Contacts of the helix formed by residues 276 - 297 (chain A) in PDB entry 3P3W
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 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASN* 4.2 25.6 + - - +
17A VAL* 5.6 1.8 - - - +
18A GLN* 3.0 34.1 + - + +
19A GLU* 4.2 17.6 + - - +
226A ASP* 3.5 22.9 - - - +
269A GLU* 5.0 7.5 + - - +
273A ALA* 5.1 9.4 - - - -
274A PRO 4.0 7.2 - - - +
275A LEU* 1.3 77.2 - - - +
277A TYR* 1.3 62.6 + - + +
278A THR* 3.9 9.4 - - - +
279A SER* 2.9 24.8 + - - +
280A ALA 3.2 8.1 + - - -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 3.1 43.9 + - - -
194A GLU* 3.9 11.4 + - - -
195A VAL* 4.2 10.5 - - + -
221A ASN* 4.1 9.8 + - - -
222A LEU* 3.7 38.2 + - + +
223A GLY* 3.4 31.6 - - - -
225A THR* 5.7 0.8 + - - -
226A ASP* 4.0 6.0 + - - -
244A ILE* 4.9 7.3 - - + +
245A VAL* 4.8 13.0 - - + -
275A LEU* 3.9 9.4 + - - +
276A LYS* 1.3 74.0 - - + +
278A THR* 1.3 76.2 + - + +
280A ALA* 3.3 6.9 + - - +
281A LEU* 3.1 41.3 + - + +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 2.7 31.9 + - - +
76A PHE* 4.7 11.2 - - + -
99A PRO* 4.2 11.6 - - + +
114A ARG* 3.8 17.0 - - - +
276A LYS* 3.9 8.7 - - - +
277A TYR* 1.3 105.4 - - + +
279A SER* 1.3 52.4 + - - +
281A LEU* 3.3 9.5 + - - +
282A THR* 2.7 36.3 + - - -
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 2.8 25.9 + - - -
19A GLU* 3.4 27.3 + - - +
22A ALA* 3.3 30.7 - - - +
255A PHE* 6.1 0.3 - - - -
259A TRP* 5.5 0.4 - - - -
275A LEU* 3.8 11.0 - - - -
276A LYS* 2.9 12.5 + - - +
278A THR* 1.3 76.0 + - - +
280A ALA* 1.3 63.6 + - - +
282A THR* 3.3 14.0 - - - -
283A HIS* 3.3 6.1 + - - +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 4.2 17.0 - - + -
255A PHE* 6.3 0.9 - - - -
275A LEU* 3.7 26.4 - - + +
276A LYS 3.2 2.8 + - - -
277A TYR 3.3 9.4 + - - +
279A SER* 1.3 78.4 - - - +
281A LEU* 1.3 58.0 + - - +
283A HIS* 3.5 8.0 + - - +
284A ASP* 2.9 32.9 + - - +
338A MET* 4.2 18.6 - - + +
339A THR* 4.6 6.1 - - + -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PRO* 3.8 31.2 - - + +
113A MET* 3.6 34.7 - - + +
114A ARG* 4.4 9.9 - - + -
115A PRO* 4.5 0.2 - - + -
244A ILE* 3.4 27.1 - - + -
277A TYR* 3.1 42.6 + - + +
278A THR* 3.6 8.5 - - - +
279A SER 3.3 0.2 - - - -
280A ALA* 1.3 73.4 - - - +
282A THR* 1.3 56.3 + - - +
284A ASP* 3.6 4.2 - - - -
285A ALA* 2.8 35.7 + - - +
339A THR* 3.8 13.7 - - + +
350A ARG* 4.5 1.3 - - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.4 35.6 - - - +
22A ALA* 4.2 1.1 - - - -
23A PHE* 3.8 20.6 - - + +
74A PHE* 3.6 36.8 - - + -
76A PHE* 4.2 2.6 - - - -
99A PRO* 4.2 0.6 - - - +
278A THR 2.7 22.3 + - - -
279A SER* 3.3 12.8 - - - -
280A ALA 3.3 0.2 - - - -
281A LEU* 1.3 77.0 - - - +
283A HIS* 1.3 61.3 + - - +
285A ALA* 3.3 15.4 + - - +
286A ILE* 3.4 12.9 + - - +
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Residues in contact with HIS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 4.4 5.8 + - + +
26A ALA* 4.1 20.0 - - + -
29A LEU* 4.2 22.6 - - + +
251A MET* 6.3 2.2 - - + -
255A PHE* 4.1 27.8 - + + -
279A SER 3.3 8.8 + - - +
280A ALA* 3.6 7.4 - - - +
281A LEU 3.3 0.2 - - - -
282A THR* 1.3 79.8 - - - +
284A ASP* 1.3 64.0 + - - +
286A ILE* 3.1 21.7 + - + +
287A LEU* 3.3 43.0 + - + +
338A MET* 3.3 35.4 - - + -
