Contacts of the helix formed by residues 306 - 327 (chain A) in PDB entry 3QJS
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 ALA 306 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR 3.6 4.4 + - - +
303A LEU* 3.5 12.1 + - + +
304A PHE 3.1 0.8 - - - -
305A VAL* 1.3 81.6 - - - +
307A VAL* 1.3 56.9 + - - +
308A PRO 3.4 1.1 - - - -
309A SER* 3.3 5.3 + - - -
310A LEU* 3.0 33.3 + - + +
364A ILE* 4.3 21.5 - - + -
801A HAS 3.7 34.4 - - + +
26B LEU* 5.5 1.6 - - + -
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.3 13.2 - - + -
303A LEU 3.9 2.0 + - - +
304A PHE* 3.3 15.3 + - + +
306A ALA* 1.3 73.1 - - - +
308A PRO* 1.4 72.6 - - + +
309A SER 3.0 1.6 - - - -
310A LEU* 3.0 11.0 + - + +
311A MET* 2.9 25.5 + - + +
19B LEU* 3.9 27.1 - - + -
22B SER* 4.9 5.4 - - - -
23B LEU* 4.0 20.4 - - + -
26B LEU* 3.6 27.1 - - + -
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Residues in contact with PRO 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A ALA* 3.8 24.4 - - - +
271A LEU* 4.0 28.3 - - + -
272A PHE* 3.7 26.5 - - + +
275A LEU* 5.3 0.4 - - + -
304A PHE 3.3 14.6 - - - +
305A VAL* 3.2 19.5 - - - +
307A VAL* 1.4 93.0 - - + +
309A SER* 1.3 55.7 + - - +
311A MET* 3.4 11.4 - - - +
312A THR* 3.0 27.9 + - - -
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Residues in contact with SER 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 5.6 0.2 - - - -
240A LEU* 4.6 2.1 - - - +
244A TYR* 2.5 31.5 + - - -
272A PHE* 4.1 9.1 - - - -
305A VAL 4.7 0.9 - - - -
306A ALA* 3.5 12.3 - - - -
307A VAL 3.0 0.4 - - - -
308A PRO* 1.3 76.1 - - - +
310A LEU* 1.3 66.4 + - - +
311A MET 3.1 1.1 - - - -
312A THR* 3.5 3.6 + - - -
313A ALA* 3.1 18.0 + - - +
356A PHE* 4.1 1.9 - - - -
801A HAS 3.7 45.3 + - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA* 3.0 24.8 + - + +
307A VAL* 3.0 12.5 + - - +
309A SER* 1.3 77.1 - - - +
311A MET* 1.3 59.2 + - + +
313A ALA* 3.3 12.3 + - - +
314A PHE 3.4 2.9 + - - -
364A ILE* 5.2 0.9 - - + -
801A HAS 3.6 22.0 - - + -
18B TRP* 2.5 50.4 + - + +
22B SER* 3.7 27.8 - - - +
25B MET* 5.4 4.7 - - + -
26B LEU* 4.1 19.7 - - + -
15C LEU* 3.9 6.1 - - + -
19C ILE* 3.9 20.4 - - + -
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 4.8 0.2 - - - -
264A MET* 3.6 40.2 - - + +
267A LEU* 3.7 28.7 - - + -
268A ALA* 5.1 4.0 - - + +
271A LEU* 4.4 5.8 - - - -
307A VAL* 2.9 32.0 + - + +
308A PRO* 3.4 15.3 - - - +
309A SER 3.1 0.2 - - - -
310A LEU* 1.3 75.4 - - + +
312A THR* 1.3 54.4 + - - +
314A PHE* 3.0 3.6 + - - -
315A THR* 2.9 38.1 + - - +
15B GLU* 3.4 18.4 - - + +
18B TRP* 3.9 7.9 - - + +
19B LEU* 4.5 23.3 - - + -
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Residues in contact with THR 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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244A TYR* 3.8 35.5 - - + +
247A ILE* 5.4 1.8 - - + -
248A TYR* 2.2 45.5 + - + +
268A ALA* 4.0 2.6 - - - +
308A PRO 3.0 14.4 + - - -
309A SER 3.7 8.5 - - - -
311A MET* 1.3 73.6 - - - +
313A ALA* 1.3 56.9 + - - +
315A THR* 4.3 2.2 - - - -
316A VAL* 2.8 52.1 + - + +
353A LEU* 5.7 2.2 - - + -
801A HAS 4.3 7.6 - - + -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER 3.1 8.3 + - - +
310A LEU 3.5 9.6 - - - +
311A MET 3.1 0.8 - - - -
312A THR* 1.3 76.3 - - - +
