Contacts of the helix formed by residues 272 - 302 (chain A) in PDB entry 2P8Q
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 ILE 272 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 3.8 32.8 - - + +
234A ARG* 4.1 21.5 - - - +
270A SER* 3.1 8.7 + - - +
271A ASP* 1.3 88.0 - - - +
273A ASP* 1.3 59.7 + - - +
274A GLU* 3.9 12.1 - - + +
275A VAL* 2.8 36.3 + - + +
276A ALA* 2.9 11.1 + - - +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER 5.3 0.9 - - - +
271A ASP 3.4 11.4 + - - +
272A ILE* 1.3 71.9 - - - +
274A GLU* 1.3 62.6 + - - +
276A ALA* 3.8 4.3 - - - +
277A LEU* 3.0 33.8 + - + +
332A LYS* 6.1 0.5 - - - +
343A ASN* 5.3 1.7 - - - +
344A PRO* 3.7 32.7 - - + +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 5.1 4.3 - - + -
235A VAL* 3.4 31.2 - - + +
272A ILE* 3.0 11.9 + - + +
273A ASP* 1.3 78.9 - - - +
275A VAL* 1.3 62.7 + - - +
277A LEU* 3.8 17.7 + - - +
278A GLN* 3.6 23.1 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A THR* 4.2 8.1 - - + -
234A ARG* 3.5 44.4 - - - +
235A VAL* 4.0 19.7 - - + -
238A LEU* 4.2 8.5 - - + -
267A ALA* 3.6 15.3 - - + +
270A SER* 3.5 18.2 - - - +
272A ILE* 2.8 26.4 + - + +
274A GLU* 1.3 76.9 - - - +
276A ALA* 1.3 63.9 + - - +
278A GLN* 3.0 14.0 + - - +
279A GLY 3.2 8.3 + - - -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ALA 3.2 14.4 + - - +
268A MET* 3.8 18.8 - - - +
270A SER* 3.9 13.7 - - - +
272A ILE 2.9 8.4 + - - +
273A ASP* 3.8 8.5 - - - +
275A VAL* 1.3 76.0 - - - +
277A LEU* 1.3 57.1 + - - +
279A GLY* 3.2 2.4 + - - -
280A ILE* 2.9 39.0 + - + +
329A THR* 6.3 0.4 - - + -
344A PRO* 4.2 19.1 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP* 3.0 27.1 + - + +
274A GLU* 3.9 20.9 - - - +
275A VAL 3.2 0.2 - - - -
276A ALA* 1.3 78.7 - - - +
278A GLN* 1.3 59.8 + - + +
280A ILE* 4.0 3.3 - - - +
281A GLU* 3.0 29.1 + - - +
342A TRP* 3.8 39.7 + - + +
343A ASN* 3.6 8.3 - - - +
344A PRO* 3.6 35.9 - - + -
347A ALA* 3.8 8.5 - - + -
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Residues in contact with GLN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A VAL* 4.0 23.9 - - + +
238A LEU* 3.6 23.5 - - + +
239A GLN* 3.4 45.3 + - - +
242A VAL* 4.0 16.7 - - - +
274A GLU* 3.6 15.3 + - - +
275A VAL 3.0 8.3 + - - +
277A LEU* 1.3 78.9 - - + +
279A GLY* 1.3 66.5 + - - +
281A GLU* 3.9 8.3 - - - +
282A PHE* 3.0 23.9 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 5.6 0.9 - - - -
264A THR* 3.8 13.9 - - - +
267A ALA* 4.0 11.5 - - - +
268A MET* 3.5 16.2 - - - -
275A VAL 3.2 6.3 + - - -
276A ALA 3.2 6.6 + - - -
278A GLN* 1.3 78.8 - - - +
280A ILE* 1.3 62.3 + - - +
282A PHE* 3.5 17.4 + - - +
283A TRP* 3.5 17.2 + - - -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A MET* 4.2 26.0 - - + +
276A ALA* 2.9 29.0 + - + +
277A LEU* 4.0 4.3 - - - +
279A GLY* 1.3 75.0 - - - +
281A GLU* 1.3 66.3 + - - +
283A TRP* 3.0 6.7 + - - +
284A SER* 3.0 21.0 + - - +
326A LEU* 4.4 2.9 - - + -
329A THR* 4.7 9.2 - - + +
344A PRO* 3.7 34.8 - - + +
347A ALA* 3.7 33.9 - - + +
348A ALA* 4.2 5.4 - - + +
351A CYS* 3.7 18.1 - - + -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 4.3 18.1 - - + +
277A LEU 3.0 19.7 + - - +
278A GLN* 3.9 11.7 - - - +
279A GLY 3.4 0.2 - - - -
280A ILE* 1.3 77.3 - - - +
282A PHE* 1.3 56.6 + - - +
284A SER* 4.3 3.1 - - - -
285A ASN* 2.8 37.8 + - - +
342A TRP* 5.9 1.4 - - - -
26B PRO* 5.5 5.3 - - - +
27B ARG* 2.7 51.4 + - - +
