Contacts of the helix formed by residues 309 - 336 (chain A) in PDB entry 4WLE
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 309 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 4.1 10.1 + - - -
308A VAL* 1.3 75.5 - - - +
310A SER* 1.3 59.2 + - - +
311A PHE* 3.5 9.5 + - - +
312A GLU* 2.9 40.8 + - - +
313A GLU* 2.8 28.9 + - - +
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Residues in contact with SER 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A SER* 1.3 71.6 - - - +
311A PHE* 1.3 60.2 + - - +
313A GLU* 3.4 7.3 + - - +
314A LYS* 3.0 29.5 + - - +
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Residues in contact with PHE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 4.6 23.8 - - + -
224A THR* 4.7 20.6 - - + -
227A THR* 4.0 23.6 - - + -
309A SER* 3.3 8.6 + - - +
310A SER* 1.3 77.7 - - - +
312A GLU* 1.3 64.7 + - + +
314A LYS* 3.6 7.0 + - + +
315A MET* 3.2 52.8 + - + +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 4.3 0.7 - - - +
207A PRO 4.2 2.2 - - - +
208A LEU* 3.8 26.0 - - + +
209A ILE* 3.1 12.6 + - - +
210A SER* 2.6 47.8 + - - -
308A VAL* 3.4 11.1 - - + +
309A SER* 2.9 30.2 + - - +
311A PHE* 1.3 79.5 - - + +
313A GLU* 1.3 63.2 + - - +
315A MET* 3.2 24.6 + - + +
316A ILE* 3.0 29.2 + - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE* 5.8 0.2 - - - +
308A VAL* 3.3 22.2 - - + +
309A SER 2.8 16.3 + - - +
310A SER* 3.4 9.6 + - - +
312A GLU* 1.3 77.6 - - - +
314A LYS* 1.3 62.0 + - - +
316A ILE* 3.2 22.3 + - - +
317A SER* 3.1 21.5 + - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A SER 3.0 17.0 + - - +
311A PHE* 3.7 9.4 - - + +
313A GLU* 1.3 72.5 - - - +
315A MET* 1.3 60.4 + - + +
317A SER* 3.3 12.0 + - - -
318A ASP* 2.8 66.9 + - - +
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Residues in contact with MET 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS 4.4 3.8 - - - +
206A ILE* 3.7 27.0 - - + +
207A PRO* 4.1 9.4 - - + +
227A THR* 3.7 27.4 - - + +
231A GLN* 3.8 18.2 - - - +
311A PHE* 3.2 38.5 + - + +
312A GLU* 3.2 32.8 + - + +
314A LYS* 1.3 76.0 - - + +
316A ILE* 1.3 63.4 + - - +
318A ASP* 3.4 10.6 + - - +
319A ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 3.9 24.2 - - + -
206A ILE* 3.7 20.9 - - + -
208A LEU* 5.3 0.2 - - + -
283A THR* 4.7 8.5 - - + -
288A PHE* 4.5 16.6 - - + -
305A ILE* 3.9 21.3 - - + -
308A VAL* 4.4 4.7 - - + -
312A GLU 3.0 17.9 + - - +
313A GLU* 3.2 30.0 + - - +
315A MET* 1.3 76.8 - - - +
317A SER* 1.3 60.5 + - - +
319A ALA* 3.2 2.9 + - - +
320A ILE* 3.2 38.3 + - + +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU 3.1 12.5 + - - -
314A LYS* 3.3 18.2 + - - +
316A ILE* 1.3 78.4 - - - +
318A ASP* 1.3 66.2 + - - +
320A ILE* 3.7 9.9 + - - +
321A PRO* 3.3 19.4 - - - +
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Residues in contact with ASP 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 3.8 33.3 + - + +
314A LYS* 2.8 49.7 + - - +
315A MET* 3.8 9.9 - - - +
316A ILE 3.3 0.2 - - - -