314A PHE* 1.3 62.8 + - - +
316A VAL* 5.0 0.2 - - - -
317A ALA* 3.0 27.5 + - - +
801A HAS 3.6 44.1 - - + +
11C VAL* 4.8 1.5 - - + +
12C ILE* 4.3 6.5 - - + -
15C LEU* 3.8 19.3 - - + -
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU 3.4 2.0 + - - -
311A MET 3.0 5.1 + - - +
313A ALA* 1.3 78.1 - - - +
315A THR* 1.3 59.2 + - - +
317A ALA* 3.7 1.5 - - - +
318A ALA* 3.0 34.9 + - + +
11B ILE* 4.1 14.1 - - + -
14B TYR* 3.5 32.3 - - + -
15B GLU* 3.5 34.3 - - - -
18B TRP* 3.6 27.6 - + + +
5C PRO* 4.2 13.9 - - + -
8C ALA* 3.7 27.1 - - + -
9C LEU* 4.5 10.5 - - + -
12C ILE* 3.8 32.6 - - + +
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 4.0 13.1 + - + -
259A LEU* 4.0 24.5 - - + -
260A VAL* 3.6 15.8 - - + +
261A SER* 4.5 2.7 - - - +
264A MET* 3.9 21.0 - - + +
311A MET* 2.9 17.6 + - - +
312A THR* 3.9 7.4 - - - -
314A PHE* 1.3 75.7 - - - +
316A VAL* 1.3 67.7 + - - +
319A SER* 3.2 24.1 + - - -
15B GLU* 3.2 21.0 + - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.6 28.7 - - + +
248A TYR* 4.4 13.7 - - + -
251A LEU* 4.6 4.0 - - + -
259A LEU* 6.2 1.1 - - + -
312A THR* 2.8 39.6 + - + +
313A ALA* 5.0 0.2 - - - -
315A THR* 1.3 69.3 - - - +
317A ALA* 1.3 66.9 + - - +
319A SER* 2.8 19.5 + - - -
320A LEU* 2.9 23.8 + - + +
353A LEU* 3.8 29.6 - - + -
801A HAS 3.9 10.5 - - + -
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Residues in contact with ALA 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 ALA 3.0 21.9 + - - +
314A PHE* 3.7 5.2 - - - +
316A VAL* 1.3 74.7 - - - +
318A ALA* 1.3 57.8 + - - +
320A LEU* 3.3 7.4 + - - +
321A GLU* 2.8 27.5 + - - +
335A TRP* 4.4 5.1 - - - -
801A HAS 3.8 10.6 - - + +
8C ALA* 3.7 23.7 - - + +
11C VAL* 4.0 24.5 - - + -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A VAL* 4.0 15.9 - - + +
314A PHE* 3.0 32.6 + - + +
315A THR 4.2 2.5 - - - +
317A ALA* 1.3 75.7 - - - +
319A SER* 1.3 58.4 + - - +
321A GLU* 3.6 5.4 - - - +
322A PHE* 2.8 30.0 + - - +
11B ILE* 4.8 8.2 - - + +
5C PRO* 4.8 8.7 - - + -
8C ALA* 3.6 15.7 - - + +
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Residues in contact with SER 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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252A PRO* 4.5 14.4 - - - +
257A GLY* 5.1 0.7 - - - -
258A ARG 3.4 14.3 + - - +
259A LEU* 3.6 7.4 - - - +
260A VAL* 3.1 35.2 + - - +
315A THR 3.2 13.8 + - - -
316A VAL* 2.8 13.4 + - - -
318A ALA* 1.3 74.3 - - - +
320A LEU* 1.3 66.6 + - - -
322A PHE* 3.2 2.8 + - - +
323A ALA* 3.0 23.9 + - - +
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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
----------------------------------------------------------
251A LEU* 4.2 14.1 - - + +
252A PRO* 5.1 4.3 - - + -
255A ALA* 4.0 25.1 - - + -
316A VAL* 2.9 30.4 + - + +
317A ALA* 3.7 6.7 - - - +
319A SER* 1.3 74.3 - - - +
321A GLU* 1.3 67.0 + - - +
323A ALA* 3.2 3.6 + - - +
324A GLY* 2.9 22.7 + - - -
335A TRP* 4.0 14.6 - - + -
339A LEU* 3.8 11.6 - - + +
346A PHE* 4.1 12.1 - - + -
350A VAL* 3.8 24.0 - - + -
353A LEU* 5.1 0.2 - - + -
801A HAS 4.0 27.8 - - + -
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Residues in contact with GLU 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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317A ALA 2.8 17.8 + - - +
