Contacts of the helix formed by residues 311 - 332 (chain A) in PDB entry 6BFN
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A PRO 3.4 3.6 + - - -
310A LEU* 1.3 76.3 - - - +
312A TRP* 1.3 60.2 + - - +
313A PRO* 3.5 11.8 - - - +
314A GLN* 3.1 36.9 + - - +
315A ARG* 3.0 29.0 + - - +
482A PRO* 4.5 8.3 - - - -
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Residues in contact with TRP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A SER* 1.3 71.9 - - - +
313A PRO* 1.4 74.6 - - + +
315A ARG* 3.2 24.8 + - + +
316A LEU* 2.9 23.9 + - - +
417A THR 4.3 6.3 - - - -
418A LEU* 3.6 43.1 - - + -
478A LEU* 4.4 6.7 - - + -
479A ASP* 3.9 10.1 - - + -
482A PRO* 3.4 35.6 + - + +
483A GLY 3.0 20.8 + - - -
484A PRO 3.7 13.5 - - - -
485A CYS* 3.5 38.2 - - + +
486A PRO* 4.2 7.4 - - + -
489A LEU* 3.7 22.7 - - + +
493A LEU* 5.2 4.9 - - + -
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Residues in contact with PRO 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 3.5 14.1 - - - +
312A TRP* 1.4 93.6 - - + +
314A GLN* 1.3 57.7 + - + +
316A LEU* 3.3 7.8 + - + +
317A ASP* 2.9 35.3 + - - +
525A VAL* 3.6 40.1 - - + -
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Residues in contact with GLN 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG* 5.4 1.0 + - - -
309A PRO 4.3 2.3 - - - +
310A LEU* 3.5 17.9 - - + +
311A SER* 3.1 36.6 + - - +
312A TRP 3.2 0.6 - - - -
313A PRO* 1.3 74.5 - - + +
315A ARG* 1.3 60.6 + - - +
317A ASP* 3.3 9.4 + - - +
318A ILE* 2.9 37.0 + - + +
352A LEU* 3.6 30.6 - - + +
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Residues in contact with ARG 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ARG 6.0 0.2 + - - -
300A LEU* 3.4 23.7 + - + +
309A PRO* 4.6 5.3 - - - +
310A LEU* 2.9 44.7 + - + +
311A SER 3.0 16.3 + - - +
312A TRP* 3.2 29.5 + - + +
314A GLN* 1.3 74.3 - - - +
316A LEU* 1.3 58.5 + - - +
318A ILE* 3.4 7.7 + - - +
319A LEU* 3.0 37.2 + - + +
417A THR* 2.8 52.5 + - + +
420A GLY 4.7 0.6 - - - +
479A ASP* 3.1 34.3 + - - +
481A ARG* 4.8 1.0 - - - +
482A PRO* 3.6 18.9 - - - +
493A LEU* 6.0 2.0 - - + -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TRP 2.9 13.4 + - - +
313A PRO* 3.5 9.6 - - + +
315A ARG* 1.3 78.4 - - - +
317A ASP* 1.3 57.3 + - - +
319A LEU* 3.3 4.9 + - - +
320A LEU* 2.9 31.5 + - + +
489A LEU* 3.7 32.1 - - + -
493A LEU* 4.4 8.6 - - + +
518A LEU* 3.9 36.8 - - + +
521A LEU* 3.8 7.6 - - + +
522A GLN* 3.6 37.9 - - + -
524A VAL* 4.5 4.9 - - + -
525A VAL* 4.8 8.3 - - + -
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PRO* 2.9 19.7 + - - +
314A GLN* 3.6 11.3 - - - +
316A LEU* 1.3 75.6 - - - +
318A ILE* 1.3 60.3 + - + +
320A LEU* 3.3 7.0 + - - +
321A GLY* 2.9 25.8 + - - -
352A LEU 5.5 3.6 - - - +
354A PRO* 4.2 5.4 - - - +
522A GLN* 2.7 32.8 + - - +