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Residues in contact with ASP 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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113A MET* 3.6 18.1 - - + +
280A ALA 2.9 18.6 + - - +
281A LEU* 3.3 2.0 + - - +
283A HIS* 1.3 81.4 + - - +
285A ALA* 1.3 62.2 + - - +
286A ILE 3.3 0.2 - - - -
287A LEU* 3.3 24.6 + - - +
288A VAL* 3.3 26.3 + - - +
337A GLY* 3.6 2.6 - - - -
338A MET* 3.1 26.6 + - - +
339A THR* 3.1 36.5 + - - +
342A ILE* 4.0 6.5 - - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 3.5 28.3 - - + -
97A VAL* 3.8 16.0 - - + +
113A MET* 3.7 15.5 - - + -
281A LEU 2.8 17.3 + - - +
282A THR 3.3 7.4 - - - +
283A HIS 3.2 0.2 - - - -
284A ASP* 1.3 75.6 - - - +
286A ILE* 1.3 63.5 + - + +
288A VAL* 3.4 4.5 + - - +
289A ILE* 3.2 28.2 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 5.0 3.6 - - + -
23A PHE* 3.7 36.6 - - + +
26A ALA* 3.4 43.3 - - + +
27A VAL* 4.9 7.2 - - + -
29A LEU* 5.9 2.2 - - + -
30A TYR* 5.6 3.4 - - + -
43A LEU* 4.9 16.1 - - + +
74A PHE* 5.4 1.3 - - + -
282A THR 3.4 20.3 + - - +
283A HIS* 3.1 10.2 + - + +
285A ALA* 1.3 79.6 - - + +
287A LEU* 1.3 61.7 + - + +
289A ILE* 3.2 15.7 + - + +
290A ALA* 2.8 38.4 + - + +
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Residues in contact with LEU 287 (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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29A LEU* 5.4 9.2 - - + -
251A MET* 5.7 4.0 - - - -
283A HIS* 3.3 34.0 + - + +
284A ASP* 3.3 33.4 - - - +
285A ALA 3.3 0.4 - - - -
286A ILE* 1.3 80.0 - - + +
288A VAL* 1.3 60.9 + - - +
290A ALA* 4.0 4.8 - - + +
291A GLU* 3.2 24.8 + - - +
294A ARG* 4.2 8.3 + - - +
335A VAL* 4.1 21.7 - - + +
336A GLN 5.4 0.2 - - - +
337A GLY* 4.1 16.4 - - - -
342A ILE* 4.9 2.5 - - + -
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 5.9 2.0 - - + -
111A ILE* 5.2 4.9 - - + -
113A MET* 4.2 5.6 - - - -
284A ASP 3.3 14.5 + - - +
285A ALA* 3.6 7.6 - - - +
286A ILE 3.2 0.6 - - - -
287A LEU* 1.3 75.4 - - - +
289A ILE* 1.3 61.8 + - + +
291A GLU* 3.3 5.6 + - - +
292A ALA* 2.9 28.8 + - - +
330A LEU* 3.7 22.4 - - + +
333A VAL* 3.7 25.5 - - + +
335A VAL* 4.8 2.9 - - + -
342A ILE* 3.8 30.7 - - + -
344A PHE* 3.8 15.9 - - + -
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Residues in contact with ILE 289 (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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6A ILE* 5.9 0.4 - - + -
8A ILE* 4.3 36.1 - - + -
43A LEU* 5.3 9.6 - - + -
72A ALA* 4.7 7.2 - - + -
74A PHE* 4.9 9.2 - - + +
97A VAL* 4.0 30.7 - - + -
285A ALA* 3.3 21.1 - - + +
286A ILE* 3.2 13.4 + - + +
288A VAL* 1.3 74.6 - - + +
290A ALA* 1.3 63.7 + - - +
292A ALA* 3.4 0.5 + - - +
293A PHE* 3.2 51.8 + - + +
330A LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 4.7 16.6 - - + -
41A PHE* 4.2 9.9 - - - -
43A LEU* 5.8 5.1 - - + +
286A ILE* 2.8 27.3 + - + +
287A LEU* 4.0 5.4 - - + +
289A ILE* 1.3 75.4 - - - +
291A GLU* 1.3 57.6 + - - +
293A PHE* 4.0 1.6 - - - +
294A ARG* 3.1 57.4 + - - +
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Residues in contact with GLU 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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287A LEU 3.2 18.8 + - - +
