Contacts of the helix formed by residues 280 - 305 (chain A) in PDB entry 4COF
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 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ARG 2.8 7.5 + - - +
142A ARG 3.5 16.6 - - - +
143A TYR 3.2 13.8 + - - +
144A PRO* 4.7 1.8 - - + -
145A LEU* 4.8 2.7 - - + -
279A LYS* 1.4 71.9 - - - +
281A ILE* 1.3 61.9 + - - +
283A MET* 3.4 8.8 + - - +
442A TYR* 3.1 30.6 + - - +
446A TYR* 3.3 42.8 - - + -
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.3 22.6 + - + +
144A PRO* 3.8 15.0 - - + -
221A PHE* 5.0 2.2 - - + -
225A THR* 3.2 32.5 - - + +
226A TYR* 3.5 33.6 + - + +
268A LEU* 3.5 34.8 - - + -
279A LYS* 3.9 14.4 - - + -
280A ALA* 1.3 78.6 - - - +
282A ASP* 1.4 61.3 + - - +
284A TYR* 3.2 4.4 + - - +
285A LEU* 3.0 35.7 + - + +
442A TYR* 3.9 1.3 + - - -
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 3.2 21.7 + - - +
268A LEU* 4.1 5.0 - - - +
269A ARG* 3.0 29.4 + - - +
278A VAL* 3.6 15.7 - - + -
279A LYS* 3.1 51.7 + - - +
281A ILE* 1.4 79.4 - - - +
283A MET* 1.3 56.8 + - - +
285A LEU* 3.8 2.7 - - - +
286A MET* 2.9 41.7 + - - +
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Residues in contact with MET 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 4.4 16.8 - - - -
279A LYS 3.3 6.8 + - - +
280A ALA 3.5 10.3 - - - +
281A ILE 3.2 0.6 - - - -
282A ASP* 1.3 78.9 - - - +
284A TYR* 1.3 59.6 + - - +
286A MET* 3.5 18.7 + - + +
287A GLY* 3.1 19.8 + - - -
438A PHE* 4.0 6.6 - - + -
442A TYR* 4.6 7.6 - - + -
446A TYR* 4.2 16.4 - - + +
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR* 3.8 27.4 - + + -
229A SER* 3.8 14.1 - - - -
230A ILE* 3.2 25.8 - - + +
280A ALA 3.5 1.8 + - - -
281A ILE 3.2 9.3 + - - +
283A MET* 1.3 78.5 - - - +
285A LEU* 1.3 67.5 + - + +
287A GLY* 3.2 3.5 + - - -
288A CYS* 3.0 46.5 + - - -
435A PHE* 3.5 7.6 - + - -
438A PHE* 3.7 22.4 - + - -
439A ASN* 2.8 31.4 + - - -
442A TYR* 3.6 44.8 - + + +
443A TRP* 4.3 5.6 + - - -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 4.7 5.6 - - - +
226A TYR* 6.1 0.2 - - + -
229A SER* 3.1 31.6 - - - +
261A MET* 4.4 11.4 - - - +
264A ILE* 3.7 20.0 - - + -
265A ASN* 3.7 46.5 + - + +
268A LEU* 3.9 25.1 - - + -
281A ILE* 3.0 25.8 + - + +
282A ASP 4.0 0.9 - - - +
284A TYR* 1.3 78.9 - - + +
286A MET* 1.4 59.4 + - - +
288A CYS* 3.5 5.3 + - - +
289A PHE* 3.1 25.5 + - - +
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Residues in contact with MET 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 4.1 15.0 - - - +
269A ARG* 5.1 4.5 - - - -
278A VAL* 4.6 15.5 - - + -
282A ASP* 2.9 32.2 + - - +
283A MET* 3.9 23.1 - - + +
285A LEU* 1.4 71.3 - - - +
287A GLY* 1.3 65.0 + - - +
289A PHE* 3.2 10.2 + - + +
290A VAL* 3.1 28.6 + - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A MET 3.1 11.1 + - - -
284A TYR 3.2 4.9 + - - -
286A MET* 1.3 74.1 - - - +
288A CYS* 1.4 55.9 + - - +
290A VAL* 3.0 24.0 + - - +
