Contacts of the helix formed by residues 305 - 335 (chain A) in PDB entry 6J95
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 PRO 305 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 1.4 89.2 - - - +
306A ARG* 1.3 66.0 + - + +
308A ARG* 3.2 6.0 + - + +
309A LYS* 2.9 26.6 + - - +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ARG* 5.1 16.5 + - - +
283A GLU* 5.9 2.5 - - - +
304A SER 3.6 1.1 - - - +
305A PRO* 1.3 84.7 - - + +
307A GLN* 1.3 59.8 + - - +
309A LYS* 3.1 8.8 + - - +
310A VAL* 2.9 34.4 + - + +
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Residues in contact with GLN 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 6.0 1.1 - - - -
304A SER* 2.9 16.8 + - - +
305A PRO 4.4 0.2 - - - -
306A ARG* 1.3 78.0 - - - +
308A ARG* 1.3 54.6 + - - +
310A VAL* 3.6 9.8 + - - +
311A ALA* 3.2 23.9 + - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A SER* 2.4 34.9 + - - +
305A PRO* 3.5 7.4 - - + +
306A ARG 3.1 0.2 - - - -
307A GLN* 1.3 67.3 - - - +
309A LYS* 1.3 59.6 + - - +
310A VAL 3.2 1.8 - - - -
311A ALA* 3.3 6.7 + - - +
312A THR* 3.0 32.6 + - - -
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Residues in contact with LYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A THR* 4.4 11.4 - - + -
282A ARG* 5.7 1.3 - - - +
305A PRO 2.9 14.2 + - - +
306A ARG* 3.1 11.0 + - - +
308A ARG* 1.3 75.7 - - - +
310A VAL* 1.3 57.6 + - - +
312A THR* 3.6 7.5 + - - -
313A SER* 2.9 32.8 + - - -
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 4.4 9.9 - - + -
279A THR* 4.4 8.5 - - + +
280A VAL* 5.2 4.0 - - + -
282A ARG* 4.2 13.9 - - - +
283A GLU* 3.9 45.1 - - + +
287A ARG* 5.6 2.5 - - - +
306A ARG* 2.9 21.9 + - + +
307A GLN* 3.7 9.4 - - - +
308A ARG 3.2 0.2 - - - -
309A LYS* 1.3 74.2 - - - +
311A ALA* 1.3 59.2 - - - +
313A SER* 3.1 4.0 + - - -
314A LEU* 2.8 46.4 + - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLN 3.2 13.0 + - - +
308A ARG* 3.3 9.4 + - - +
310A VAL* 1.3 79.9 - - - +
312A THR* 1.3 57.8 + - - +
314A LEU* 3.5 9.8 + - - +
315A LYS* 3.0 27.9 + - - +
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ARG* 3.0 18.4 + - - +
309A LYS* 3.8 8.1 - - - +
311A ALA* 1.3 74.7 - - - +
313A SER* 1.3 66.4 + - - +
315A LYS* 3.2 7.6 + - - +
316A LEU* 3.0 25.0 + - + +
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Residues in contact with SER 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 3.6 37.2 - - - +
279A THR* 3.5 20.2 + - - +
280A VAL* 4.0 6.1 - - - -
309A LYS* 2.9 19.6 + - - +
310A VAL 3.6 3.6 - - - -
312A THR* 1.3 76.3 - - - +
314A LEU* 1.3 62.8 + - - +
316A LEU* 3.3 2.4 + - - +
317A ILE* 3.1 31.2 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 3.7 28.0 - - + +
184A VAL* 4.1 23.6 - - + +
280A VAL* 3.6 21.8 - - + -
310A VAL* 2.8 36.2 + - + +
311A ALA* 3.7 8.7 - - - +
313A SER* 1.3 72.7 - - - +
315A LYS* 1.3 57.9 + - - +
317A ILE* 3.5 4.8 + - + +
318A ASN* 3.0 44.1 + - - +
372A MET* 5.4 7.4 - - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA 3.0 18.1 + - - +
312A THR* 3.2 7.8 + - - +
314A LEU* 1.3 77.4 - - - +
316A LEU* 1.3 56.9 + - - +
318A ASN* 3.4 6.1 + - + +
319A ASP* 2.8 65.3 + - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLY* 3.5 36.8 - - - +