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Residues in contact with PHE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 6.4 0.2 - - + -
241A LEU* 3.7 31.0 - - + -
242A VAL* 3.8 26.7 - - + +
245A MET* 3.4 30.2 - - + +
256A MET* 4.1 15.3 - - + -
260A LEU* 4.5 11.4 - - + -
264A THR* 3.7 37.2 - - + -
278A GLN 3.0 18.9 + - - +
279A GLY 3.5 7.2 - - - +
280A ILE 3.2 0.2 - - - -
281A GLU* 1.3 77.8 - - - +
283A TRP* 1.3 75.4 + + - +
285A ASN* 3.5 5.2 + - - +
286A VAL* 3.1 39.0 + - + +
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A MET* 4.0 24.9 - - + -
261A PHE* 4.0 17.7 - + - -
264A THR* 3.2 24.7 + - - -
265A ILE* 3.4 12.2 - - + +
268A MET* 3.6 9.4 - - - -
279A GLY 3.5 18.3 + - - +
280A ILE 3.0 8.0 + - - +
282A PHE* 1.3 83.5 - + - +
284A SER* 1.3 63.5 + - - +
285A ASN 3.3 0.2 - - - -
286A VAL* 3.9 22.0 - - + +
287A CYS* 3.3 26.3 + - - -
314A TYR* 3.8 26.2 - - + -
315A ALA* 4.1 4.3 - - + -
318A ALA* 3.4 27.8 - - + -
322A LEU* 3.5 40.6 - - + +
351A CYS* 4.2 10.9 - - - -
355A LEU* 5.0 0.9 - - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.0 13.0 + - - +
281A GLU* 3.2 9.1 + - - -
283A TRP* 1.3 75.7 - - - +
285A ASN* 1.3 63.5 + - - +
287A CYS* 3.2 7.0 + - - +
288A ASP* 3.1 24.3 + - - +
347A ALA 4.7 0.9 + - - -
350A VAL* 4.6 0.5 - - - +
351A CYS* 3.3 34.3 + - - +
354A LEU* 3.6 20.6 - - - +
27B ARG* 3.9 22.0 - - - -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A VAL* 3.2 28.0 + - + +
245A MET* 4.4 8.3 - - - +
246A SER* 2.7 33.4 + - - +
281A GLU* 2.8 29.0 + - - +
282A PHE* 3.7 4.6 + - - +
284A SER* 1.3 76.2 - - - +
286A VAL* 1.3 64.6 + - - +
288A ASP* 3.3 6.5 + - - +
289A GLU* 3.0 30.4 + - - +
27B ARG* 3.9 10.0 + - - +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A MET* 3.9 28.0 - - + -
249A TYR* 5.1 2.0 - - + -
256A MET* 5.1 1.8 - - + -
282A PHE* 3.1 37.0 + - + +
283A TRP* 4.0 22.7 - - + +
284A SER 3.3 0.4 - - - -
285A ASN* 1.3 75.9 - - - +
287A CYS* 1.3 65.2 + - - +
289A GLU* 3.3 5.7 + - - -
290A GLU* 2.9 50.5 + - + +
314A TYR* 4.2 5.2 - - + -
315A ALA* 4.0 14.4 - - + +
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP 3.3 18.8 + - - -
284A SER* 3.2 10.7 + - - +
286A VAL* 1.3 81.1 - - - +
288A ASP* 1.3 55.9 + - - +
290A GLU 3.4 0.7 + - - -
291A MET* 2.9 38.0 + - + +
315A ALA* 4.2 6.5 - - - -
351A CYS 4.9 0.4 - - - -
354A LEU* 3.8 23.8 - - + +
355A LEU* 3.5 44.4 - - - -
358A CYS* 3.9 14.8 - - + -
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Residues in contact with ASP 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER 3.1 11.7 + - - -
285A ASN* 3.6 11.9 - - - +
286A VAL 3.3 0.2 - - - -
287A CYS* 1.3 75.9 - - - +
289A GLU* 1.3 64.6 + - + +
291A MET* 3.3 22.4 + - - +
292A ASP* 3.1 31.4 + - - +
354A LEU* 3.8 10.6 - - - +
27B ARG* 2.8 39.8 + - - -
30B GLN* 5.5 0.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A MET* 4.5 7.2 - - + +
246A SER* 3.3 43.7 + - - +
249A TYR* 4.4 19.7 - - + +
285A ASN* 3.0 31.3 + - - +
286A VAL* 3.9 5.4 - - - +
288A ASP* 1.3 76.6 - - - +
290A GLU* 1.3 59.9 + - - +
292A ASP* 3.3 12.1 + - - +
293A LEU* 2.9 32.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 2.6 37.2 + - + +
286A VAL* 2.9 24.4 + - - +
287A CYS 4.1 2.5 - - - +
289A GLU* 1.3 76.1 - - - +
291A MET* 1.3 64.0 + - - +
293A LEU* 3.4 7.1 + - + +
294A ALA* 3.1 21.5 + - - +
311A SER* 3.8 10.5 + - - +
313A PHE* 3.5 11.3 + - + -
314A TYR* 2.8 30.6 + - - -
315A ALA* 3.1 29.5 + - - +
316A LYS 4.6 0.3 + - - -
