Contacts of the helix formed by residues 314 - 340 (chain A) in PDB entry 3NC0
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 ASP 314 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 4.5 9.7 - - - +
259A MET* 5.5 3.2 - - - -
261A ARG* 2.8 36.5 + - - +
262A ASN* 3.6 17.5 - - - +
312A LYS* 2.7 10.9 + - + -
313A ASP* 1.3 77.5 - - - +
315A GLU* 1.3 61.1 + - - +
316A GLN 3.1 4.6 + - - -
317A ASN 3.7 1.3 + - - +
318A PHE* 3.3 22.5 + - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ARG* 3.9 23.8 - - - +
298A LEU* 5.4 8.5 - - + +
307A ALA* 3.4 40.9 - - + +
310A ASN 3.8 11.1 - - - +
311A GLY* 4.0 4.5 - - - -
312A LYS* 3.3 12.2 + - - +
314A ASP* 1.3 78.4 + - - +
316A GLN* 1.3 57.9 + - - +
318A PHE* 4.1 4.2 - - + +
319A ILE* 3.3 25.3 + - + +
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Residues in contact with GLN 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 2.9 72.7 + - + +
309A SER* 5.0 2.0 + - - +
311A GLY* 3.8 19.6 + - - -
312A LYS 3.0 21.9 + - - +
313A ASP* 4.5 9.2 - - - +
315A GLU* 1.3 77.7 - - - +
317A ASN* 1.3 72.4 + - - +
318A PHE 3.2 1.6 - - - -
319A ILE* 3.1 14.9 + - - +
320A GLN* 3.2 10.3 + - - +
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Residues in contact with ASN 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 3.7 18.6 - - - +
313A ASP* 3.5 32.3 + - - +
314A ASP 3.7 1.5 + - - +
316A GLN* 1.3 79.0 - - - +
318A PHE* 1.3 52.8 + - - +
320A GLN* 3.1 11.8 + - - +
321A ASN* 2.7 43.7 + - - +
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Residues in contact with PHE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A LEU* 4.6 5.8 - - + -
261A ARG* 3.5 56.3 - - + +
262A ASN* 3.1 19.3 - - - +
265A LEU* 4.1 18.3 - - + +
294A LEU* 4.6 12.8 - - + -
297A MET* 3.6 29.6 - - + -
298A LEU* 3.6 35.0 - - + -
314A ASP 3.3 16.5 + - - +
315A GLU* 4.1 6.3 - - + +
316A GLN 3.2 0.4 - - - -
317A ASN* 1.3 78.7 - - - +
319A ILE* 1.3 53.9 + - + +
321A ASN* 3.2 2.5 + - - +
322A LEU* 2.7 37.8 + - + +
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 5.2 11.4 - - + -
304A ILE* 4.0 31.9 - - + +
307A ALA* 4.4 6.7 - - + -
308A TYR* 3.4 39.0 - - + +
315A GLU* 3.3 21.3 - - + +
316A GLN 3.1 5.3 + - - +
318A PHE* 1.3 78.9 - - + +
320A GLN* 1.3 57.3 + - - +
322A LEU* 3.1 9.7 + - + +
323A SER* 2.9 30.1 + - - -
357A VAL* 4.5 13.6 - - + +
360A VAL* 4.3 7.9 - - + -
365A ILE* 4.1 15.7 - - + -
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 5.5 2.0 - - - +
316A GLN 3.2 8.2 + - - +
317A ASN* 3.1 15.1 + - - +
319A ILE* 1.3 78.3 - - - +
321A ASN* 1.3 68.2 + - - +
323A SER* 3.2 9.5 + - - -
324A LEU* 3.1 37.5 + - - +
364A GLU* 4.4 16.3 - - - +
365A ILE* 3.5 26.8 - - + +
368A ILE* 4.4 14.6 - - + +
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASN* 3.0 27.3 + - - +
265A LEU* 3.7 18.1 - - + +
266A LYS* 3.6 34.7 - - + +
269A THR* 4.0 2.6 + - - -
317A ASN* 2.7 25.3 + - - +
318A PHE 3.6 5.2 - - - +
320A GLN* 1.3 80.0 - - - +
322A LEU* 1.3 59.9 + - - +
324A LEU* 3.5 19.4 + - - +
325A PHE* 2.9 29.6 + - - +
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.7 12.1 - - + +
294A LEU* 4.0 33.0 - - + -
298A LEU* 4.5 21.5 - - + -
304A ILE* 5.8 2.7 - - + -
318A PHE* 2.7 18.2 + - + +
319A ILE* 3.1 12.3 + - + +
321A ASN* 1.3 74.9 - - - +
323A SER* 1.3 64.7 - - - +
325A PHE* 4.4 5.2 - - + +
