Contacts of the helix formed by residues 263 - 285 (chain J) in PDB entry 6C6U
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 263 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250J ARG* 5.0 6.6 - - - -
251J PRO* 3.9 23.9 + - - +
252J LEU* 4.7 0.4 - - - +
253J VAL* 5.6 2.5 - - - +
261J ALA 3.9 0.2 + - - -
262J THR* 1.3 97.0 + - - +
264J ASP* 1.3 72.0 + - - +
265J LEU* 3.2 16.9 + - - +
266J ASN* 3.6 14.1 + - - +
267J ASP* 3.7 2.9 + - - +
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Residues in contact with ASP 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J THR 4.5 4.3 - - - +
263J SER* 1.3 78.4 + - - +
265J LEU* 1.3 59.8 + - - +
267J ASP* 3.3 9.2 + - - +
268J LEU* 3.0 30.1 + - - +
322J ARG* 5.6 8.0 + - - -
324J LEU* 3.5 27.1 - - + +
325J LYS* 3.0 47.8 + - + +
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Residues in contact with LEU 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245J LEU* 3.7 24.5 - - + -
249J LEU 4.7 0.2 - - - +
250J ARG* 3.9 23.1 - - + -
263J SER* 3.2 8.6 - - - +
264J ASP* 1.3 75.6 - - + +
266J ASN* 1.3 60.6 + - - +
268J LEU* 3.2 8.3 + - + +
269J TYR* 2.9 47.5 + - + -
306J LEU* 5.8 1.1 - - + +
325J LYS* 4.1 15.0 - - + +
326J SER* 4.3 5.6 - - - -
327J LEU* 3.8 25.6 - - + -
330J MET* 3.6 33.2 - - + -
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Residues in contact with ASN 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J THR* 5.1 6.4 - - + +
56J LEU* 3.7 22.1 - - + +
57J PHE* 3.7 23.5 - - + -
250J ARG* 3.3 47.6 + - - -
251J PRO 4.6 0.2 + - - -
252J LEU* 4.2 6.2 - - + +
262J THR* 3.6 23.1 + - - +
263J SER* 3.6 8.1 + - - -
264J ASP 3.4 0.6 - - - -
265J LEU* 1.3 75.4 - - - +
267J ASP* 1.3 57.2 + - - +
269J TYR* 4.6 0.2 - - - -
270J ARG* 2.9 32.4 + - - +
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Residues in contact with ASP 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A G 5.2 1.4 - - - +
24B C 5.2 6.1 + - - -
262J THR* 4.8 11.6 + - + +
263J SER 3.7 6.7 + - - +
264J ASP* 3.3 15.0 + - - +
265J LEU 3.2 0.2 - - - -
266J ASN* 1.3 78.6 - - - +
268J LEU* 1.3 58.0 + - - +
270J ARG* 3.4 30.9 + - - +
271J ARG* 3.0 45.2 + - - +
318J GLY* 4.8 6.4 - - - -
324J LEU* 3.7 23.3 - - + +
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Residues in contact with LEU 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ASP 3.0 13.4 + - - +
265J LEU* 3.2 11.4 + - + +
267J ASP* 1.3 77.4 - - - +
269J TYR* 1.3 62.6 + - + +
271J ARG* 3.2 10.8 + - + +
272J VAL* 3.0 26.9 + - - +
302J ALA 5.3 1.1 - - - +
305J ALA* 4.0 25.4 - - + +
306J LEU* 4.0 20.9 - - + +
316J ILE* 3.7 29.8 - - + -
324J LEU* 3.7 11.2 - - + -
325J LYS 3.4 26.0 - - - +
326J SER* 3.9 14.4 - - - +
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Residues in contact with TYR 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1332I SER* 4.5 3.1 + - - -
56J LEU* 3.8 19.5 - - + -
105J ILE* 4.3 10.1 - - + -
242J LEU* 4.2 5.2 - - + -
243J PRO 3.5 23.1 + - - -
244J VAL* 3.6 25.3 - - + -
245J LEU* 3.5 26.5 + - + +
250J ARG* 4.2 15.0 - - - -
265J LEU* 2.9 46.3 + - + +
268J LEU* 1.3 76.0 - - + +
270J ARG* 1.3 57.4 + - - +
272J VAL* 3.3 2.5 + - - +
273J ILE* 2.9 38.2 + - + +
306J LEU* 3.8 27.4 - - + +
327J LEU* 4.1 18.5 - - + +
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Residues in contact with ARG 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A C 6.1 1.6 - - - -
