.3 + - + +
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Residues in contact with ALA 301 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194U GLN* 3.6 20.4 - - - +
228V GLY 4.8 2.9 - - - +
229V LEU* 5.5 1.1 - - - +
230V THR 4.6 8.5 - - - +
231V LEU* 3.5 27.1 - - + -
297V VAL 2.7 23.0 + - - +
298V GLN 3.7 0.2 - - - +
299V CYS 3.4 0.2 - - - -
300V LEU* 1.3 73.1 - - - +
302V ALA* 1.3 62.5 + - - +
304V LEU* 3.3 4.9 + - - +
305V ASP* 3.0 30.5 + - - +
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Residues in contact with ALA 302 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428P TRP* 4.7 3.6 - - + -
249U PHE* 3.1 37.2 - - + -
231V LEU* 4.2 10.5 - - + +
234V TYR* 3.3 26.2 - - - +
298V GLN 3.3 7.3 + - - +
299V CYS* 3.8 3.4 - - - +
300V LEU 3.2 0.4 - - - -
301V ALA* 1.3 77.1 - - - +
303V MET* 1.3 64.6 + - - +
305V ASP* 3.0 5.4 + - - +
306V THR 2.9 23.2 + - - -
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Residues in contact with MET 303 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363O MET* 5.0 0.8 - - - +
473S GLN* 5.6 1.1 - - - +
332T SER* 3.4 13.4 + - - +
335T LEU* 4.1 30.1 - - + -
336T ALA* 5.2 10.7 - - + +
339T VAL* 3.7 27.4 - - + -
249U PHE* 3.6 31.4 - - + -
253U THR* 4.1 15.9 - - - +
299V CYS* 3.1 30.0 + - - +
300V LEU* 3.1 16.9 + - + +
302V ALA* 1.3 74.8 - - - +
304V LEU* 1.3 59.4 + - + +
306V THR* 3.0 18.3 + - - -
307V VAL* 3.1 14.6 - - - +
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Residues in contact with LEU 304 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363O MET* 3.8 33.4 - - + -
367O VAL* 3.9 15.7 - - + -
336T ALA* 6.0 1.8 - - + -
194U GLN* 3.1 40.2 - - + +
198U LEU* 4.3 18.4 - - + -
229V LEU* 4.9 4.3 - - + -
300V LEU* 3.1 24.0 + - + +
301V ALA 3.6 4.7 - - - +
302V ALA 3.0 0.8 - - - -
303V MET* 1.3 78.1 - - + +
305V ASP* 1.3 62.4 + - - +
306V THR 3.2 0.2 - - - -
307V VAL* 3.8 3.4 - - - -
308V VAL* 2.7 45.4 + - + +
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Residues in contact with ASP 305 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428P TRP* 3.0 40.0 - - + -
432P LEU* 3.7 9.0 - - + +
229V LEU* 2.3 57.8 - - - +
231V LEU* 4.0 10.7 - - - +
301V ALA 3.0 19.7 + - - +
302V ALA 3.0 2.9 + - - +
304V LEU* 1.3 76.4 - - - +
306V THR* 1.3 56.9 + - - +
309V PHE* 2.9 39.7 + - + +
310V LYS* 3.6 1.2 + - - -
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Residues in contact with THR 306 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428P TRP* 4.6 3.7 - - - -
332T SER* 3.8 11.4 + - - -
245U PHE* 6.2 2.5 - - - -
249U PHE* 3.7 21.1 - - - -
302V ALA 2.9 12.6 + - - -
303V MET* 3.0 17.8 + - - -
305V ASP* 1.3 74.9 - - - +
307V VAL* 1.3 59.6 + - - +
310V LYS* 1.9 53.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 307 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359O ASP* 4.6 4.0 - - - +
363O MET* 3.5 29.2 - - + -
332T SER* 2.3 50.5 - - - +
333T THR* 4.7 2.0 - - + +
303V MET 3.1 15.3 - - - +
304V LEU* 3.3 6.3 - - - +
306V THR* 1.3 79.5 + - - +
308V VAL* 1.3 82.9 + - + +
310V LYS* 3.1 14.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 308 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 4.2 8.4 - - + +
359O ASP* 2.9 45.5 - - + +
360O VAL* 4.7 9.2 - - + +
363O MET* 3.3 36.1 - - + -
198U LEU* 5.3 5.6 - - + -
201U LEU* 5.2 3.6 - - + -
229V LEU* 5.5 5.4 - - + -
304V LEU* 2.7 38.1 + - + +
305V ASP* 4.7 0.2 - - - -
307V VAL* 1.3 80.7 - - + +
309V PHE* 1.3 75.4 + - + +
310V LYS* 3.0 7.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 309 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356O TRP* 3.4 43.7 - + - +
428P TRP* 5.2 0.7 - - + -
432P LEU* 3.1 36.8 - - + -
435P LEU* 4.8 11.9 - - + -
436P MET* 3.9 25.6 - - + -
201U LEU* 4.1 10.5 - - + -
237U LEU* 5.8 2.7 - - + -
238U PRO* 4.2 24.7 - - + -
229V LEU* 3.8 26.0 - - + -
305V ASP* 2.9 19.8 + - + +
308V VAL* 1.3 80.9 - - + +
310V LYS* 1.3 89.1 + - - +
----------------------------------------------------------
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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).
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