288A VAL 3.3 3.5 + - - +
290A ALA* 1.3 77.1 - - - +
292A ALA* 1.3 63.2 + - - +
294A ARG* 3.3 23.1 + - - +
295A TYR* 3.3 20.8 + - - +
298A ARG* 3.6 24.3 + - - -
333A VAL* 4.1 13.8 - - + +
334A GLN 5.5 1.1 - - - +
335A VAL* 3.8 27.4 - - + +
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Residues in contact with ALA 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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288A VAL 2.9 16.7 + - - +
289A ILE 3.8 3.1 - - - +
290A ALA 3.3 0.2 - - - -
291A GLU* 1.3 78.1 - - - +
293A PHE* 1.3 61.2 + - + +
295A TYR* 3.3 6.6 + - - +
296A LEU* 3.0 32.5 + - + +
329A ALA* 3.7 24.7 - - + +
330A LEU* 3.7 30.5 - - + +
333A VAL* 4.1 3.1 - - + +
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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
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6A ILE* 3.7 42.4 - - + -
41A PHE* 3.4 32.3 - + + -
71A TYR* 3.7 32.1 - + + -
72A ALA* 4.7 7.9 - - + -
289A ILE* 3.2 42.0 + - + +
292A ALA* 1.3 78.5 - - + +
294A ARG* 1.3 63.1 + - - +
295A TYR 3.2 0.2 - - - -
296A LEU* 3.3 40.6 + - + +
297A ARG* 3.4 10.0 + - - +
303A VAL* 4.6 6.7 - - + -
326A ILE* 4.5 9.6 - - + -
330A LEU* 5.2 11.0 - - + -
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Residues in contact with ARG 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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30A TYR* 3.3 23.2 - - - +
37A THR 4.6 4.7 - - - +
38A GLU* 3.2 39.8 + - - +
40A PRO* 4.2 21.6 - - + +
41A PHE* 3.9 6.3 - - + -
287A LEU* 4.2 8.1 + - - +
290A ALA* 3.1 30.9 + - - +
291A GLU* 3.3 45.2 + - - +
292A ALA 3.4 0.2 - - - -
293A PHE* 1.3 76.2 - - - +
295A TYR* 1.3 62.7 - - - +
297A ARG* 3.8 2.6 + - - +
298A ARG* 3.3 39.0 + - - +
335A VAL* 6.2 0.8 - - - +
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Residues in contact with TYR 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 GLU* 3.3 12.3 + - - +
292A ALA* 3.4 10.8 - - - +
293A PHE 3.2 0.4 - - - -
294A ARG* 1.3 77.6 - - - +
296A LEU* 1.3 59.4 + - + +
298A ARG* 3.2 31.2 + - - +
299A GLN* 3.0 65.0 + - + +
328A ARG* 5.5 7.7 + - - -
329A ALA* 3.9 28.5 - - + +
332A MET* 5.1 16.9 - - + +
333A VAL* 6.3 0.2 - - + -
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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
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292A ALA* 3.0 20.4 + - + +
293A PHE* 3.4 46.7 - - + +
294A ARG 3.2 0.8 - - - -
295A TYR* 1.3 79.7 - - + +
297A ARG* 1.3 56.7 + - - +
298A ARG 3.2 0.2 - - - -
299A GLN* 3.5 6.9 + - + +
300A ARG 3.1 4.7 + - - -
301A VAL* 3.0 37.4 + - + +
303A VAL* 3.8 24.9 - - + -
325A ASP* 4.8 7.6 - - - +
326A ILE* 4.1 15.3 - - + +
329A ALA* 3.4 26.9 - - + -
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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
----------------------------------------------------------
40A PRO* 4.2 35.4 + - + +
41A PHE* 6.1 3.1 - - + -
293A PHE 3.4 10.2 + - - +
294A ARG 3.8 3.8 + - - +
296A LEU* 1.3 74.0 - - - +
298A ARG* 1.3 63.0 + - - +
299A GLN 3.2 0.9 - - - -
300A ARG* 3.3 19.8 + - + +
301A VAL 4.7 0.9 - - - +
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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