Contacts of the helix formed by residues 279 - 301 (chain A) in PDB entry 4UQJ
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 LYS 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLN* 3.4 20.9 + - - +
25A GLU* 5.0 2.0 - - - +
229A ASP* 3.2 18.1 - - + +
278A ILE* 1.3 78.4 - - - +
280A TYR* 1.3 61.9 + - + +
281A THR* 3.8 17.3 - - - +
282A SER* 2.9 5.3 + - - +
283A ALA* 2.9 23.9 + - - +
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Residues in contact with TYR 280 (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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99A PRO 5.4 2.2 - - - -
114A ARG* 5.4 4.3 - - + -
141A ARG* 4.9 13.5 - - - -
197A GLU* 6.1 1.6 - - - -
198A ARG* 6.0 6.7 - - + -
224A ASN* 4.8 13.6 - - + +
225A LEU* 3.7 40.6 - - + +
226A GLY* 3.6 17.3 - - - -
229A ASP* 2.9 22.8 + - + +
246A GLN* 5.9 0.4 - - - +
247A ILE* 3.5 24.4 - - + +
248A VAL* 4.2 13.7 - - + -
278A ILE 3.5 1.2 + - - -
279A LYS* 1.3 72.4 - - + +
281A THR* 1.3 81.0 + - + +
283A ALA* 3.7 0.9 - - - +
284A LEU* 3.0 46.1 + - + +
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.8 30.7 + - - +
76A PHE* 5.2 8.3 - - + -
99A PRO* 3.9 11.3 - - + +
100A SER* 6.5 0.2 - - - -
279A LYS* 3.8 10.3 - - + +
280A TYR* 1.3 110.8 - - + +
282A SER* 1.3 59.1 + - - +
284A LEU* 3.5 7.9 + - - +
285A THR* 3.0 25.0 + - - -
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.3 38.8 + - - +
25A GLU* 3.3 23.3 + - - +
28A ALA* 3.4 8.2 - - - +
278A ILE* 3.6 19.5 - - - -
279A LYS* 2.9 8.9 + - - +
281A THR* 1.3 78.5 + - - +
283A ALA* 1.3 63.5 + - - +
285A THR* 3.1 18.2 + - - -
286A TYR 3.1 10.0 + - - -
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Residues in contact with ALA 283 (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 ILE* 6.0 0.2 - - + -
248A VAL* 3.6 30.7 - - + -
278A ILE* 3.6 15.6 - - + +
279A LYS 2.9 12.3 + - - +
280A TYR 3.7 3.4 - - - +
282A SER* 1.3 76.6 - - - +
284A LEU* 1.3 58.4 + - + +
286A TYR* 3.4 3.8 + - - +
287A ASP* 3.1 32.7 + - - +
341A LEU* 4.0 24.5 - - + +
342A SER* 5.5 0.9 - - - +
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Residues in contact with LEU 284 (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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99A PRO* 3.7 27.4 - - + +
113A MET* 3.3 29.2 - - + +
114A ARG* 3.6 32.1 - - + +
115A PRO* 4.8 3.6 - - + -
225A LEU* 5.3 0.9 - - + -
247A ILE* 5.4 3.6 - - + -
280A TYR* 3.0 39.0 + - + +
281A THR* 3.8 0.9 - - - +
283A ALA* 1.3 74.5 - - + +
285A THR* 1.3 55.8 + - - +
287A ASP* 3.2 5.5 + - + +
288A ALA* 2.8 34.4 + - - +
342A SER* 3.5 33.4 - - - +
353A ARG* 3.9 1.6 - - - +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.4 0.7 - - + -
25A GLU* 3.3 27.9 + - - +
28A ALA* 4.6 0.4 - - - -
29A PHE* 3.6 21.8 - - + -
74A PHE* 3.4 27.7 - - + -
76A PHE* 3.7 8.7 - - - -
99A PRO* 3.7 11.2 - - - +
281A THR 3.0 14.9 + - - -
282A SER* 3.1 10.8 + - - -
284A LEU* 1.3 79.8 - - - +
286A TYR* 1.3 61.7 + - - +
288A ALA* 3.1 16.6 + - - +
289A VAL* 3.3 10.9 + - - +
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Residues in contact with TYR 286 (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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28A ALA* 3.9 18.8 + - + +
31A VAL* 4.2 7.6 - - + -
32A GLY* 3.7 25.4 - - - -
35A GLN* 3.3 26.2 - - + +
36A PHE* 3.4 30.9 - + - -
254A LEU* 5.8 4.4 - - + +
258A PHE* 3.4 34.8 - + + -
282A SER 3.1 9.0 + - - +
283A ALA 3.6 7.2 - - - +
285A THR* 1.3 79.4 - - - +
