Contacts of the helix formed by residues 316 - 340 (chain A) in PDB entry 4O6M
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 LEU 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A CYS* 2.8 27.0 + - + +
314A VAL* 3.7 22.7 - - + +
315A ASN* 1.3 86.1 - - - +
317A PRO* 1.3 65.8 - - - +
318A SER* 3.0 12.6 - - - +
319A LEU* 2.9 34.8 + - + +
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Residues in contact with PRO 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 4.4 11.9 - - + -
200A THR* 4.1 19.5 - - + +
250A ILE* 3.8 25.3 - - + +
254A LEU* 5.2 9.2 - - + -
311A CYS* 3.9 9.1 - - + +
312A SER* 4.2 15.7 - - - +
315A ASN* 3.2 13.7 - - - +
316A LEU* 1.3 88.7 - - - +
318A SER* 1.3 61.3 + - - +
320A ALA* 3.1 20.2 + - + +
321A LEU* 3.3 10.9 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 3.4 34.4 - - - +
261A TYR* 3.6 28.2 + - - -
316A LEU* 3.0 14.1 + - - +
317A PRO* 1.3 81.7 - - - +
319A LEU* 1.3 63.9 + - - +
321A LEU* 3.2 7.3 + - - +
322A VAL* 3.2 25.7 + - - +
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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
----------------------------------------------------------
311A CYS* 3.9 14.6 - - - -
314A VAL* 6.2 1.3 - - + -
316A LEU* 2.9 34.7 + - + +
318A SER* 1.3 78.2 + - - +
320A ALA* 1.3 61.3 + - - +
322A VAL* 3.2 14.3 + - + +
323A ILE* 2.9 56.7 + - + +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 5.7 1.1 - - + -
307A ILE* 3.9 9.2 - - + +
308A ILE* 3.8 33.0 - - + -
311A CYS* 3.6 24.7 - - + -
316A LEU 3.6 1.8 + - - -
317A PRO* 3.1 14.0 + - + +
319A LEU* 1.3 78.9 - - - +
321A LEU* 1.3 57.8 + - + +
323A ILE* 3.8 0.9 - - - +
324A ILE* 2.9 37.6 + - - +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 4.0 30.7 - - + -
250A ILE* 3.8 32.3 - - + -
251A THR* 3.6 21.5 - - - +
254A LEU* 3.9 15.7 - - + -
261A TYR* 4.9 7.6 - - + +
264A ILE* 3.9 11.7 - - + -
265A GLY* 4.2 9.4 - - - +
268A ALA* 3.6 12.8 - - + +
308A ILE* 6.0 1.6 - - + -
317A PRO 3.3 10.7 + - - +
318A SER 3.2 7.2 + - - +
320A ALA* 1.3 77.6 - - + +
322A VAL* 1.3 60.2 + - - +
324A ILE* 4.7 3.1 - - + -
325A ALA* 2.8 33.1 + - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 5.0 4.9 - - + -
264A ILE* 4.0 31.2 - - + -
318A SER 3.2 14.4 + - - +
319A LEU* 3.2 18.6 + - + +
321A LEU* 1.3 76.8 - - - +
323A ILE* 1.3 59.9 + - + +
325A ALA* 3.7 1.3 - - - +
326A LEU* 2.9 50.2 + - + +
407A MPG 4.6 7.6 - - + -
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Residues in contact with ILE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.9 39.7 - - + -
311A CYS* 4.3 5.8 - - - -
319A LEU* 2.9 45.9 + - + +
320A ALA 3.8 3.4 - - - +
322A VAL* 1.3 78.2 - - + +
324A ILE* 1.3 57.1 + - - +
326A LEU* 4.7 4.7 - - + -
327A LEU* 2.9 50.6 + - + +
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Residues in contact with ILE 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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247A VAL* 5.5 5.4 - - + -
268A ALA* 3.7 16.8 - - + +
271A ALA* 3.7 5.6 - - + +
272A SER* 3.5 24.0 - - - +
299A ILE* 4.3 19.5 - - + -
304A ARG* 3.9 30.7 - - + +
307A ILE* 4.6 7.6 - - + -
308A ILE* 3.9 34.3 - - + -
320A ALA 2.9 21.3 + - - +