291A PHE* 3.0 23.9 + - - -
438A PHE* 3.6 24.0 - - - -
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Residues in contact with CYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 4.1 8.3 - - - -
233A THR* 3.8 7.6 + - - +
261A MET* 3.8 23.3 - - + -
284A TYR* 3.0 45.3 + - - +
285A LEU* 3.8 8.3 - - - +
287A GLY* 1.4 73.7 - - - +
289A PHE* 1.4 56.9 + - - +
291A PHE* 3.4 8.1 + - - +
292A VAL* 3.0 33.4 + - - +
435A PHE* 3.6 24.7 - - - -
438A PHE* 4.8 1.1 - - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.9 22.0 - - + -
261A MET* 4.2 10.9 - - + +
262A THR* 3.5 30.3 - - + -
285A LEU 3.1 15.5 + - - +
286A MET* 3.2 14.3 + - + +
288A CYS* 1.4 75.0 - - - +
290A VAL* 1.3 61.7 + - + +
292A VAL* 3.3 8.4 + - + +
293A PHE* 2.8 69.3 + + + +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A MET* 3.1 15.9 + - + +
287A GLY* 3.0 10.4 + - - +
289A PHE* 1.3 83.6 - - + +
291A PHE* 1.3 58.0 + - + +
293A PHE* 3.4 3.8 + - - +
294A LEU* 3.0 54.8 + - + +
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A THR* 4.1 15.5 - - + -
236A SER* 4.5 2.9 + - - -
237A TRP* 5.3 0.8 + - - +
287A GLY* 3.0 28.0 + - - -
288A CYS 3.7 6.3 - - - +
289A PHE 3.3 0.2 - - - -
290A VAL* 1.3 78.0 - - + +
292A VAL* 1.4 61.0 - - - +
294A LEU* 4.7 7.6 - - + -
295A ALA* 3.5 17.2 + - - +
431A PHE* 3.6 33.4 - + + -
434A THR* 3.4 43.1 - - + -
435A PHE* 3.5 40.4 - + + -
438A PHE* 3.7 28.3 - + + -
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE 4.2 1.3 - - - +
233A THR* 3.8 23.1 - - - +
236A SER* 3.8 25.4 - - - +
254A GLY* 4.9 0.7 - - - +
257A THR* 3.7 30.1 + - - +
258A VAL* 3.6 19.3 - - + +
261A MET* 3.6 25.4 - - + -
288A CYS 3.0 19.4 + - - +
289A PHE* 3.4 14.4 - - + +
291A PHE* 1.4 73.2 - - - +
293A PHE* 1.4 64.2 + - - +
295A ALA* 3.6 4.3 + - - +
296A LEU* 3.6 14.4 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.8 23.1 - - + -
289A PHE* 2.8 49.4 + + + +
290A VAL* 3.9 4.9 - - - +
292A VAL* 1.4 76.1 - - - +
294A LEU* 1.3 65.8 + - + +
296A LEU* 3.2 13.5 + - + +
297A LEU* 3.0 51.9 + - + +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 3.0 41.8 + - + +
291A PHE* 3.7 6.9 + - + +
292A VAL 3.4 0.2 - - - -
293A PHE* 1.3 78.9 - - + +
295A ALA* 1.4 50.8 + - - +
297A LEU* 3.1 22.1 + - + +
298A GLU* 2.6 36.4 + - - +
431A PHE* 3.9 21.0 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.9 25.4 - - - +
239A SER* 5.3 4.8 + - - -
240A PHE* 3.7 31.6 - - + -
254A GLY* 5.9 1.6 - - - -
291A PHE 3.5 12.4 + - - +
292A VAL 3.9 8.7 - - - +
293A PHE 3.3 0.8 - - - -
294A LEU* 1.4 75.5 - - - +
296A LEU* 1.3 62.2 + - - +
298A GLU* 3.3 7.2 + - - +
299A TYR* 3.1 19.8 + - - +
431A PHE* 3.7 5.7 - - + -
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ARG 4.7 2.2 - - - +
251A VAL* 4.3 28.3 - - + +
254A GLY* 3.9 40.7 - - - +
255A ILE* 4.1 11.0 - - + +
258A VAL* 4.4 10.3 - - + -
292A VAL 3.6 7.3 + - - +
293A PHE* 3.2 17.6 + - + +