326A LEU* 2.9 56.0 + - + +
353A TYR* 4.5 14.6 - - + -
357A VAL* 3.9 23.8 - - + -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE 2.9 13.1 + - - -
320A GLN* 3.3 10.8 - - - -
322A LEU* 1.3 76.0 - - - +
324A LEU* 1.3 57.3 + - - +
326A LEU* 4.2 0.3 - - - +
327A CYS* 2.9 35.7 + - - +
354A MET* 4.6 8.9 - - - +
357A VAL* 3.2 31.2 - - - +
365A ILE* 3.4 11.7 - - - +
368A ILE* 3.8 26.9 - - - +
369A CYS* 4.5 3.4 - - - -
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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
----------------------------------------------------------
266A LYS* 6.4 0.2 - - + -
269A THR* 4.2 14.4 - - + -
320A GLN* 3.1 25.6 + - - +
321A ASN* 3.7 22.9 - - - +
322A LEU 3.2 0.2 - - - -
323A SER* 1.3 76.3 - - - +
325A PHE* 1.3 57.5 + - - +
327A CYS* 4.7 1.1 - - - -
328A THR* 2.9 40.8 + - - +
368A ILE* 3.5 32.1 - - + -
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 3.7 20.6 - - + -
268A LEU* 4.3 13.9 - - + -
269A THR* 3.0 37.2 + - - +
272A ALA* 4.2 18.1 - - + +
286A LEU* 5.1 4.9 - - + -
287A PHE* 4.6 20.6 - + - -
290A THR* 3.7 36.8 - - + -
294A LEU* 4.7 2.5 - - + -
321A ASN 2.9 15.8 + - - +
322A LEU* 3.8 8.5 - - + +
324A LEU* 1.3 77.5 - - - +
326A LEU* 1.3 85.6 + - + +
328A THR* 3.9 1.0 - - - -
329A PHE* 3.1 34.0 + + + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 5.0 3.4 - - + -
291A MET* 4.5 11.0 - - + -
294A LEU* 4.5 9.2 - - + -
322A LEU* 2.9 45.1 + - + +
325A PHE* 1.3 94.8 - - + +
327A CYS* 1.3 63.3 + - - +
329A PHE* 3.9 1.9 - - - +
330A LEU* 3.1 35.5 + - + +
350A ALA* 4.2 15.9 - - + +
353A TYR* 3.4 32.1 - - + -
354A MET* 3.4 26.7 - - + +
357A VAL* 5.2 1.3 - - + -
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Residues in contact with CYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER 2.9 20.9 + - - +
324A LEU* 4.1 1.6 - - - +
326A LEU* 1.3 78.1 - - - +
328A THR* 1.3 66.3 + - - +
330A LEU* 5.3 0.2 - - - -
331A LYS* 3.0 42.0 + - - +
354A MET* 4.3 7.5 - - + -
368A ILE* 3.8 31.2 - - + +
371A GLU* 4.5 10.8 - - - -
372A TYR* 4.0 30.2 - - + -
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Residues in contact with THR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A THR* 4.1 20.9 - - + +
272A ALA* 4.2 2.0 - - + +
273A GLY* 3.8 28.7 - - - +
324A LEU* 2.9 32.8 + - - +
325A PHE 4.0 2.0 - - - -
327A CYS* 1.3 78.3 - - - +
329A PHE* 1.3 62.4 + - - +
331A LYS* 3.7 5.6 + - - +
332A GLU* 3.3 23.2 + - + +
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA* 3.3 33.9 - - + -
283A PHE* 3.6 23.3 - + - -
284A GLU* 5.5 0.2 - - - -
286A LEU* 4.9 7.0 - - + -
287A PHE* 3.4 52.9 - + + -
325A PHE* 3.1 27.9 + + + +
326A LEU* 3.9 2.9 - - - +
328A THR* 1.3 76.0 - - - +
330A LEU* 1.3 63.0 + - + +
332A GLU 2.9 1.2 + - - -
333A HIS* 2.7 67.0 + + + -
334A GLY 3.3 1.9 + - - -
336A LEU* 6.4 0.7 - - + -
337A LEU* 3.9 21.1 - - + -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 4.4 14.1 - - + -
326A LEU* 3.1 22.7 + - + +
329A PHE* 1.3 77.3 - - + +
331A LYS* 1.3 61.9 + - - +
332A GLU 4.0 0.2 - - - -
334A GLY* 3.0 29.0 + - - -
335A GLN* 4.2 2.1 + - - +
337A LEU* 3.8 25.6 - - + -
347A LEU* 4.0 14.4 - - + -
350A ALA* 4.6 10.1 - - + -
351A LEU* 3.9 17.9 - - + -
354A MET* 4.5 13.0 - - + -
372A TYR* 3.3 38.6 + - + +
375A HIS* 5.2 1.6 + - - -
