Contacts of the helix formed by residues 313 - 345 (chain A) in PDB entry 2AY6
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 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU 5.2 0.2 - - - -
311A THR 3.2 11.8 - - - +
312A THR* 1.3 82.5 - - + +
314A GLU* 1.3 78.3 + - - +
316A ARG* 3.8 9.6 - - + +
317A ALA* 3.0 33.7 + - - +
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Residues in contact with GLU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 3.3 22.1 - - + +
313A PRO* 1.3 93.3 - - - +
315A LEU* 1.3 69.3 + - + +
317A ALA* 3.9 3.8 - - - +
318A ASP* 3.4 19.8 + - - +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.8 22.7 - - + +
55A ALA* 4.1 19.1 - - + -
56A ALA* 4.8 2.7 - - - -
59A ARG* 4.5 19.5 - - - +
308A THR* 4.0 22.7 - - + +
309A VAL* 3.8 18.6 - - + -
312A THR* 2.7 36.0 + - + +
314A GLU* 1.3 80.6 - - + +
316A ARG* 1.3 65.9 + - - +
318A ASP* 2.8 10.2 + - + +
319A TRP* 2.8 23.0 + - - +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 5.6 0.8 + - - -
85A GLU* 5.7 3.0 - - - +
86A LEU* 4.0 28.6 - - - +
309A VAL* 3.0 25.6 + - - +
310A LEU* 3.2 35.7 + - + +
312A THR 2.9 11.5 + - - +
313A PRO* 3.8 9.2 - - + +
315A LEU* 1.3 73.4 - - - +
317A ALA* 1.3 64.0 + - - +
319A TRP* 3.2 6.8 + - + +
320A MET* 3.0 71.4 + - + +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PRO 3.0 19.2 + - - +
314A GLU* 3.9 5.4 - - - +
316A ARG* 1.3 76.4 - - - +
318A ASP* 1.3 63.3 + - - +
320A MET* 3.5 8.3 + - - +
321A ALA* 3.1 22.9 + - - +
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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
----------------------------------------------------------
51A ARG* 3.2 52.1 + - - +
52A ALA* 3.7 10.1 + - + -
314A GLU 3.4 11.0 + - - +
315A LEU* 2.8 12.5 + - + +
317A ALA* 1.3 78.8 - - - +
319A TRP* 1.3 60.3 + - - +
321A ALA* 3.3 8.4 + - - +
322A GLU* 3.0 19.6 + - - +
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Residues in contact with TRP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.8 19.7 - - + -
52A ALA* 3.8 13.0 - - + +
53A VAL* 5.4 1.6 - - + -
86A LEU* 4.3 14.1 - - + -
233A LEU* 3.6 35.2 - - + -
259A ASN* 2.9 28.0 + - - -
260A PHE* 3.5 42.8 - + - -
309A VAL* 3.6 22.2 - - + -
310A LEU* 3.9 21.5 - - + -
315A LEU 2.8 9.2 + - - +
316A ARG* 3.6 10.3 - - + +
318A ASP* 1.3 70.7 - - - +
320A MET* 1.3 86.0 + - + +
322A GLU* 3.0 7.1 + - - +
323A LEU* 2.9 41.5 + - + +
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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
----------------------------------------------------------
86A LEU* 5.6 1.6 - - + -
233A LEU* 3.6 30.5 - - + -
234A GLU* 6.4 1.6 - - + -
316A ARG* 3.0 57.1 + - + +
317A ALA* 3.9 7.0 - - - +
319A TRP* 1.3 92.4 - - + +
321A ALA* 1.3 58.1 + - - +
323A LEU* 3.8 5.4 - - - +
324A GLU* 2.9 35.3 + - + +
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Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 4.6 7.4 - - - +
317A ALA 3.1 13.5 + - - +
318A ASP* 3.3 15.3 - - - +
319A TRP 3.0 0.6 - - - -
320A MET* 1.3 79.4 - - - +
322A GLU* 1.3 60.1 + - - +
324A GLU* 3.5 5.8 + - - +
325A ALA* 3.2 22.2 + - - +
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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
----------------------------------------------------------
48A PRO* 5.4 7.1 - - - +
49A ILE 4.5 2.9 - - - +
50A MET* 3.4 36.4 - - + +
51A ARG* 3.0 58.4 + - - +
52A ALA 4.5 1.4 + - - -
318A ASP* 3.0 7.7 + - - +
319A TRP* 3.0 10.1 + - - +
321A ALA* 1.3 73.4 - - - +
323A LEU* 1.3 67.6 + - - +
325A ALA* 3.2 8.5 + - + +
326A VAL* 3.1 31.2 + - + +
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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
----------------------------------------------------------
50A MET* 4.0 10.4 - - + +