317A SER* 1.3 78.2 + - - +
319A ALA* 1.3 61.2 + - - +
321A PRO* 3.5 11.7 - - - +
322A GLU* 4.6 3.3 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 3.8 6.7 - - - +
204A THR* 3.8 26.4 - - + +
206A ILE* 3.8 18.6 - - + -
288A PHE* 5.7 0.9 - - + -
315A MET 3.1 16.8 + - - +
316A ILE 3.2 5.3 + - - +
318A ASP* 1.3 77.3 - - - +
320A ILE* 1.3 65.6 + - + +
322A GLU* 3.2 6.6 + - - +
323A LEU* 3.0 31.8 + - + +
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A THR* 4.8 13.2 - - + +
284A GLU* 3.6 31.4 - - + +
285A CYS* 4.0 19.3 - - - -
288A PHE* 5.3 3.6 - - + -
316A ILE* 3.2 34.0 + - + +
317A SER* 4.0 7.6 - - - +
319A ALA* 1.3 76.5 - - - +
321A PRO* 1.3 72.1 - - + +
323A LEU* 3.3 1.7 + - - +
324A LYS* 2.9 42.1 + - + +
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Residues in contact with PRO 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER 3.3 17.5 - - - +
318A ASP* 3.5 12.3 - - - +
320A ILE* 1.3 95.1 - - + +
322A GLU* 1.3 60.8 + - - +
324A LYS* 3.5 7.6 + - + +
325A ALA* 3.1 22.5 + - - +
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Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 5.0 0.6 + - - +
201A ALA* 3.9 20.3 - - - +
202A GLY* 5.6 0.2 - - - -
203A LYS* 3.3 31.5 + - + +
204A THR* 3.7 21.1 - - + +
318A ASP 4.6 4.9 + - - +
319A ALA 3.2 8.7 + - - +
321A PRO* 1.3 76.7 - - - +
323A LEU* 1.3 61.6 + - - +
325A ALA* 3.2 8.0 + - + +
326A SER* 2.9 35.5 + - - +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 3.4 36.6 - - + +
198A GLY* 4.2 10.1 - - - +
199A GLY* 4.0 7.2 - - - +
204A THR* 3.9 12.3 - - + -
277A PHE* 4.1 11.0 - - + -
285A CYS* 3.9 13.0 - - - -
287A TYR 4.7 2.2 - - - +
288A PHE* 3.7 37.0 - - + -
319A ALA* 3.0 26.5 + - + +
320A ILE 3.3 4.0 + - - +
322A GLU* 1.3 75.9 - - - +
324A LYS* 1.3 57.1 + - - +
326A SER* 3.2 4.8 + - - -
327A ILE* 2.8 40.0 + - + +
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Residues in contact with LYS 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 3.3 32.4 + - + +
285A CYS* 4.0 19.3 - - - -
320A ILE* 2.9 37.2 + - + +
321A PRO* 3.8 6.7 - - + +
323A LEU* 1.3 74.6 - - - +
325A ALA* 1.3 57.2 + - - +
327A ILE* 3.4 8.6 + - + +
328A LYS* 3.0 30.5 + - - +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO 3.1 14.5 + - - +
322A GLU* 3.5 11.4 - - + +
323A LEU 3.2 0.2 - - - -
324A LYS* 1.3 76.5 - - - +
326A SER* 1.3 62.4 + - - +
328A LYS* 3.5 5.7 + - - +
329A LYS* 3.1 23.3 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 4.9 7.2 + - - +
143A PRO* 6.1 0.7 - - - +
145A ASN* 3.6 29.6 + - - +
146A SER* 2.7 32.2 + - - -
322A GLU* 2.9 23.5 + - - +
323A LEU* 3.6 7.9 - - - -
325A ALA* 1.3 76.5 - - - +
327A ILE* 1.3 62.2 + - - +
329A LYS* 3.4 6.4 + - - +
330A GLY 3.3 11.6 + - - -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN 3.8 15.0 - - - +
149A PRO* 3.8 5.8 - - + +
277A PHE* 4.6 3.6 - - + -
285A CYS* 4.2 6.3 - - + -
286A THR* 3.4 24.9 - - - +
287A TYR* 3.7 52.0 - - + +
323A LEU* 2.8 28.7 + - + +
324A LYS* 3.8 7.4 - - - +