5A T 3.6 30.2 + - - +
6A G 4.3 1.6 + - - -
24B C 3.8 17.0 - - - +
41J PRO* 3.6 37.9 - - + +
43J THR* 5.4 7.0 - - - +
56J LEU* 4.5 6.5 - - + +
266J ASN 2.9 20.8 + - - +
267J ASP* 3.4 28.1 + - - +
268J LEU 3.2 0.2 - - - -
269J TYR* 1.3 76.0 - - - +
271J ARG* 1.3 58.0 + - - +
273J ILE 3.9 0.2 - - - -
274J ASN* 2.9 44.5 + - - +
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Residues in contact with ARG 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A G 4.4 26.4 + - - -
267J ASP* 3.0 33.5 + - - +
268J LEU* 3.5 13.0 - - + +
270J ARG* 1.3 74.9 - - - +
272J VAL* 1.3 63.4 + - + +
274J ASN* 3.5 8.3 + - + +
275J ARG* 3.0 30.7 + - + +
302J ALA* 4.5 18.6 - - + +
305J ALA* 5.7 1.5 - - - +
316J ILE* 3.3 47.1 - - - +
317J THR 4.8 10.3 + - - -
324J LEU* 5.4 0.6 - - - +
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Residues in contact with VAL 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J ILE* 4.7 16.4 - - + -
107J LEU* 4.6 16.2 - - + -
242J LEU* 5.2 3.8 - - + -
268J LEU 3.0 16.3 + - - +
269J TYR* 3.3 5.6 + - - +
271J ARG* 1.3 74.6 - - - +
273J ILE* 1.3 59.0 + - + +
275J ARG* 3.4 2.5 + - - +
276J ASN* 2.9 33.2 + - + +
299J LEU* 5.2 3.8 - - + +
302J ALA* 3.8 33.9 - - + +
303J VAL* 4.2 20.0 - - + +
306J LEU* 3.7 20.6 - - + -
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Residues in contact with ILE 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J VAL* 3.6 27.1 - - + +
39J LYS* 3.9 8.5 - - - +
40J LYS 3.7 20.4 - - - +
41J PRO* 3.9 4.7 - - + -
56J LEU* 3.7 19.7 - - + -
105J ILE* 4.0 30.1 - - + -
269J TYR* 2.9 21.9 + - + +
270J ARG 4.1 2.5 - - - +
272J VAL* 1.3 75.5 - - - +
274J ASN* 1.3 64.9 + - - +
276J ASN* 4.0 4.8 - - + +
277J ASN* 3.0 48.8 + - - +
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Residues in contact with ASN 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A C 5.6 10.9 + - - +
5A T 5.6 11.3 + - - +
41J PRO* 3.3 21.1 - - - +
270J ARG* 2.9 42.8 + - - +
271J ARG* 3.7 7.5 - - + +
273J ILE* 1.3 77.4 - - - +
275J ARG* 1.3 62.8 + - - +
277J ASN* 3.9 4.8 - - - +
278J ARG* 3.0 36.9 + - - +
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Residues in contact with ARG 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A G 4.1 21.0 + - - -
271J ARG* 3.0 23.8 + - + +
272J VAL* 4.0 4.5 - - - +
274J ASN* 1.3 76.7 - - - +
276J ASN* 1.3 57.5 + - - +
278J ARG* 3.4 33.9 + - - +
279J LEU* 3.0 27.2 + - - +
295J GLU* 3.3 32.6 + - - +
298J MET* 3.5 40.8 + - - +
299J LEU* 3.8 31.9 - - + +
302J ALA* 5.0 4.7 - - + -
13N GLN* 6.2 0.4 - - - +
68N TYR* 5.6 1.4 + - - -
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Residues in contact with ASN 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J ILE* 3.6 19.8 - - - +
106J GLU 3.2 23.1 + - - +
107J LEU* 3.6 13.6 - - + +
108J ALA* 3.2 27.4 + - - +
272J VAL* 2.9 20.7 + - + +
273J ILE* 4.0 4.9 - - + +
275J ARG* 1.3 75.4 - - - +
277J ASN* 1.3 62.4 + - - +
279J LEU* 3.2 1.0 + - - -
280J LYS* 2.9 31.7 + - - +
299J LEU* 3.7 19.2 - - + +
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Residues in contact with ASN 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39J LYS* 3.0 29.4 + - - +
40J LYS* 4.3 0.4 - - - +
41J PRO* 4.1 10.3 - - - +
273J ILE* 3.0 33.7 + - - +
274J ASN* 3.9 3.8 - - - +
276J ASN* 1.3 77.1 - - - +
278J ARG* 1.3 59.8 + - + +
280J LYS* 3.3 19.1 + - - +
281J ARG* 3.0 28.6 + - - +