273A VAL* 3.8 14.4 - - + +
276A ALA* 4.2 5.8 - - + -
312A THR* 3.0 18.1 + - + +
313A SER* 3.3 5.1 + - - +
315A LYS* 1.3 77.0 - - - +
317A ILE* 1.3 59.4 + - - +
319A ASP* 3.4 9.5 + - + +
320A THR* 2.8 42.5 + - - +
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Residues in contact with ILE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 6.3 0.4 - - + -
264A PHE* 6.4 1.1 - - + -
273A VAL* 4.7 7.4 - - + +
276A ALA* 3.7 35.9 - - + +
277A VAL* 3.7 21.5 - - + +
280A VAL* 4.0 15.0 - - + -
313A SER 3.1 18.1 + - - +
314A LEU* 4.0 4.5 - - + +
316A LEU* 1.3 74.4 - - - +
318A ASN* 1.3 58.1 - - - +
320A THR* 3.2 7.7 + - - -
321A LEU* 2.8 41.1 + - + +
372A MET* 3.6 35.7 - - + -
375A LEU* 5.0 7.9 - - + -
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Residues in contact with ASN 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LEU* 3.0 32.1 + - - +
315A LYS* 3.8 6.6 - - + +
317A ILE* 1.3 77.4 - - - +
319A ASP* 1.3 58.4 + - - +
321A LEU* 3.3 3.4 + - - +
322A ASP* 2.8 35.0 + - - +
368A ARG* 3.4 36.2 + - - +
369A ASP* 5.5 1.4 - - - +
372A MET* 3.7 20.1 - - - +
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LYS* 2.8 60.7 + - - +
316A LEU* 3.7 10.0 - - + +
318A ASN* 1.3 73.9 - - - +
320A THR* 1.3 63.8 + - - +
322A ASP* 3.2 13.7 + - - +
323A ASP* 3.0 30.7 + - - +
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 6.2 0.7 - - + -
262A TYR* 4.0 37.0 - - + +
264A PHE* 6.2 0.2 - - + -
273A VAL* 3.9 23.5 - - + +
316A LEU* 2.8 30.6 + - - +
317A ILE* 3.2 8.7 + - + -
319A ASP* 1.3 75.7 - - - +
321A LEU* 1.3 65.6 + - + +
323A ASP* 3.2 14.3 + - + +
324A LEU* 3.1 24.8 + - + +
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Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.7 47.3 - - + -
317A ILE* 2.8 27.2 + - + +
318A ASN* 3.7 6.1 - - - +
320A THR* 1.3 74.1 - - + +
322A ASP* 1.3 59.0 + - - +
324A LEU* 3.1 9.2 + - + +
325A ILE* 2.8 38.0 + - + +
368A ARG* 4.1 32.8 - - + +
371A LEU* 4.4 11.7 - - + -
372A MET* 3.6 34.5 - - + +
375A LEU* 6.2 0.2 - - + -
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Residues in contact with ASP 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 2.8 20.1 + - - +
319A ASP* 3.2 18.4 + - - +
321A LEU* 1.3 75.9 - - - +
323A ASP* 1.3 63.8 + - - +
325A ILE* 3.4 9.9 + - - +
326A ALA* 3.0 24.8 + - - +
364A SER* 4.8 4.9 + - - -
368A ARG* 3.0 35.8 + - - +
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Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ASP* 3.0 20.0 + - - +
320A THR* 3.2 10.2 + - - +
322A ASP* 1.3 78.9 - - - +
324A LEU* 1.3 58.5 + - + +
326A ALA* 3.3 6.1 + - - +
327A THR* 2.9 33.8 + - - +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.6 50.7 - - + +
261A ASN* 4.1 12.1 - - + +
262A TYR* 3.8 30.7 - - + -
320A THR* 3.1 18.2 + - + +
321A LEU* 3.1 15.3 + - + +
323A ASP* 1.3 77.0 - - + +
325A ILE* 1.3 56.4 - - - +
327A THR* 3.4 9.0 + - + -
328A CYS* 2.8 31.4 + - - +
352A LEU* 4.1 8.6 - - + +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 2.8 22.8 + - - +
322A ASP* 3.8 11.2 - - - +
324A LEU* 1.3 75.4 - - - +
326A ALA* 1.3 59.0 + - - +
328A CYS* 3.3 2.0 + - - +
329A LYS* 2.9 56.5 + - - +
352A LEU* 4.1 18.2 - - + -
356A LEU* 4.4 3.6 - - + -