358A CYS* 4.2 12.2 - - - -
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A CYS* 2.9 27.1 + - + +
288A ASP* 3.5 28.5 - - - +
290A GLU* 1.3 77.5 - - - +
292A ASP* 1.3 66.1 + - - +
294A ALA* 3.3 8.1 + - - +
295A ILE* 3.3 26.8 + - - +
354A LEU* 3.6 21.5 - - + -
357A THR* 3.3 33.4 - - - +
358A CYS* 4.0 18.4 - - + -
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ASP* 3.1 16.0 + - - +
289A GLU* 3.5 16.7 - - - +
291A MET* 1.3 78.9 - - - +
293A LEU* 1.3 65.1 + - + +
295A ILE* 3.4 10.0 + - - +
296A GLU* 3.2 22.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A TYR* 3.6 43.3 - - + -
289A GLU* 2.9 22.4 + - + +
290A GLU* 3.7 7.4 - - - +
291A MET 3.3 0.4 - - - -
292A ASP* 1.3 77.0 - - + +
294A ALA* 1.3 58.2 + - - +
296A GLU* 3.2 15.5 + - - +
297A ALA* 2.8 30.2 + - - +
309A HIS* 3.8 39.2 - - + +
310A THR 4.1 0.7 - - - +
311A SER* 3.7 28.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU 3.1 13.3 + - - +
291A MET* 3.5 11.7 - - - +
292A ASP 3.2 0.4 - - - -
293A LEU* 1.3 78.9 - - - +
295A ILE* 1.3 59.1 + - + +
297A ALA* 3.7 7.6 - - - +
298A SER* 3.0 28.6 + - - -
311A SER* 5.5 1.3 - - - -
313A PHE* 6.3 3.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A MET 3.3 16.1 + - - +
292A ASP* 3.7 11.2 - - - +
293A LEU 3.2 0.8 - - - -
294A ALA* 1.3 77.6 - - + +
296A GLU* 1.3 61.6 + - - +
298A SER* 3.4 7.7 + - - -
299A GLU* 2.9 49.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP 3.2 13.8 + - - +
293A LEU* 3.2 21.8 + - + +
295A ILE* 1.3 78.5 - - - +
297A ALA* 1.3 57.7 + - - +
299A GLU* 3.4 7.9 + - - +
300A ALA* 2.9 32.0 + - + +
307A PRO* 4.4 5.2 - - + -
308A GLU* 3.5 10.8 + - - +
309A HIS* 2.9 52.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU 2.8 16.8 + - - +
294A ALA* 3.7 9.2 - - - +
295A ILE 3.3 0.2 - - - -
296A GLU* 1.3 77.2 - - - +
298A SER* 1.3 62.1 + - - +
300A ALA* 3.8 2.3 - - - +
301A ALA* 3.1 23.6 + - - +
307A PRO* 4.1 23.7 - - + +
309A HIS 5.8 0.4 - - - +
----------------------------------------------------------
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Residues in contact with SER 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA 3.0 17.9 + - - -
295A ILE* 3.6 10.5 - - - -
297A ALA* 1.3 74.5 - - - +
299A GLU* 1.3 65.8 + - - +
301A ALA* 3.4 13.5 + - - +
302A GLU* 3.4 25.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 2.9 35.9 + - + +
296A GLU* 3.9 7.8 - - - +
298A SER* 1.3 75.6 - - - +
300A ALA* 1.3 66.8 + - - +
302A GLU* 3.1 24.3 + - - +
303A GLN* 3.4 29.1 + - - +
854A LYS* 3.6 23.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 2.9 18.4 + - + +
297A ALA 3.8 4.5 - - - +
299A GLU* 1.3 77.3 - - - +
301A ALA* 1.3 61.2 + - - +
303A GLN* 3.1 12.2 + - - +
305A ARG* 2.7 49.4 + - + +
306A PRO 3.9 2.2 - - - +
307A PRO* 3.6 26.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ALA 3.1 13.9 + - - +
298A SER* 3.6 11.7 - - - +
299A GLU 3.1 0.6 - - - -
300A ALA* 1.3 73.6 - - - +
302A GLU* 1.3 60.5 + - + +
303A GLN 3.0 7.9 + - - -
304A GLY* 3.2 12.0 + - - -
305A ARG 4.3 3.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A SER* 3.5 21.6 + - - +
299A GLU* 3.1 18.9 + - - +
301A ALA* 1.3 77.4 - - + +
303A GLN* 1.3 61.0 + - + +
304A GLY 3.4 1.1 + - - -
852A ARG* 4.7 9.4 + - - -
854A LYS* 5.9 2.9 - - - -
----------------------------------------------------------
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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