326A SER* 1.3 74.1 - - - +
328A LYS* 1.3 64.4 - - - +
330A GLY* 3.3 2.8 + - - -
331A GLU* 3.0 40.3 + - - +
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Residues in contact with LYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS 3.0 18.1 + - - +
325A ALA* 3.9 5.8 - - - +
327A ILE* 1.3 77.1 - - - +
329A LYS* 1.3 54.0 + - - +
331A GLU* 3.6 14.5 - - - +
332A ASP* 2.7 67.1 + - - +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 2.8 45.9 + - - +
114A PHE* 3.5 38.6 - - + +
115A ASN* 5.5 2.9 - - - +
146A SER* 4.1 4.9 - - - +
325A ALA 3.1 14.1 + - - +
326A SER* 3.4 12.3 - - - +
328A LYS* 1.3 76.1 - - - +
330A GLY* 1.3 61.1 + - - +
332A ASP* 3.9 6.7 - - - +
333A PHE* 3.1 17.5 + - - +
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Residues in contact with GLY 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.0 8.2 - - - -
146A SER* 3.6 23.7 - - - -
149A PRO* 4.4 4.0 - - - -
150A ILE* 3.5 23.8 - - - +
326A SER 3.3 7.9 + - - -
327A ILE 3.3 2.6 + - - -
329A LYS* 1.3 76.5 - - - +
331A GLU* 1.3 65.2 + - - +
333A PHE* 3.4 7.8 + - - +
334A VAL* 3.5 10.4 + - - +
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 4.3 9.4 - - + +
153A GLU* 4.3 27.7 - - + +
286A THR* 4.1 5.9 + - - +
287A TYR* 4.1 11.0 + - + -
327A ILE* 3.0 35.2 + - - +
328A LYS* 3.6 18.1 - - + +
330A GLY* 1.3 77.6 - - - +
332A ASP* 1.3 64.0 + - - +
334A VAL* 3.3 5.0 + - - +
335A LYS* 3.3 38.9 + - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LYS* 2.7 57.5 + - - +
329A LYS* 3.9 6.4 + - - +
331A GLU* 1.3 72.2 - - - +
333A PHE* 1.3 66.4 + - - +
335A LYS* 3.1 12.0 + - - +
336A THR* 3.0 28.8 + - + +
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Residues in contact with PHE 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 3.6 19.7 - + + -
115A ASN* 5.4 6.1 - - - -
118A ALA* 3.6 35.4 - - + -
119A THR* 3.7 23.6 - - - -
122A ALA* 4.1 8.1 - - + -
150A ILE* 4.0 16.2 - - + -
329A LYS 3.1 17.8 + - - +
330A GLY 3.6 5.4 - - - +
331A GLU 3.3 0.2 - - - -
332A ASP* 1.3 76.3 - - - +
334A VAL* 1.3 65.1 + - + +
336A THR* 2.5 30.3 + - - -
337A LEU* 3.6 35.4 - - + +
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA* 5.9 0.4 - - + -
150A ILE* 4.0 26.7 - - + +
153A GLU* 3.8 38.6 - - + +
154A VAL* 4.6 8.7 - - + +
157A LYS* 5.9 3.8 - - + -
330A GLY 3.5 12.5 + - - +
331A GLU 3.3 7.5 + - - +
332A ASP 3.3 0.4 - - - -
333A PHE* 1.3 83.9 - - + +
335A LYS* 1.3 64.5 + - + +
337A LEU* 3.2 33.1 + - + +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A GLU* 4.1 23.4 + - - -
331A GLU* 3.3 29.5 + - - +
332A ASP* 3.1 15.5 + - - +
334A VAL* 1.3 84.0 - - + +
336A THR* 1.3 58.7 + - + +
337A LEU 3.2 7.8 + - - +
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Residues in contact with THR 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ASP* 3.0 18.0 + - + +
333A PHE* 2.5 30.0 + - - -
335A LYS* 1.3 76.9 - - + +
337A LEU* 1.3 65.5 + - - +
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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