Contacts of the helix formed by residues 305 - 328 (chain A) in PDB entry 4QBT
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 HIS 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 5.9 1.3 - - + +
283A TRP* 4.0 49.8 + + + +
299A PHE* 4.4 1.1 - - - -
302A GLU* 4.0 20.7 + - - -
303A VAL* 4.8 4.5 - - - -
304A VAL* 1.3 77.1 - - - +
306A PRO* 1.3 73.7 - - + +
308A ASP* 3.0 23.7 + - - +
309A LEU* 2.8 21.1 + - - +
501A PO4 3.4 34.9 + - - +
507A PO4 5.4 0.4 - - - -
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Residues in contact with PRO 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A CYS* 3.4 41.3 - - + +
251A GLU 4.4 0.7 - - - -
252A PRO* 3.9 35.7 - - + -
299A PHE* 4.3 4.0 - - + -
304A VAL 4.3 2.7 - - - +
305A HIS* 1.3 84.9 - - + +
307A GLY* 1.3 56.0 + - - +
309A LEU* 3.3 4.4 + - + +
310A LYS* 2.9 40.7 + - + +
501A PO4 3.3 12.8 - - - +
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO* 1.3 78.0 - - - +
308A ASP* 1.3 58.4 + - - +
310A LYS* 3.6 8.9 + - - +
311A ASN* 3.1 28.4 + - - +
501A PO4 2.9 28.8 + - - -
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Residues in contact with ASP 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 4.7 10.1 - - + -
278A LEU 3.4 21.5 - - - +
279A ARG* 3.7 23.1 - - + +
280A ASP* 4.7 6.0 + - - +
283A TRP* 5.3 2.9 - - - -
304A VAL* 5.0 0.4 - - + -
305A HIS* 3.0 29.0 + - - +
307A GLY* 1.3 75.8 - - - +
309A LEU* 1.3 64.0 + - - +
311A ASN* 3.9 5.7 + - - +
312A SER* 2.7 31.6 + - - -
501A PO4 3.7 10.1 + - - -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A CYS* 3.8 17.9 - - - -
260A VAL* 3.5 24.9 - - + -
261A LEU* 3.7 31.0 - - + -
264A ILE* 3.6 22.0 - - + -
277A ILE* 3.8 23.6 - - + -
295A LEU* 4.1 6.1 - - + -
299A PHE* 3.8 9.2 - - + -
304A VAL* 4.0 13.3 - - + +
305A HIS 2.8 12.7 + - - +
306A PRO* 3.6 9.0 - - + +
308A ASP* 1.3 78.2 - - - +
310A LYS* 1.3 62.9 + - - +
312A SER* 3.1 2.3 + - - -
313A VAL* 3.1 21.1 + - - +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.4 39.2 + - + +
246A LYS* 3.6 17.2 + - - +
248A ALA* 3.0 32.8 + - - -
250A CYS* 3.8 20.0 + - + +
260A VAL* 4.3 21.1 - - + -
306A PRO* 2.9 27.9 + - - +
307A GLY* 3.9 7.0 - - - +
309A LEU* 1.3 72.3 - - - +
311A ASN* 1.3 51.1 + - - +
313A VAL* 3.2 4.4 + - - +
314A GLU* 2.7 37.7 + - - +
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Residues in contact with ASN 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 5.5 2.8 + - - -
278A LEU* 3.6 27.3 + - - +
307A GLY 3.1 15.7 + - - +
308A ASP* 4.0 7.1 + - - +
310A LYS* 1.3 78.6 - - - +
312A SER* 1.3 60.7 + - - +
314A GLU* 4.0 16.2 - - - +
315A VAL* 3.1 30.3 + - - +
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.7 18.2 - - - -
276A VAL 3.4 21.4 - - - +
277A ILE* 3.5 5.0 - - - +
278A LEU* 2.9 35.9 + - - +
308A ASP 2.7 22.7 + - - -
309A LEU 3.7 3.8 - - - -
311A ASN* 1.3 76.2 - - - +
313A VAL* 1.3 61.9 + - - +
315A VAL* 3.8 2.6 + - - +
316A ALA* 3.4 22.3 + - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 4.5 18.4 - - + -
245A LEU* 4.6 10.5 - - + -
260A VAL* 3.7 15.0 - - + +
263A PHE* 4.3 20.2 - - + -
264A ILE* 3.5 39.3 - - + -
268A LEU* 4.3 8.4 - - + +
275A PHE* 4.2 1.3 - - + -
309A LEU 3.1 10.7 + - - +
310A LYS* 3.5 8.1 - - - +
312A SER* 1.3 76.3 - - - +
314A GLU* 1.3 55.7 + - - +