294A LEU 3.2 0.2 - - - -
295A ALA* 1.3 76.1 - - - +
297A LEU* 1.4 62.5 + - + +
299A TYR* 3.1 9.3 + - + -
300A ALA* 2.9 28.2 + - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.0 48.3 + - + +
294A LEU* 3.5 25.4 - - + +
296A LEU* 1.4 74.0 - - + +
298A GLU* 1.4 55.2 + - - +
300A ALA* 3.2 12.3 + - + +
301A PHE* 2.8 36.1 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 3.6 13.6 - - + -
250A ARG* 3.3 17.8 + - - -
294A LEU 2.6 20.2 + - - +
295A ALA* 3.4 10.7 - - - +
296A LEU 3.2 0.2 - - - -
297A LEU* 1.4 71.8 - - - +
299A TYR* 1.4 59.9 + - - +
301A PHE* 3.2 8.2 + - - +
302A VAL* 2.9 29.8 + - - +
423A ILE* 3.5 18.3 - - + +
424A ASP* 2.7 30.6 - - - +
427A SER* 3.3 27.8 + - - +
431A PHE* 4.6 6.7 - - + -
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER* 4.7 3.1 - - - +
244A TYR* 2.7 36.9 + - + -
246A ALA 4.3 0.4 - - - -
247A SER* 3.1 34.6 - - - -
250A ARG* 3.3 48.2 - - + +
251A VAL* 3.8 22.7 - - + -
295A ALA 3.1 8.0 + - - +
296A LEU* 3.1 13.8 + - + +
298A GLU* 1.4 80.0 + - - +
300A ALA* 1.3 59.0 + - - +
302A VAL* 3.3 4.9 + - + -
303A ASN* 2.7 72.1 + - + +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 2.9 15.6 + - + +
297A LEU* 3.4 19.5 - - + +
299A TYR* 1.3 77.1 - - - +
301A PHE* 1.3 57.5 + - - +
303A ASN* 3.4 6.1 + - - +
304A TYR* 2.9 32.0 + - - +
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Residues in contact with PHE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU 2.8 19.7 + - - +
298A GLU* 3.5 7.0 - - - +
300A ALA* 1.3 73.2 - - - +
302A VAL* 1.4 61.6 + - - +
304A TYR* 3.2 17.0 + + - +
305A ILE* 3.0 47.5 + - + +
312A ARG* 6.6 0.2 - - - -
423A ILE* 3.4 39.0 - - + -
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 3.6 41.1 - - + -
298A GLU* 2.9 42.0 + - - +
299A TYR* 3.8 9.6 - - + +
301A PHE* 1.4 69.5 - - - +
303A ASN* 1.3 60.1 + - - +
305A ILE* 3.1 8.3 + - - +
306A PHE* 2.9 30.7 + - - -
313A ALA* 3.9 15.9 - - + +
423A ILE* 3.8 20.6 - - + -
424A ASP* 3.9 12.3 - - - +
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 4.2 10.9 - - - -
299A TYR* 2.7 57.9 + - + +
300A ALA* 3.6 6.7 - - - +
302A VAL* 1.3 73.7 - - - +
304A TYR* 1.3 60.9 + - - +
305A ILE 3.6 0.3 + - - -
306A PHE* 3.7 29.7 + - - -
307A PHE 5.4 0.9 + - - -
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Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 2.9 18.3 + - - +
301A PHE* 3.4 16.4 - + - +
303A ASN* 1.3 79.1 + - - +
305A ILE* 1.4 71.8 + - + +
307A PHE 5.5 0.6 + - - -
308A SER* 5.2 1.4 + - - -
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.0 42.4 + - + +
302A VAL* 3.1 8.3 + - - +
304A TYR* 1.4 96.4 - - + +
306A PHE* 1.4 61.5 + - - +
307A PHE 3.2 3.4 + - - -
308A SER* 3.5 8.3 + - - -
309A GLN* 2.9 52.1 + - + +
312A ARG* 3.9 14.1 - - + -
313A ALA* 3.4 33.4 - - + +
423A ILE* 4.1 10.5 - - + -
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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