Contacts of the helix formed by residues 314 - 341 (chain A) in PDB entry 6AF6
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 ALA 314 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA 3.6 24.7 - - - +
307A LYS* 4.1 5.8 - - + -
308A HIS* 3.8 22.9 - - + +
312A GLN 3.2 3.4 + - - +
313A ASP* 1.3 74.5 + - - +
315A GLU* 1.3 65.3 + - - +
316A ALA 3.4 2.5 - - - -
317A ASP* 3.1 10.3 + - + +
318A ILE* 2.9 36.7 + - + +
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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
----------------------------------------------------------
238A HIS* 2.8 37.9 + - - +
242A ILE* 3.9 25.1 - - + +
245A LYS* 5.2 1.2 + - - +
313A ASP* 3.4 15.4 + - - +
314A ALA* 1.3 77.4 - - - +
316A ALA* 1.3 64.1 + - - +
318A ILE* 3.3 2.7 + - - +
319A ALA* 3.0 21.8 + - - +
374A ILE* 3.9 23.6 - - + +
377A ARG* 3.8 20.2 + - - -
378A LYS* 3.9 20.5 + - - +
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Residues in contact with ALA 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 5.1 0.6 + - - -
314A ALA 3.4 0.4 - - - -
315A GLU* 1.3 78.4 - - - +
317A ASP* 1.3 62.5 + - - +
319A ALA* 3.3 7.4 + - - +
320A MET* 2.9 41.9 + - + +
374A ILE* 5.1 1.1 - - - -
375A ILE* 4.2 11.4 - - + +
378A LYS* 3.8 34.5 - - + +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 4.7 2.8 - - + +
303A ARG* 4.0 11.3 + - - +
304A ALA* 3.7 22.9 - - + +
307A LYS* 2.9 34.5 + - - +
313A ASP 3.5 20.8 - - - +
314A ALA* 3.1 8.9 + - - +
316A ALA* 1.3 80.5 + - - +
318A ILE* 1.3 57.9 + - - +
320A MET* 3.4 22.5 + - + +
321A SER* 2.9 31.7 + - - -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.4 36.6 - - + +
245A LYS* 3.6 18.3 - - + +
246A GLY* 3.6 34.8 - - - +
304A ALA* 3.8 22.2 - - + +
305A CYS* 5.8 1.3 - - - -
308A HIS* 5.0 7.6 - - + -
314A ALA* 2.9 34.5 + - + +
315A GLU 3.8 3.8 - - - +
317A ASP* 1.3 74.2 - - - +
319A ALA* 1.3 60.1 - - - +
321A SER* 3.2 4.1 + - - -
322A LYS* 2.9 29.1 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 4.5 4.0 - - - +
315A GLU 3.0 16.6 + - - +
316A ALA 3.7 4.5 - - - +
318A ILE* 1.3 76.1 - - - +
320A MET* 1.3 62.7 + - - +
322A LYS* 3.4 3.0 + - - +
323A LEU* 3.0 25.3 + - - +
371A GLN* 3.4 30.4 - - - +
374A ILE* 4.0 16.6 - - + -
375A ILE* 3.8 19.5 - - + -
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Residues in contact with MET 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 3.8 28.3 - - + -
303A ARG* 4.7 5.8 - - - +
316A ALA* 2.9 21.3 + - + +
317A ASP* 3.7 35.0 - - - +
319A ALA* 1.3 76.1 - - - +
321A SER* 1.3 59.0 + - - +
323A LEU* 3.4 4.6 + - - +
324A LEU* 3.0 37.3 + - + +
375A ILE* 3.6 31.4 - - + -
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS 5.4 0.9 - - - -
300A MET* 3.0 37.6 + - - +
301A LEU* 3.5 27.2 - - - -
304A ALA* 3.8 1.5 - - - +
317A ASP 2.9 17.8 + - - -
318A ILE* 3.2 7.8 + - - -
320A MET* 1.3 74.8 - - - +
322A LYS* 1.3 61.2 + - - +
324A LEU* 3.9 2.1 - - - +
325A ILE* 2.8 39.7 + - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 3.8 31.1 + - + +
249A SER* 3.7 23.8 - - - +
318A ILE 2.9 16.8 + - - +
319A ALA* 3.8 3.6 - - - +
321A SER* 1.3 75.8 - - - +
323A LEU* 1.3 61.0 + - - +
325A ILE* 4.2 0.6 - - - +
326A SER* 2.8 30.5 + - - -
361A SER 3.0 25.6 + - - -
362A ARG 3.5 7.7 + - - -
364A PHE* 3.2 21.8 + - - -
365A SER* 5.0 0.7 - - - -
366A GLY 2.8 24.7 + - - -
368A ASN* 3.0 21.5 + - - +
371A GLN* 3.9 11.7 - - + +