226A GLN 4.1 2.5 - - - +
227A GLY* 3.7 19.3 - - - +
228A PHE* 4.0 31.0 - - + -
233A LEU* 4.0 21.8 - - + -
259A ASN* 3.5 25.8 - - + +
319A TRP* 2.9 44.1 + - + +
320A MET* 3.8 5.6 - - - +
322A GLU* 1.3 77.5 - - - +
324A GLU* 1.3 57.2 + - - +
326A VAL* 3.2 8.9 + - + +
327A ARG* 2.9 26.3 + - - +
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Residues in contact with GLU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY 4.8 1.6 - - - +
230A ASP 4.4 0.6 - - - +
231A GLY* 4.2 10.9 - - - -
233A LEU 5.2 0.5 + - - -
320A MET* 2.9 19.5 + - + +
321A ALA* 3.7 7.2 - - - +
323A LEU* 1.3 75.1 - - - +
325A ALA* 1.3 60.3 + - - +
327A ARG* 2.9 46.7 + - - +
328A SER* 2.8 40.1 + - - -
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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 ALA 3.2 11.3 + - - +
322A GLU* 3.2 12.4 + - + +
324A GLU* 1.3 77.7 - - - +
326A VAL* 1.3 54.3 + - + +
328A SER* 3.3 6.2 + - - -
329A GLY* 2.8 32.6 + - - -
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Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.5 50.4 + - + +
50A MET* 4.5 12.3 - - + -
228A PHE* 4.0 22.2 - - + -
322A GLU* 3.1 21.7 + - + +
323A LEU* 3.3 12.1 - - + +
325A ALA* 1.3 77.8 - - + +
327A ARG* 1.3 62.6 + - - +
329A GLY* 3.3 2.0 + - - -
330A MET* 3.0 28.1 + - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLY 3.5 21.3 - - - +
228A PHE* 3.7 11.4 - - - +
229A GLY 2.8 39.5 + - - +
230A ASP* 3.3 32.2 + - - +
231A GLY 3.6 0.4 - - - +
323A LEU* 2.9 13.6 + - + +
324A GLU* 2.9 43.3 + - - +
326A VAL* 1.3 76.8 - - - +
328A SER* 1.3 71.2 + - - +
330A MET* 3.4 11.3 + - - +
331A LEU* 3.1 50.5 + - - +
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 2.8 33.6 + - - -
325A ALA* 3.7 6.1 - - - -
327A ARG* 1.3 80.7 + - - +
329A GLY* 1.3 64.8 + - - +
331A LEU* 3.3 7.9 + - - +
332A ARG* 3.0 52.2 + - - +
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Residues in contact with GLY 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA 2.8 20.9 + - - -
326A VAL 3.7 1.6 - - - -
328A SER* 1.3 72.5 - - - +
330A MET* 1.3 62.2 + - - +
332A ARG* 3.1 23.9 + - - +
333A LEU* 3.0 24.7 + - - +
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Residues in contact with MET 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.2 29.2 - - + -
228A PHE* 3.5 46.0 - - + +
326A VAL* 3.0 21.6 + - - +
327A ARG* 3.9 7.4 - - - +
329A GLY* 1.3 75.7 - - - +
331A LEU* 1.3 64.5 + - - +
333A LEU* 3.1 14.0 + - + +
334A ARG* 3.0 25.6 + - - +
358A GLY 4.2 16.6 - - - +
359A MET* 3.6 24.5 - - - -
389A ILE* 3.6 12.0 - - + +
390A ALA* 4.7 10.5 - - + -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLY 4.9 0.4 - - - +
230A ASP* 5.5 0.4 - - - +
327A ARG* 3.1 45.3 + - - +
328A SER* 3.6 7.0 - - - +
330A MET* 1.3 75.5 - - - +
332A ARG* 1.3 64.0 + - + +
334A ARG* 3.1 17.0 + - + +
335A GLU* 3.0 46.8 + - + +
354A ALA 5.3 3.6 - - - +
357A ARG* 4.4 33.2 - - - +
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Residues in contact with ARG 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A SER* 3.0 42.6 + - - +
329A GLY* 3.4 13.9 - - - +
331A LEU* 1.3 76.8 - - + +
333A LEU* 1.3 57.0 + - + +
335A GLU* 3.1 16.3 + - - +
336A GLN* 2.8 41.3 + - + +
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Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLY* 3.0 35.0 + - - +
330A MET* 3.1 12.8 + - + +
332A ARG* 1.3 75.0 - - + +
334A ARG* 1.3 57.4 + - - +
336A GLN* 3.2 14.7 + - - +
337A LEU* 2.8 31.5 + - - +
389A ILE* 3.8 20.4 - - + +
390A ALA* 5.7 3.4 - - - +
392A LEU* 3.9 28.0 - - + +
393A ASN* 4.0 8.1 - - - -
394A ASP* 5.1 0.7 - - - +
397A ILE* 3.8 24.9 - - + +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A MET* 3.0 19.2 + - - +
331A LEU* 3.1 18.6 + - + +
333A LEU* 1.3 76.0 - - - +
335A GLU* 1.3 63.6 + - + +