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LEU* 4.2 27.8 - - + -
310A LEU* 3.9 34.1 - - + -
314A GLN 2.9 22.7 + - - +
315A ARG* 3.7 6.3 - - - +
317A ASP* 1.3 75.5 - - - +
319A LEU* 1.3 64.1 + - + +
321A GLY 3.3 0.7 + - - -
322A THR* 2.9 34.1 + - - +
346A VAL* 4.2 4.7 - - + -
348A LEU* 3.7 29.8 - - + -
352A LEU* 3.8 17.0 - - + +
354A PRO* 3.4 19.6 - - + +
417A THR* 6.1 0.7 - - + -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ARG 3.0 22.5 + - - +
316A LEU* 3.7 4.5 - - - +
318A ILE* 1.3 79.9 - - + +
320A LEU* 1.3 56.9 + - - +
322A THR* 3.4 3.5 + - - +
323A ALA* 2.9 31.5 + - - +
410A PHE* 3.5 14.4 - - + -
413A VAL* 4.1 14.6 - - + -
414A VAL* 4.1 31.4 - - + +
417A THR* 3.6 35.4 - - + +
418A LEU* 6.1 0.2 - - + -
493A LEU* 4.1 34.8 - - + -
518A LEU* 4.0 10.5 - - + -
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A LEU* 2.9 19.1 + - + +
317A ASP* 3.5 7.0 - - - +
318A ILE 3.2 0.2 - - - -
319A LEU* 1.3 78.0 - - - +
321A GLY* 1.3 57.4 + - - +
323A ALA* 3.4 2.9 + - - +
324A ARG* 2.9 46.4 + - - +
515A TYR* 3.5 28.8 - - + +
518A LEU* 3.8 16.7 - - + +
519A GLU* 3.6 35.4 - - + +
522A GLN* 3.5 39.5 - - + +
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASN* 3.3 21.2 - - - +
317A ASP 2.9 11.8 + - - -
318A ILE 3.3 0.2 + - - -
320A LEU* 1.3 74.1 - - - +
322A THR* 1.3 65.1 + - - +
324A ARG* 3.1 16.6 + - - +
325A ALA 3.0 18.4 + - - -
354A PRO* 3.5 21.3 - - - -
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ASN* 5.4 0.7 - - - -
296A LEU* 5.8 0.3 - - - +
318A ILE* 2.9 19.9 + - - +
319A LEU* 3.7 6.4 - - - +
321A GLY* 1.3 75.9 - - - +
323A ALA* 1.3 62.3 + - - +
325A ALA* 3.1 7.9 + - - +
326A ILE* 3.0 36.1 + - + +
341A ILE* 5.3 2.9 - - + -
346A VAL* 3.7 41.1 - - + +
354A PRO* 3.7 5.6 - - - +
356A LEU* 4.8 11.9 - - + +
410A PHE* 3.9 18.6 - - + -
413A VAL* 5.5 3.7 - - + +
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU 2.9 17.7 + - - +
320A LEU 3.6 5.2 - - - +
322A THR* 1.3 76.1 - - - +
324A ARG* 1.3 57.7 + - - +
326A ILE* 3.3 0.7 + - - +
327A GLN* 2.9 35.0 + - - +
410A PHE* 3.7 10.5 - - + -
511A MET* 3.9 20.2 - - + +
514A VAL* 4.5 0.4 - - + -
515A TYR* 4.2 13.7 - - - -
518A LEU* 3.7 20.6 - - + -
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A HIS* 3.8 8.5 - - + -
270A ASN* 2.8 32.1 + - - +
320A LEU* 2.9 28.1 + - - +
321A GLY* 3.1 20.7 + - - +
323A ALA* 1.3 76.7 - - - +
325A ALA* 1.3 62.6 + - - +
327A GLN* 2.9 19.2 + - - +
328A PHE* 2.9 22.2 + - - +
515A TYR* 3.1 41.6 + - + -
233B ASN 3.2 20.4 + - - +
234B THR* 3.7 18.1 - - - +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A HIS* 4.3 6.7 - - - -
270A ASN* 3.5 37.6 - - + +
271A ILE* 4.2 10.5 - - + +
321A GLY 3.0 7.8 + - - +
322A THR* 3.1 9.8 + - - +
324A ARG* 1.3 75.3 - - - +
326A ILE* 1.3 63.4 + - - +
328A PHE* 3.2 6.4 + - - +
329A LEU* 3.0 27.8 + - - +
356A LEU* 4.2 14.8 - - + -