287A ASP* 1.3 79.9 + - - +
288A ALA 3.3 0.3 + - - -
289A VAL* 3.3 15.8 + - - +
290A GLN* 3.5 8.7 + - - -
340A GLY* 5.8 0.7 - - - -
341A LEU* 3.7 25.1 - - + -
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Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 4.3 4.0 - - - -
283A ALA 3.1 17.9 + - - +
284A LEU* 3.7 7.4 - - + +
286A TYR* 1.3 87.4 - - - +
288A ALA* 1.3 63.6 + - - +
290A GLN* 3.4 9.7 + - - +
291A VAL* 3.1 28.3 + - - +
340A GLY* 3.3 12.3 - - - -
341A LEU* 2.8 21.7 + - - -
342A SER* 2.9 38.1 + - - +
345A ILE* 3.7 16.0 - - + +
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Residues in contact with ALA 288 (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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74A PHE* 3.4 32.8 - - + -
97A ILE* 3.9 6.0 - - + +
113A MET* 3.7 19.5 - - + -
284A LEU 2.8 13.9 + - - +
285A THR 3.1 11.4 + - - +
287A ASP* 1.3 75.5 - - - +
289A VAL* 1.3 65.2 + - + +
291A VAL* 3.1 4.7 + - - +
292A MET* 3.0 28.7 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 43.1 - - + +
32A GLY* 3.4 32.3 - - - +
33A MET* 3.8 15.9 - - - +
36A PHE* 4.1 4.3 - - + -
43A LEU* 4.9 4.6 - - + +
285A THR 3.3 13.6 + - - +
286A TYR* 3.6 8.3 - - - +
287A ASP 3.3 0.2 - - - -
288A ALA* 1.3 78.2 - - - +
290A GLN* 1.3 56.8 + - - +
292A MET* 3.3 10.7 + - - +
293A THR* 3.0 38.8 + - - +
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Residues in contact with GLN 290 (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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36A PHE* 3.4 49.8 - - + -
286A TYR* 3.5 5.0 + - - +
287A ASP* 3.4 14.4 + - - +
288A ALA 3.2 0.6 - - - -
289A VAL* 1.3 78.8 - - - +
291A VAL* 1.3 57.6 + - - +
293A THR* 3.4 2.8 + - - -
294A GLU* 3.0 27.7 + - - +
338A VAL* 3.4 35.5 - - + +
339A GLU 3.2 26.7 + - - +
340A GLY* 4.0 9.7 - - - -
345A ILE* 5.3 0.2 - - - +
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Residues in contact with VAL 291 (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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97A ILE* 5.8 1.8 - - + -
111A ILE* 5.0 3.1 - - + -
113A MET* 4.3 14.6 - - + -
287A ASP 3.1 16.8 - - - +
288A ALA* 3.1 8.2 + - - +
290A GLN* 1.3 78.2 - - - +
292A MET* 1.3 58.1 + - + +
294A GLU 3.5 0.3 + - - -
295A ALA* 3.0 27.5 + - - +
333A LEU* 4.2 20.0 - - + +
336A VAL* 3.5 32.5 - - + +
338A VAL* 4.7 3.6 - - + -
345A ILE* 4.2 28.3 - - + -
347A PHE* 4.2 10.1 - - + -
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Residues in contact with MET 292 (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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14A ILE* 3.7 43.3 - - + -
29A PHE* 5.4 4.5 - - - -
43A LEU* 4.5 12.6 - - + +
72A ALA* 4.1 19.5 - - + -
74A PHE* 4.1 26.2 - - + -
97A ILE* 4.3 26.7 - - + -
288A ALA 3.0 20.3 + - - +
289A VAL* 3.3 8.5 + - - +
291A VAL* 1.3 75.5 - - + +
293A THR* 1.3 61.6 + - - +
295A ALA* 3.7 1.2 - - - +
296A PHE* 3.1 24.9 + - - +
333A LEU* 4.0 11.9 - - + -
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Residues in contact with THR 293 (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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36A PHE* 3.7 38.3 + - + +
38A THR* 5.4 4.3 - - + -
41A PHE* 3.5 24.3 - - + -
43A LEU* 4.2 14.9 - - + +
289A VAL* 3.0 19.5 + - - +
290A GLN* 3.7 6.1 - - - -
292A MET* 1.3 75.5 - - - +
294A GLU* 1.3 61.6 + - - +
296A PHE 3.3 1.4 + - - -
297A ARG* 3.0 31.0 + - + +