337A LEU* 3.2 4.6 + - - +
338A ALA* 2.9 25.7 + - - +
353A VAL* 2.9 39.1 + - + +
354A ALA* 4.5 8.3 - - - -
356A HIS* 3.3 28.3 + - - +
357A ARG* 4.0 4.8 - - - +
358A GLY 2.8 35.9 + - - +
360A PHE 3.0 24.4 + - - -
361A SER* 2.9 19.8 + - - -
389A ILE* 3.7 29.0 - - + +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.0 40.9 + - + +
332A ARG* 3.5 17.4 + - - +
334A ARG* 1.3 75.2 - - + +
336A GLN* 1.3 58.4 + - + +
338A ALA* 3.7 5.9 - - - +
339A GLY* 2.9 26.7 + - - -
354A ALA* 4.8 11.0 - - + -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 2.8 22.0 + - + +
333A LEU* 3.5 23.9 - - - +
335A GLU* 1.3 74.1 - - + +
337A LEU* 1.3 60.1 + - - +
339A GLY* 3.2 1.4 + - - -
340A GLU* 2.8 30.8 + - - +
394A ASP* 3.3 27.1 + - - +
397A ILE* 3.7 22.0 - - + +
----------------------------------------------------------
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU 2.8 20.3 + - - +
334A ARG 3.6 3.6 - - - +
336A GLN* 1.3 71.3 - - - +
338A ALA* 1.3 58.7 + - - +
340A GLU* 3.1 2.9 + - - +
341A LEU* 2.8 54.6 + - + +
353A VAL* 3.7 22.9 - - + -
363A LEU* 5.5 0.9 - - + -
387A ILE* 4.4 13.9 - - + -
389A ILE* 4.9 5.6 - - + -
392A LEU* 4.9 7.9 - - + -
397A ILE* 3.9 33.3 - - + +
400A LEU* 4.0 31.2 - - + -
401A ALA* 4.4 6.1 - - + +
404A ILE* 5.4 1.3 - - + -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ARG 2.9 16.2 + - - +
335A GLU* 3.7 4.3 - - - +
337A LEU* 1.3 76.7 - - - +
339A GLY* 1.3 56.5 - - - +
341A LEU* 3.2 8.0 + - - +
342A ARG* 2.9 29.3 + - - +
350A PHE* 4.4 15.2 - - - +
351A GLY* 4.8 5.6 - - - +
353A VAL* 4.6 4.0 - - + +
354A ALA* 4.0 28.0 - - + +
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Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU 2.9 17.8 + - - -
336A GLN* 3.6 1.6 - - - -
338A ALA* 1.3 76.9 - - - +
340A GLU* 1.3 63.4 + - - +
342A ARG* 3.1 18.0 + - - +
343A ASP* 3.2 21.4 + - - +
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN 2.8 16.5 + - - +
337A LEU 3.5 4.3 - - - +
339A GLY* 1.3 75.4 - - - +
341A LEU* 1.3 61.7 + - - +
343A ASP* 3.3 7.5 + - - +
344A LEU* 3.0 46.9 + - + +
397A ILE* 4.0 15.6 - - + +
398A PRO* 3.6 30.4 - - + +
401A ALA* 3.4 22.4 - - + -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 2.8 38.3 + - + +
338A ALA* 3.6 5.4 - - - +
340A GLU* 1.3 77.8 - - - +
342A ARG* 1.3 51.3 + - - +
344A LEU* 3.9 3.2 - - - +
345A SER* 2.6 39.3 + - - -
350A PHE* 3.8 40.6 - - + -
353A VAL* 4.6 8.7 - - + -
363A LEU* 6.1 0.4 - - + -
401A ALA* 3.8 36.3 - - + +
404A ILE* 4.1 20.6 - - + -
405A ILE* 4.3 14.4 - - + -
----------------------------------------------------------
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA 2.9 13.2 + - - +
339A GLY* 3.1 12.3 + - - +
341A LEU* 1.3 75.2 - - - +
343A ASP* 1.3 63.7 + - - +
346A GLY* 2.8 29.8 + - - -
347A SER* 3.1 26.4 + - - +
348A ASP* 2.9 51.1 + - - +
351A GLY* 5.7 4.2 - - - -
----------------------------------------------------------
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLY 3.2 15.7 + - - +
340A GLU* 3.3 10.6 + - - +
342A ARG* 1.3 81.1 - - - +
344A LEU* 1.3 68.8 + - + +
346A GLY* 4.2 3.8 + - - -
----------------------------------------------------------
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 3.0 47.4 + - - +
341A LEU* 4.1 2.7 - - - +
343A ASP* 1.3 86.9 - - + +
345A SER* 1.3 56.6 + - - +
398A PRO 6.0 0.2 - - - +
401A ALA* 4.8 9.9 - - + +
402A ARG* 4.9 17.5 - - + +
405A ILE* 3.2 32.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU 2.6 22.8 + - - -
344A LEU* 1.3 77.9 - - - +
346A GLY* 1.3 65.5 + - - +
347A SER* 3.5 28.9 + - - -
349A ARG* 4.0 21.2 + - - +
350A PHE* 4.3 9.5 - - - -
405A ILE* 3.8 14.6 - - - -
----------------------------------------------------------
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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