318A ALA* 3.6 5.2 - - - +
320A LEU* 1.3 78.0 - - - +
322A PHE* 1.3 61.3 - - - +
324A GLY* 3.7 0.5 - - - -
325A ARG* 2.5 61.8 + - + +
335A TRP* 3.6 32.8 - - + +
5C PRO* 3.2 33.6 - - - +
6C LYS 3.6 3.1 + - - -
7C GLY* 2.7 23.3 + - - -
8C ALA* 3.3 5.9 + - - +
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Residues in contact with PHE 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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258A ARG* 3.8 44.4 - - + -
260A VAL* 4.3 15.7 - - + -
318A ALA 2.8 17.3 + - - +
319A SER 3.8 2.2 - - - +
320A LEU 3.2 0.2 - - - -
321A GLU* 1.3 77.7 - - - +
323A ALA* 1.3 64.2 + - - +
325A ARG* 3.2 8.3 + - + +
326A LEU* 3.1 58.1 + - + +
512A ILE* 4.6 3.6 - - + -
3B ASP* 3.5 29.2 - - - -
4B GLN* 3.5 32.1 - - + -
11B ILE* 6.1 2.2 - - + -
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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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252A PRO* 5.6 0.4 - - + -
255A ALA* 3.5 32.9 - - + +
256A GLY 4.4 1.1 - - - +
257A GLY* 3.6 26.0 - - - +
319A SER 3.0 13.2 + - - +
320A LEU 3.5 7.6 - - - +
322A PHE* 1.3 76.5 - - - +
324A GLY* 1.3 63.4 + - - +
326A LEU* 3.2 12.2 - - - +
327A ARG* 3.0 24.2 + - - +
339A LEU* 4.2 2.7 - - + -
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Residues in contact with GLY 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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320A LEU 2.9 17.9 + - - -
321A GLU 3.7 1.3 - - - -
323A ALA* 1.3 73.5 - - - +
325A ARG* 1.3 57.9 + - - +
327A ARG* 3.1 9.5 + - - -
329A GLY* 2.9 22.5 + - - -
335A TRP* 3.6 31.2 - - - -
338A ALA* 3.4 6.2 - - - +
339A LEU* 3.5 8.1 - - - +
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Residues in contact with ARG 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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321A GLU* 2.5 50.6 + - + +
322A PHE* 3.6 9.9 - - + +
324A GLY* 1.3 73.4 - - - +
326A LEU* 1.3 60.1 + - + +
328A GLY* 3.0 21.7 + - - -
329A GLY 3.3 21.8 + - - +
330A ARG 5.1 5.8 + - - -
331A GLY 3.5 22.6 + - - -
332A LEU* 4.3 1.4 + - - +
335A TRP* 3.7 19.6 - - - +
2C GLU* 2.4 48.0 + - + +
4C LYS 4.5 7.5 + - - -
6C LYS* 4.6 10.3 - - - +
7C GLY 4.2 3.8 - - - +
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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
----------------------------------------------------------
256A GLY 3.6 22.4 - - - +
257A GLY* 4.5 2.0 - - - -
258A ARG* 5.2 9.4 - - - +
322A PHE* 3.1 54.5 + - + +
323A ALA 3.2 11.0 - - - +
325A ARG* 1.3 78.4 - - + +
327A ARG* 1.3 58.3 + - + +
328A GLY 3.3 3.0 + - - -
3B ASP* 4.4 9.6 - - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA 4.5 14.1 - - - +
256A GLY* 5.2 8.3 - - - +
323A ALA 3.0 15.2 + - - +
324A GLY* 3.8 4.3 - - - +
325A ARG 3.1 1.0 - - - -
326A LEU* 1.3 78.3 - - + +
328A GLY* 1.3 60.3 + - - +
329A GLY 3.3 3.1 - - - -
330A ARG* 4.1 5.2 + - - -
338A ALA* 3.1 39.4 + - + +
339A LEU 4.1 0.6 + - - -
340A PRO* 3.9 27.2 - - - +
342A ASP* 5.6 0.8 + - - -
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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) + - + + + + + -
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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