321A LEU* 4.1 4.3 - - + +
323A ILE* 1.3 75.5 - - - +
325A ALA* 1.3 59.9 + - - +
328A GLY* 2.8 28.6 + - - -
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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
----------------------------------------------------------
264A ILE* 4.0 7.0 - - + +
267A LEU* 4.0 13.9 - - + -
268A ALA* 3.8 24.4 - - - +
321A LEU 2.8 19.2 + - - +
322A VAL 3.7 3.8 - - - +
324A ILE* 1.3 76.9 - - - +
326A LEU* 1.3 60.5 + - - +
329A ASN* 2.9 34.9 + - - +
407A MPG 4.0 16.5 - - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 2.9 39.2 + - + +
323A ILE* 3.9 4.3 - - + +
325A ALA* 1.3 76.0 - - - +
327A LEU* 1.3 75.4 + - + +
329A ASN* 4.2 0.3 - - - +
330A PHE* 3.1 45.3 + - + -
407A MPG 3.7 35.9 - - + -
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 3.7 28.8 - - + +
298A PRO* 4.6 10.1 - - + +
299A ILE* 3.9 19.3 - - + -
307A ILE* 4.9 3.4 - - + -
323A ILE* 2.9 41.8 + - + +
326A LEU* 1.3 83.4 - - + +
328A GLY* 1.3 57.9 + - - +
330A PHE* 3.9 2.9 - - - +
331A GLU* 2.9 31.5 + - - +
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Residues in contact with GLY 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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271A ALA* 3.8 14.8 - - - +
275A ILE* 3.6 12.1 - - - +
299A ILE* 3.8 20.0 - - - +
304A ARG* 6.3 0.2 - - - -
324A ILE* 2.8 23.9 + - - -
327A LEU* 1.3 74.9 - - - +
329A ASN* 1.3 54.5 + - - +
331A GLU 3.4 0.7 + - - -
332A ALA* 3.0 28.2 + - - +
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Residues in contact with ASN 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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267A LEU* 3.3 40.2 + - - +
270A PHE* 3.5 27.0 - - - -
271A ALA* 3.7 5.0 - - - +
325A ALA* 2.9 27.4 + - - +
326A LEU 4.2 0.2 - - - +
328A GLY* 1.3 73.4 - - - +
330A PHE* 1.3 65.2 + - - +
332A ALA* 3.5 4.8 + - - +
333A LEU* 3.2 22.3 + - - +
407A MPG 4.0 26.9 - - + +
241B TYR* 4.5 7.3 + - - -
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Residues in contact with PHE 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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297A ILE* 3.8 18.6 - - + +
326A LEU* 3.1 45.4 + - + +
327A LEU* 4.8 0.7 - - - -
329A ASN* 1.3 75.7 - - - +
331A GLU* 1.3 57.8 + - - +
333A LEU* 3.3 20.5 + - + +
334A ARG* 2.8 28.2 + - - +
407A MPG 3.7 27.1 - - + -
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Residues in contact with GLU 331 (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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275A ILE* 3.5 20.2 - - + -
290A TYR* 5.3 0.2 - - - -
296A ALA* 3.9 4.2 - - - +
297A ILE* 2.9 34.4 + - + +
299A ILE* 3.7 18.6 - - + -
327A LEU 2.9 19.4 + - - +
330A PHE* 1.3 73.2 - - - +
332A ALA* 1.3 65.3 + - - +
334A ARG* 2.9 43.5 + - - -
335A ARG* 2.9 48.2 + - - +
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Residues in contact with ALA 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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270A PHE* 6.1 0.2 - - + -
271A ALA* 6.2 0.2 - - - -
274A MET* 4.6 17.0 - - + -
275A ILE* 4.0 10.3 - - + +
278A THR* 4.9 11.9 - - + +
328A GLY 3.0 17.1 + - - +
329A ASN* 3.8 5.6 - - - +