316A ALA* 3.3 1.9 + - - +
317A LEU* 2.7 41.6 + - + +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LYS 4.5 2.8 - - - +
241A VAL* 4.4 3.0 - - + +
242A LYS* 3.1 60.9 + - - +
245A LEU* 3.7 24.5 - - + +
310A LYS* 2.7 21.0 + - - +
311A ASN* 3.4 18.5 + - - +
313A VAL* 1.3 72.0 - - - +
315A VAL* 1.3 58.6 + - + +
317A LEU* 3.3 3.8 + - - +
318A ASN* 2.9 44.5 + - - +
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 3.7 23.3 - - + -
311A ASN* 3.1 24.0 + - - +
312A SER 4.0 4.7 - - - +
314A GLU* 1.3 79.3 - - + +
316A ALA* 1.3 63.5 + - - +
318A ASN* 3.4 5.1 + - - +
319A LYS* 3.1 28.7 + - + +
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Residues in contact with ALA 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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268A LEU* 3.8 24.5 - - + +
272A LYS* 4.0 21.6 + - - +
275A PHE* 4.8 4.3 - - + -
312A SER 3.4 14.7 + - - +
313A VAL 3.3 4.3 + - - +
315A VAL* 1.3 80.7 - - - +
317A LEU* 1.3 62.1 + - - +
319A LYS* 3.3 10.6 + - - +
320A LEU* 3.1 24.9 + - - +
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Residues in contact with LEU 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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50A VAL* 4.3 13.2 - - + -
53A PHE* 4.7 1.1 - - + -
218A LEU* 4.1 22.7 - - + -
232A ILE* 4.4 10.1 - - + -
241A VAL* 4.1 21.8 - - + -
245A LEU* 4.9 5.8 - - + -
263A PHE* 3.8 28.0 - - + -
268A LEU* 5.2 0.2 - - - +
313A VAL* 2.7 25.4 + - + +
314A GLU 3.8 2.7 - - - +
316A ALA* 1.3 72.2 - - - +
318A ASN* 1.3 59.6 + - - +
320A LEU* 2.9 18.6 + - + +
321A LEU* 2.9 47.7 + - + +
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Residues in contact with ASN 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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238A LYS* 3.7 33.1 + - - +
241A VAL* 3.9 19.5 - - - +
314A GLU* 2.9 41.2 + - - +
315A VAL* 3.9 5.3 - - - +
317A LEU* 1.3 76.6 - - - +
319A LYS* 1.3 59.9 + - - +
321A LEU* 4.5 1.5 - - - +
322A ASP* 2.9 34.2 + - - +
325A ARG* 2.9 35.7 + - - +
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Residues in contact with LYS 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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107A SER* 4.2 0.5 + - - -
272A LYS* 6.0 2.5 - - - +
315A VAL* 3.1 22.6 + - + +
316A ALA* 3.4 13.7 - - - +
317A LEU 3.2 0.2 - - - -
318A ASN* 1.3 76.6 - - - +
320A LEU* 1.3 62.1 + - + +
322A ASP* 3.4 19.6 + - - +
323A PRO* 3.5 13.9 - - - +
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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
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53A PHE* 4.0 28.5 - - + -
107A SER* 2.6 36.4 + - - +
108A ILE* 3.4 29.2 - - + -
263A PHE* 4.6 0.4 - - + -
267A VAL* 4.0 26.0 - - + -
268A LEU* 4.3 10.1 - - + -
271A LEU* 3.9 19.5 - - + -
316A ALA 3.1 15.0 + - - +
317A LEU* 2.9 18.9 + - + +
319A LYS* 1.3 79.5 - - + +
321A LEU* 1.3 61.5 + - - +
322A ASP 3.5 0.5 + - - -
323A PRO* 4.0 1.4 - - - +
324A ILE* 3.7 7.7 - - - +
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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
----------------------------------------------------------
50A VAL* 4.3 9.6 - - + -
53A PHE* 3.9 25.6 - - + -
233A ASP 4.2 13.0 - - - +