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Residues in contact with GLU 294 (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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290A GLN* 3.0 17.6 + - + +
293A THR* 1.3 79.2 - - - +
295A ALA* 1.3 57.3 + - - +
297A ARG* 3.7 7.4 - - - +
298A ASN* 3.1 60.3 + - - +
336A VAL* 3.9 20.0 - - + -
337A GLN 5.1 0.9 - - - +
338A VAL* 3.9 27.7 - - + +
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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
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291A VAL 3.0 19.3 + - - +
292A MET 3.7 3.4 - - - +
293A THR 3.1 0.2 - - - -
294A GLU* 1.3 74.8 - - - +
296A PHE* 1.3 64.0 + - - +
297A ARG 3.1 2.2 + - - -
298A ASN* 3.3 12.0 + - - +
299A LEU* 3.4 21.3 + - - +
332A ALA* 3.9 6.9 - - + +
333A LEU* 3.5 35.4 - - + +
336A VAL* 3.6 14.8 - - + +
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Residues in contact with PHE 296 (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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12A ILE* 3.6 32.5 - - + +
41A PHE* 4.1 13.2 - - + -
43A LEU* 5.6 1.8 - - + -
292A MET 3.1 14.4 + - - +
293A THR 4.0 2.9 - - - +
295A ALA* 1.3 78.3 - - - +
297A ARG* 1.3 59.6 + - - +
299A LEU* 3.6 13.7 + - + +
300A ARG* 3.5 17.7 + - - +
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Residues in contact with ARG 297 (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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41A PHE* 3.7 21.3 - - + -
293A THR* 3.0 19.7 + - + +
294A GLU* 3.7 13.0 - - - +
296A PHE* 1.3 75.3 - - - +
298A ASN* 1.3 63.8 + - - +
299A LEU 3.1 5.2 - - - -
300A ARG* 3.3 4.9 + - - +
301A LYS* 3.2 23.9 + - - +
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Residues in contact with ASN 298 (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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294A GLU* 3.1 47.9 + - - +
295A ALA* 3.3 7.4 + - - +
297A ARG* 1.3 78.4 - - - +
299A LEU* 1.3 63.2 + - + +
300A ARG 3.5 0.2 - - - -
301A LYS* 4.2 6.9 - - - +
302A GLN* 3.0 25.3 + - - +
332A ALA* 5.3 4.9 + - + +
335A GLN* 5.4 4.8 + - - +
336A VAL* 5.0 10.9 - - - +
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Residues in contact with LEU 299 (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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295A ALA 3.4 11.2 + - - +
296A PHE* 3.8 15.3 - - - +
297A ARG 3.1 0.4 - - - -
298A ASN* 1.3 86.1 - - + +
300A ARG* 1.3 61.4 + - - +
301A LYS 3.4 0.4 - - - -
302A GLN* 3.5 2.6 + - - -
303A ARG 3.4 2.4 + - - -
304A ILE* 3.1 61.5 + - + +
306A ILE* 3.9 29.8 - - + -
328A GLU* 4.6 5.8 - - + +
329A ILE* 4.5 14.8 - - + +
332A ALA* 3.4 32.5 - - + -
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Residues in contact with ARG 300 (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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10A ASN* 5.8 3.6 - - - +
41A PHE* 5.4 8.7 - - + -
296A PHE 3.5 9.8 + - - +
297A ARG* 3.3 11.0 + - - +
299A LEU* 1.3 80.0 - - - +
301A LYS* 1.3 59.5 + - - +
302A GLN 3.1 0.9 - - - -
303A ARG* 3.3 13.0 + - - -
304A ILE 5.2 0.7 - - - +
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Residues in contact with LYS 301 (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 ARG 3.2 13.1 + - - +
298A ASN* 4.7 6.3 - - - +
300A ARG* 1.3 78.9 - - - +
302A GLN* 1.3 58.1 + - - +
303A ARG* 3.3 2.4 + - - +
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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