330A PHE 3.3 0.2 - - - -
331A GLU* 1.3 75.3 - - - +
333A LEU* 1.3 63.1 + - - +
335A ARG* 3.2 11.6 + - - +
336A ILE* 3.1 25.2 + - - +
241B TYR* 3.3 22.7 - - + +
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Residues in contact with LEU 333 (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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329A ASN 3.2 10.7 + - - +
330A PHE* 3.5 26.9 - - + +
332A ALA* 1.3 76.8 - - - +
334A ARG* 1.3 65.1 + - - +
336A ILE* 3.2 22.1 + - + +
337A VAL* 3.1 34.3 + - + +
407A MPG 6.4 2.0 - - + -
241B TYR* 4.2 3.2 + - - +
407B MPG 5.6 4.3 - - + -
412B MPG 5.1 13.2 - - + -
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TYR* 3.7 13.5 + - - -
292A PRO* 4.3 0.6 - - - +
295A PHE* 3.5 36.1 + - - -
296A ALA* 3.4 15.7 - - - +
297A ILE* 5.0 5.4 - - + -
330A PHE 2.8 20.3 + - - +
331A GLU* 2.9 43.9 + - - +
333A LEU* 1.3 73.3 - - - +
335A ARG* 1.3 61.0 + - - +
337A VAL* 3.2 7.2 + - + +
338A ALA* 2.8 45.2 + - + +
413A SO4 2.7 31.5 + - - -
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 3.0 35.4 + - - +
278A THR* 2.9 30.8 + - - -
279A GLY* 3.8 8.9 - - - +
290A TYR* 3.3 46.6 + - - +
297A ILE 5.7 0.6 + - - -
299A ILE* 6.0 0.2 - - - +
300A THR* 4.0 17.6 - - - +
331A GLU* 2.9 44.9 + - - +
332A ALA* 3.2 9.4 + - - +
334A ARG* 1.3 78.1 - - - +
336A ILE* 1.3 63.4 + - - +
338A ALA* 4.5 5.2 - - - -
339A LEU* 3.0 33.8 + - + +
411A SO4 5.4 0.8 + - - -
233B TRP* 4.0 12.8 - - + -
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Residues in contact with ILE 336 (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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278A THR* 5.5 0.7 - - + -
332A ALA 3.1 15.4 + - - +
333A LEU* 3.4 18.4 - - + +
335A ARG* 1.3 78.4 - - - +
337A VAL* 1.3 66.5 + - + +
339A LEU 3.7 4.3 + - - -
230B TYR* 3.0 34.9 + - - +
233B TRP* 3.7 21.5 - - + -
234B LEU* 4.0 8.7 - - + -
237B VAL* 4.0 21.5 - - + -
238B LEU* 4.6 10.8 - - + -
241B TYR* 4.0 20.6 - - + +
407B MPG 3.9 27.6 - - + -
412B MPG 5.0 6.1 - - + -
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.1 27.6 + - + +
334A ARG* 3.7 7.9 - - - +
336A ILE* 1.3 81.1 - - + +
338A ALA* 1.3 63.6 + - - +
340A ARG* 3.3 20.9 + - - +
341A SER* 4.5 2.3 + - - -
407B MPG 6.1 5.2 - - + -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A TYR* 6.2 0.2 - - - +
334A ARG* 2.8 36.1 + - + +
335A ARG* 4.0 3.6 - - - +
337A VAL* 1.3 75.0 - - - +
339A LEU* 1.3 59.3 + - + +
341A SER* 3.0 24.1 + - - -
342A TYR* 3.4 8.0 + - - +
413A SO4 3.5 32.2 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR 5.5 0.2 - - - +
282A PHE* 3.5 38.8 - - + -
286A TYR* 4.1 6.0 + - + +
290A TYR* 4.6 16.8 - - + +
335A ARG* 3.0 17.3 + - + +
337A VAL 3.3 0.2 - - - -
338A ALA* 1.3 73.0 - - - +
340A ARG* 1.3 62.7 + - - +
341A SER 2.9 8.9 + - - -
342A TYR* 3.2 37.3 + - + +
413A SO4 4.6 6.5 - - - +
230B TYR* 3.5 25.8 - - + +
233B TRP* 3.5 42.0 - - + -
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE 3.7 1.1 + - - +
337A VAL* 3.3 16.3 + - - +
338A ALA 3.2 0.6 - - - -
339A LEU* 1.3 78.3 - - - +
341A SER* 1.3 56.6 + - - +
230B TYR* 3.5 36.5 - - + +
407B MPG 5.0 8.1 - - + -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il