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Residues in contact with ARG 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A T 3.9 25.3 + - - -
6A G 4.9 6.7 + - - -
274J ASN* 3.0 27.3 + - - +
275J ARG* 3.4 38.2 - - - +
277J ASN* 1.3 76.3 - - + +
279J LEU* 1.3 58.8 + - - +
281J ARG* 3.4 22.1 + - - +
282J LEU* 2.9 32.6 + - - +
295J GLU* 3.7 18.4 + - - +
16N SER* 5.0 5.6 + - - -
66N PRO* 2.8 48.9 + - + +
68N TYR* 5.3 3.6 - - - -
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Residues in contact with LEU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ALA* 3.7 15.3 - - + -
109J SER* 4.6 7.0 - - - +
275J ARG 3.0 15.6 + - - +
276J ASN* 3.2 7.2 + - - +
278J ARG* 1.3 75.7 - - - +
280J LYS* 1.3 59.8 + - - +
282J LEU* 3.8 2.5 - - + +
283J LEU* 2.9 50.9 + - + +
292J VAL* 5.2 3.4 - - + +
295J GLU* 3.5 47.7 - - + +
296J LYS* 3.6 25.4 - - + +
299J LEU* 3.8 16.2 - - + -
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Residues in contact with LYS 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J GLU* 3.9 19.2 + - - -
39J LYS* 5.6 4.9 - - - +
106J GLU* 3.8 24.5 + - - +
108J ALA* 3.7 19.5 - - + +
276J ASN* 2.9 26.2 + - - +
277J ASN* 3.3 18.4 + - - +
279J LEU* 1.3 76.6 - - - +
281J ARG* 1.3 58.3 + - - +
283J LEU* 3.4 4.8 + - - +
284J ASP* 2.9 28.8 + - - +
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Residues in contact with ARG 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ASN 3.0 16.9 + - - +
278J ARG* 3.9 17.9 + - - +
279J LEU 3.3 0.4 - - - -
280J LYS* 1.3 77.4 - - - +
282J LEU* 1.3 66.6 + - + +
284J ASP* 3.2 6.9 + - - +
285J LEU* 3.2 40.4 + - + +
63N LYS 4.4 13.2 + - - +
64N PHE* 5.3 6.1 - - - +
66N PRO* 3.4 42.4 - - - +
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Residues in contact with LEU 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J ARG 2.9 20.9 + - - +
279J LEU* 4.0 4.9 - - - +
281J ARG* 1.3 81.3 - - + +
283J LEU* 1.3 62.3 + - - +
284J ASP 3.6 0.2 + - - -
285J LEU* 4.0 3.0 + - + -
286J ALA 3.8 1.4 + - - -
287J ALA* 3.2 48.0 + - + +
291J ILE* 4.2 17.3 - - + +
292J VAL* 4.0 11.2 - - + +
295J GLU* 3.7 31.2 - - + +
64N PHE* 5.3 4.3 - - + -
65N PHE* 4.1 22.9 - - + -
66N PRO* 4.2 24.7 - - + -
68N TYR* 5.2 0.7 - - + -
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Residues in contact with LEU 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ALA* 4.4 18.8 - - + +
279J LEU* 2.9 40.4 + - + +
280J LYS* 4.0 4.7 - - - +
282J LEU* 1.3 74.8 - - - +
284J ASP* 1.3 64.1 + - - +
286J ALA* 4.1 6.3 + - - +
292J VAL* 4.0 27.1 - - + -
296J LYS* 4.8 14.1 - - - +
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Residues in contact with ASP 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280J LYS 2.9 17.8 + - - +
281J ARG* 3.4 9.8 - - - +
282J LEU 3.2 0.6 - - - -
283J LEU* 1.3 81.3 - - - +
285J LEU* 1.3 71.9 - - + +
286J ALA* 3.2 6.6 + - - +
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Residues in contact with LEU 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J ARG* 3.2 31.2 + - + +
282J LEU* 4.0 3.1 + - + +
283J LEU 3.6 0.2 - - - -
284J ASP* 1.3 92.9 - - + +
286J ALA* 1.3 65.0 + - - +
287J ALA* 3.6 2.2 - - - -
47N GLU* 4.9 7.9 - - - +
64N PHE* 4.5 31.2 - - + -
65N PHE* 5.9 2.9 - - + -
114N ARG* 3.2 38.2 + - - +
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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