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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
----------------------------------------------------------
319A ALA 3.0 15.8 + - - +
320A MET* 3.6 5.2 - - - +
322A LYS* 1.3 77.0 - - - +
324A LEU* 1.3 69.3 + - + +
326A SER* 3.3 1.0 + - - -
327A GLU* 3.1 39.1 + - + +
368A ASN* 3.4 46.0 - - + +
371A GLN* 4.3 6.7 - - + +
372A LYS* 3.8 35.2 - - + -
375A ILE* 4.0 19.5 - - + -
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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
----------------------------------------------------------
296A GLN* 5.8 1.6 - - + -
297A CYS* 4.3 7.2 - - + -
300A MET* 3.9 38.1 - - + -
320A MET* 3.0 23.2 + - + +
321A SER* 4.0 2.0 - - - +
323A LEU* 1.3 82.4 - - + +
325A ILE* 1.4 64.1 + - - +
327A GLU* 4.7 2.5 - - + -
328A TYR* 2.8 68.0 + - + +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER* 3.6 38.4 - - - +
252A PHE* 3.7 21.1 - - + -
253A VAL* 3.6 23.1 - - + +
256A LEU* 5.9 0.3 - - - +
297A CYS* 3.7 31.4 - - + +
301A LEU* 4.1 24.9 - - + -
321A SER* 2.8 25.6 + - - +
322A LYS 4.2 2.2 - - - +
324A LEU* 1.4 75.6 - - - +
326A SER* 1.3 58.9 + - - +
328A TYR* 3.7 0.9 - - - +
329A ALA* 2.8 28.2 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE* 5.9 0.2 - - - -
322A LYS* 2.8 22.1 + - - -
323A LEU 3.3 0.3 + - - -
325A ILE* 1.3 77.2 - - - +
327A GLU* 1.3 64.0 + - - +
329A ALA* 3.3 3.5 + - - +
330A VAL* 3.1 28.6 + - - +
361A SER* 3.1 44.6 + - - -
362A ARG* 3.7 4.9 - - - -
368A ASN* 2.9 29.8 + - - -
----------------------------------------------------------
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 3.1 28.4 + - + +
324A LEU* 3.9 4.3 - - + +
326A SER* 1.3 77.8 + - - +
328A TYR* 1.3 65.6 + - + +
330A VAL* 3.3 2.9 + - - +
331A GLN* 3.0 39.1 + - + +
362A ARG* 3.4 28.6 + - - +
368A ASN* 2.8 30.6 + - - +
372A LYS* 5.7 1.6 - - - -
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Residues in contact with TYR 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 4.7 7.9 - - + -
293A ARG* 3.4 66.6 - - + +
296A GLN* 4.0 21.3 + - + +
297A CYS* 3.8 18.6 - - + -
324A LEU* 2.8 52.8 + - + +
325A ILE* 3.9 3.8 - - - +
327A GLU* 1.3 81.0 - - + +
329A ALA* 1.3 58.9 + - - +
331A GLN* 4.6 2.5 - - + -
332A SER* 2.8 36.4 + - - -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PHE* 4.4 16.2 - - + +
256A LEU* 5.1 9.4 - - + +
259A LEU* 5.3 0.2 - - - +
325A ILE 2.8 22.7 + - - +
326A SER* 3.7 7.2 - - - +
327A GLU 3.3 0.2 - - - -
328A TYR* 1.3 74.0 - - - +
330A VAL* 1.3 61.6 - - - +
332A SER* 4.0 3.3 - - - -
333A GLY* 3.1 19.8 + - - -
354A HIS* 4.7 2.7 + - - +
358A MET* 3.8 37.1 - - + +
361A SER* 4.6 1.6 - - - +
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Residues in contact with VAL 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A SER 3.1 16.5 + - - +
327A GLU 3.8 3.1 - - - +
329A ALA* 1.3 74.8 - - - +
331A GLN* 1.3 72.8 + - + +
333A GLY 3.1 2.3 + - - -
334A LEU* 3.1 27.8 + - + +
355A LEU* 3.5 21.8 - - + +
358A MET* 3.6 30.3 - - + +
359A ILE* 4.1 11.0 - - + -
362A ARG* 4.0 36.3 - - - +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.8 28.7 - - - +
327A GLU* 3.0 25.9 + - + +
328A TYR* 4.1 3.1 - - + +
330A VAL* 1.3 82.7 - - + +
332A SER* 1.3 57.9 + - - +
334A LEU* 3.3 23.9 + - - +
335A ASP* 3.0 33.0 + - - +
362A ARG* 5.0 7.1 + - - -
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Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.4 32.4 - - - +