364A SER* 5.0 9.9 - - - +
367A LEU* 4.0 35.7 - - + -
368A ARG* 3.9 27.6 - - + -
371A LEU* 4.4 8.1 - - + -
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASP 3.0 18.1 + - - +
323A ASP* 3.7 6.3 - - - +
325A ILE* 1.3 74.9 - - - +
327A THR* 1.3 65.5 + - - +
329A LYS* 3.3 10.2 + - - +
330A ARG* 3.1 33.5 + - - +
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Residues in contact with THR 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 2.9 19.6 + - - +
324A LEU* 3.7 9.5 - - + -
326A ALA* 1.3 74.5 - - - +
328A CYS* 1.3 64.5 + - - +
330A ARG* 3.3 33.2 + - - +
331A MET* 3.0 23.3 + - + +
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Residues in contact with CYS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU 2.8 18.7 + - - +
325A ILE 3.8 0.2 - - - +
326A ALA 3.2 0.2 - - - -
327A THR* 1.3 77.6 - - - +
329A LYS* 1.3 59.2 + - - +
331A MET* 3.1 7.9 + - - +
332A VAL* 2.8 35.2 + - - +
348A ASP* 3.6 9.6 - - - +
352A LEU* 4.2 10.3 - - + -
353A HIS* 3.4 49.4 - - - -
356A LEU* 3.6 21.1 - - + -
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 2.9 42.4 + - + +
326A ALA* 3.3 8.0 + - - +
328A CYS* 1.3 76.8 - - - +
330A ARG* 1.3 56.4 + - - +
332A VAL* 3.2 7.4 + - - +
333A GLU* 2.8 30.5 + - - +
356A LEU* 3.7 26.5 - - + -
364A SER* 4.7 11.1 + - - -
367A LEU* 5.6 1.1 - - - -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA* 3.1 16.7 + - - +
327A THR* 3.5 49.6 + - - +
329A LYS* 1.3 75.5 - - - +
331A MET* 1.3 62.0 + - - +
333A GLU* 3.4 7.3 + - + +
334A GLU* 3.2 47.7 + - + +
----------------------------------------------------------
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Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASN* 5.7 1.6 - - - -
327A THR* 3.0 16.0 + - + +
328A CYS* 3.4 9.6 - - - +
330A ARG* 1.3 73.3 - - - +
332A VAL* 1.3 65.3 + - - +
334A GLU* 3.3 5.7 + - - +
335A GLU* 3.0 24.9 + - + +
345A ASN* 3.6 20.0 - - - +
347A ARG* 3.6 32.1 - - + +
348A ASP* 3.7 21.1 - - + +
353A HIS* 3.6 19.1 - - + -
----------------------------------------------------------
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A CYS* 2.8 25.0 + - - +
329A LYS* 3.6 6.5 - - - +
331A MET* 1.3 71.9 - - - +
333A GLU* 1.3 64.8 + - - +
334A GLU 3.3 0.3 + - - -
335A GLU* 3.3 26.7 + - - +
353A HIS* 3.8 26.2 - - + +
356A LEU* 4.1 27.6 - - + +
357A ALA* 4.1 24.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LYS 2.8 16.3 + - - +
330A ARG* 3.8 7.6 - - - +
332A VAL* 1.3 79.4 - - - +
334A GLU* 1.3 62.6 + - + +
335A GLU 3.8 3.6 + - - +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 3.2 35.5 + - - +
331A MET* 3.8 4.8 - - - +
332A VAL 3.2 0.2 - - - -
333A GLU* 1.3 79.2 - - + +
335A GLU* 1.3 64.7 + - - +
336A GLU* 4.1 8.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET* 3.0 12.2 + - + +
332A VAL* 3.3 25.5 + - + +
333A GLU 4.2 3.5 - - - +
334A GLU* 1.3 81.5 - - - +
336A GLU* 1.3 64.2 + - - +
337A LEU* 3.8 19.8 + - + +
343A TYR* 2.6 31.7 + - - -
345A ASN* 2.7 35.2 + - - +
353A HIS* 2.9 16.5 + - - -
357A ALA* 4.2 5.7 - - - +
----------------------------------------------------------
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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