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A THR* 3.0 24.6 + - + +
323A ALA 3.3 3.1 + - - +
325A ALA* 1.3 76.2 - - - +
327A GLN* 1.3 57.6 + - - +
329A LEU* 3.1 12.2 + - + +
330A HIS* 2.9 54.2 + - + +
338A HIS* 6.0 0.7 - - + -
341A ILE* 3.6 35.4 - - + -
356A LEU* 4.1 13.7 - - + -
406A ASP* 4.4 2.5 - - + +
410A PHE* 3.6 33.7 - - + -
511A MET* 3.7 16.4 - - + -
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ALA 2.9 25.3 + - - +
324A ARG* 2.9 26.1 + - - +
326A ILE* 1.3 69.7 - - - +
328A PHE* 1.3 72.5 + - - +
330A HIS* 3.3 4.6 + - - +
331A GLN* 2.9 46.0 + - - +
511A MET* 3.6 33.6 - - - +
512A THR* 3.8 9.2 - - + +
515A TYR* 4.1 10.5 - - + -
232B ARG* 2.9 23.2 + - - +
233B ASN* 2.9 34.2 + - - +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PHE* 3.8 28.9 - + + -
267A ARG 4.5 10.8 - - - -
268A HIS* 3.4 38.1 - + + -
271A ILE* 4.6 0.4 - - + -
324A ARG 2.9 15.6 + - - +
325A ALA 3.3 9.0 - - - +
327A GLN* 1.3 84.9 - - - +
329A LEU* 1.3 71.2 + - + +
331A GLN* 3.2 16.3 + - - +
332A ASP* 3.7 6.6 + - - +
198B PHE* 4.2 21.3 - + - -
200B TRP* 4.1 8.5 - + - -
232B ARG* 3.9 35.2 + - + -
234B THR* 4.6 0.4 - - - -
236B TYR* 3.5 21.8 - - - -
275B ALA 6.2 0.2 - - - -
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PHE* 3.6 37.2 - - + -
271A ILE* 3.8 17.5 - - + -
325A ALA 3.0 18.4 + - - +
326A ILE* 3.1 9.8 + - + +
328A PHE* 1.3 77.2 - - + +
330A HIS* 1.3 63.3 + - + +
331A GLN 3.4 0.7 + - - -
332A ASP* 3.5 11.3 + - - +
336A LEU* 3.2 43.0 + - + +
338A HIS* 4.2 22.2 - - + -
356A LEU* 4.4 8.3 - - + -
359A PHE* 3.6 31.0 - - + -
406A ASP* 5.8 0.2 - - - +
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Residues in contact with HIS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 2.9 30.2 + - + +
327A GLN* 3.9 6.5 - - - +
328A PHE 3.2 0.2 - - - -
329A LEU* 1.3 78.5 - - + +
331A GLN* 1.3 61.4 + - - +
332A ASP 3.2 1.5 + - - +
335A SER* 2.8 24.9 + - - -
336A LEU 3.3 17.0 + - - -
403A VAL* 3.4 50.1 - - + +
406A ASP* 3.0 32.2 + - + +
407A THR* 4.5 0.4 + - - -
511A MET* 3.6 24.5 + - + +
512A THR* 6.3 1.8 - - + -
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLN* 2.9 34.8 + - - +
328A PHE* 3.2 7.5 + - - +
330A HIS* 1.3 76.1 - - - +
332A ASP* 1.3 64.3 + - - +
333A SER* 5.2 1.0 - - - -
512A THR* 3.8 18.9 - - - +
232B ARG* 3.9 47.3 + - + +
233B ASN* 4.4 2.9 + - - -
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ARG* 3.0 32.0 + - - -
266A PHE* 3.3 28.5 - - + -
328A PHE 3.7 3.3 + - - +
329A LEU 3.5 13.2 + - - +
330A HIS 3.2 4.4 - - - +
331A GLN* 1.3 82.9 - - - +
333A SER* 1.3 64.7 + - - +
334A PRO 2.9 26.2 - - - +
335A SER* 3.1 6.6 + - - -
364A PHE* 4.4 4.9 - - - -
198B PHE* 3.7 5.2 - - - -
232B ARG* 3.4 21.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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