259A LEU* 3.5 9.6 - - - +
290A MET* 3.8 13.0 - - - +
293A ARG* 3.1 27.0 + - - +
328A TYR 2.8 24.1 + - - -
329A ALA 4.1 1.6 - - - -
331A GLN* 1.3 74.5 - - - +
333A GLY* 1.3 60.3 + - - +
335A ASP* 3.7 4.2 - - - +
336A ALA* 2.9 25.5 + - - +
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Residues in contact with GLY 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.9 13.6 - - - +
329A ALA 3.1 16.2 + - - -
330A VAL 3.1 4.0 + - - -
332A SER* 1.3 77.0 - - - +
334A LEU* 1.3 60.7 + - - +
336A ALA* 3.4 2.4 + - - +
337A ILE* 3.1 32.3 + - - +
351A LEU 5.1 0.7 - - - +
354A HIS* 4.3 11.9 - - - -
355A LEU* 4.3 10.3 - - - -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A VAL* 3.1 20.2 + - + +
331A GLN* 3.3 28.2 + - - +
333A GLY* 1.3 76.0 - - - +
335A ASP* 1.3 59.1 + - - +
337A ILE* 3.4 11.1 + - + +
338A GLN* 3.0 27.6 + - - +
355A LEU* 3.7 27.1 - - + +
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 3.8 36.4 + - + +
289A ASP* 4.3 2.8 - - - +
290A MET* 3.9 15.3 - - + -
293A ARG* 2.8 32.8 + - - -
331A GLN* 3.0 19.5 + - - +
332A SER 3.2 7.4 + - - +
334A LEU* 1.3 75.5 - - - +
336A ALA* 1.3 63.7 + - - +
338A GLN* 3.3 7.4 + - - +
339A THR* 2.9 28.4 + - - -
----------------------------------------------------------
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.6 26.7 - - + -
263A THR* 3.5 26.5 - - - +
290A MET* 4.1 2.2 - - + -
332A SER 2.9 14.9 + - - +
333A GLY 3.8 4.3 - - - +
335A ASP* 1.3 72.7 - - - +
337A ILE* 1.3 68.8 + - + +
339A THR* 3.1 14.4 + - - -
340A PHE* 3.2 21.0 + - + -
351A LEU* 4.6 8.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLY 3.1 16.2 + - - +
334A LEU* 3.5 13.5 - - + +
335A ASP 3.3 0.2 - - - -
336A ALA* 1.3 77.7 - - - +
338A GLN* 1.4 69.3 + - - +
340A PHE 3.1 10.6 + - - -
341A GLY* 3.1 11.4 + - - +
344A ALA* 3.6 24.4 - - + +
345A MET* 4.2 13.0 - - + -
351A LEU* 4.0 33.7 - - + +
352A VAL* 4.2 13.2 - - + -
355A LEU* 3.9 27.1 - - + -
----------------------------------------------------------
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 3.9 36.8 + - - +
334A LEU 3.0 13.7 + - - +
335A ASP* 3.7 8.7 - - - +
336A ALA 3.2 0.2 - - - -
337A ILE* 1.4 83.6 - - - +
339A THR* 1.3 62.6 + - - +
341A GLY* 3.4 13.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR* 3.7 29.6 - - + +
266A TYR* 3.9 6.9 - - + -
267A ALA* 4.3 7.2 - - + -
277A ILE* 3.5 32.8 - - + +
283A VAL* 4.4 7.4 + - + +
286A ARG* 4.5 13.8 + - - +
287A ILE* 4.2 20.8 - - + +
290A MET* 5.1 0.2 - - - -
335A ASP 2.9 16.3 + - - -
336A ALA 3.1 8.5 + - - -
338A GLN* 1.3 78.2 - - - +
340A PHE* 1.3 62.0 + - + +
----------------------------------------------------------
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.8 23.3 - - + -
263A THR* 4.1 21.8 - - + -
266A TYR* 3.4 63.1 + + + -
336A ALA 3.2 19.2 + - - -
337A ILE 3.1 7.6 + - - +
339A THR* 1.3 81.9 - - - +
341A GLY* 1.3 63.6 + - - +
342A GLY 3.5 0.5 + - - -
343A ALA* 3.3 20.1 + - + +
344A ALA* 3.7 17.5 - - + +
349A LEU* 3.8 26.9 - - + -
351A LEU* 3.3 22.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 3.1 10.6 + - - +
338A GLN* 3.4 11.2 + - - -
339A THR 3.4 4.0 + - - -
340A PHE* 1.3 76.6 - - - +
342A GLY* 1.3 64.3 + - - -
344A ALA* 2.9 20.4 + - - +
345A MET* 4.4 4.8 + - - +
----------------------------------------------------------
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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