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A CYS* 3.0 34.6 + - - +
328A THR* 3.8 6.3 - - - +
330A LEU* 1.3 75.7 - - - +
332A GLU* 1.3 60.9 + - + +
335A GLN* 4.2 7.8 - - - +
371A GLU* 3.0 41.1 + - - +
372A TYR* 4.0 6.0 - - + -
375A HIS* 3.9 56.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 4.2 15.0 - - - +
273A GLY* 4.6 11.7 - - - +
274A VAL 3.6 19.5 - - - +
275A SER* 4.1 20.1 + - - -
276A VAL 5.1 0.9 + - - +
328A THR* 3.3 17.3 + - + +
329A PHE 2.9 3.9 + - - +
331A LYS* 1.3 79.8 - - + +
333A HIS* 1.3 67.9 + - + +
334A GLY 3.3 3.4 - - - -
335A GLN* 3.0 32.1 - - - +
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Residues in contact with HIS 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 3.0 28.0 + - - -
274A VAL 3.3 24.0 + - - -
276A VAL 4.7 6.4 + - - -
283A PHE* 3.2 41.4 - + + -
329A PHE* 2.7 46.8 + + + +
332A GLU* 1.3 84.4 + - + +
334A GLY* 1.3 58.2 + - - -
335A GLN 3.0 5.6 - - - -
336A LEU* 3.1 40.2 + - + +
337A LEU* 3.3 10.1 + - - +
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Residues in contact with GLY 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A PHE 3.3 3.0 + - - -
330A LEU* 3.0 30.9 + - - -
333A HIS* 1.3 78.6 - - - +
335A GLN* 1.3 60.4 + - - +
336A LEU 3.1 0.2 - - - -
337A LEU* 3.3 26.0 + - - +
338A GLU* 3.4 20.1 - - - +
347A LEU* 5.2 2.7 - - - +
409A TYR* 4.6 1.4 + - - -
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 5.0 2.9 - - - +
331A LYS 4.2 8.3 - - - +
332A GLU* 3.0 27.9 - - - +
333A HIS* 3.0 0.6 - - - -
334A GLY* 1.3 79.1 - - - +
336A LEU* 1.3 58.1 + - + +
337A LEU 3.5 0.2 - - - -
338A GLU* 3.9 22.3 + - - +
339A LYS* 4.4 5.5 + - - +
375A HIS* 5.9 3.8 + - - +
379A GLU* 5.7 6.5 - - + +
405A ARG* 5.4 8.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 4.0 26.0 - - + +
283A PHE* 5.2 4.7 - - + -
284A GLU* 3.8 35.9 - - + +
329A PHE* 6.4 0.4 - - + -
333A HIS* 3.1 39.2 + - + +
335A GLN* 1.3 77.7 - - + +
337A LEU* 1.3 74.2 + - + +
338A GLU 3.1 2.2 - - - -
339A LYS* 3.3 40.3 - - - +
340A ARG* 3.8 8.1 + - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A GLU* 5.4 2.9 - - - -
287A PHE* 3.5 45.8 - - + -
329A PHE* 3.9 12.8 - - + -
330A LEU* 3.8 25.1 - - + -
333A HIS 3.3 10.0 + - - +
334A GLY* 3.3 16.5 + - - +
336A LEU* 1.3 85.0 - - + +
338A GLU* 1.3 59.8 + - - +
340A ARG 3.8 8.3 - - - +
343A LEU* 3.8 45.3 - - + +
344A ARG* 4.4 2.1 + - - -
347A LEU* 4.1 23.2 - - + +
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLY 3.4 19.0 - - - +
335A GLN* 3.9 13.0 - - - +
336A LEU 3.1 0.4 - - - -
337A LEU* 1.3 79.3 - - - +
339A LYS* 1.3 62.6 + - - +
340A ARG 2.8 15.3 - - - +
344A ARG* 5.5 4.6 - - - +
347A LEU* 4.4 6.5 - - + -
405A ARG* 3.2 53.9 + - - +
408A LEU* 3.8 24.9 - - + +
409A TYR* 2.7 31.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 3.0 38.9 + - - +
335A GLN 4.4 3.5 + - - +
336A LEU* 3.3 36.3 - - - +
338A GLU* 1.3 80.2 - - - +
340A ARG* 1.3 87.0 + - + +
341A LEU* 3.9 1.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLU* 2.7 33.0 + - - -
284A GLU* 3.4 27.0 + - - +
336A LEU 3.8 9.1 + - - +
337A LEU 3.8 5.2 - - - +
338A GLU 2.8 19.1 - - - +
339A LYS* 1.3 90.7 - - + +
341A LEU* 1.3 61.0 + - - +
342A ASN* 3.4 16.6 - - - +
343A LEU* 3.6 19.1 - - + -
344A ARG* 4.5 5.4 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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