234A LEU* 3.6 30.7 - - + +
236A ASP 4.6 0.7 - - - +
241A VAL* 4.0 26.7 - - + -
317A LEU* 2.9 31.1 + - + +
318A ASN* 4.6 1.3 - - - +
320A LEU* 1.3 76.2 - - - +
322A ASP* 1.3 65.7 + - - +
323A PRO 3.6 0.4 - - - -
324A ILE* 3.4 9.6 + - + +
325A ARG* 3.0 45.8 + - - +
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LYS* 4.2 11.2 + - - +
318A ASN* 2.9 24.5 + - - +
319A LYS* 3.9 14.7 + - - +
320A LEU 3.3 0.2 - - - -
321A LEU* 1.3 77.6 - - - +
323A PRO* 1.3 78.3 - - + +
325A ARG* 2.9 32.5 + - - +
326A GLU* 3.0 21.8 + - - +
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Residues in contact with PRO 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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103A ALA* 5.4 2.0 - - + +
106A GLU* 6.4 0.7 - - + -
107A SER* 3.9 31.4 - - - +
319A LYS 3.5 9.0 - - - +
320A LEU 4.0 0.7 - - - +
322A ASP* 1.3 94.7 - - + +
324A ILE* 1.3 62.4 + - + +
326A GLU* 2.9 10.5 + - + +
327A LYS* 2.8 32.7 + - + +
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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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53A PHE* 4.0 12.8 - - + -
100A VAL* 4.6 5.8 - - + -
103A ALA* 4.0 35.9 - - + +
104A MET* 3.9 30.5 - - + +
107A SER* 4.3 1.3 - - - -
234A LEU* 4.1 15.9 - - + +
235A LEU* 3.9 16.4 - - + -
320A LEU 3.7 22.2 - - - +
321A LEU* 3.7 15.9 - - + +
322A ASP 3.2 0.8 - - - -
323A PRO* 1.3 76.3 - - - +
325A ARG* 1.3 62.6 + - - +
327A LYS* 3.5 1.2 + - - +
328A PHE* 3.1 36.5 + - + +
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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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234A LEU 4.0 11.0 - - - +
235A LEU* 3.5 24.0 - - - +
236A ASP 2.5 39.4 + - - -
237A ARG* 3.5 5.0 - - - +
238A LYS* 3.3 24.9 - - - +
241A VAL* 3.9 5.5 - - - +
318A ASN* 2.9 39.4 + - - +
321A LEU* 3.0 25.2 + - - +
322A ASP* 2.9 30.9 + - - +
324A ILE* 1.3 72.9 - - - +
326A GLU* 1.3 68.2 + - - +
328A PHE* 3.8 1.7 - - - +
329A ASN* 3.2 19.9 + - - +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP 3.0 12.4 + - - +
323A PRO* 2.9 14.8 + - + +
325A ARG* 1.3 76.4 - - - +
327A LYS* 1.3 55.1 + - + +
329A ASN* 2.7 45.9 + - - +
330A THR* 5.5 0.2 - - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 5.3 7.2 - - + -
106A GLU* 3.2 32.4 + - - +
323A PRO* 2.8 22.6 + - + +
324A ILE* 3.8 5.6 - - - +
326A GLU* 1.3 73.5 - - + +
328A PHE* 1.3 68.5 + - + +
329A ASN 3.2 3.5 + - - -
330A THR* 3.8 13.7 + - - +
333A LEU* 3.4 17.4 - - + +
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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
----------------------------------------------------------
96A TYR* 3.7 28.3 - + - -
99A ASN* 3.4 35.2 - - + -
100A VAL* 3.4 24.9 - - + -
103A ALA* 4.2 11.2 - - + -
235A LEU* 3.7 33.0 - - + -
324A ILE* 3.1 24.9 + - + +
325A ARG 3.8 2.7 - - - +
327A LYS* 1.3 83.1 - - + +
329A ASN* 1.3 55.9 + - - +
330A THR 3.1 18.3 + - - +
333A LEU* 3.9 36.8 - - + +
334A LYS* 4.5 8.5 + - - +
337A ALA* 5.8 1.1 - - + -
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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) + - + + + + + -
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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