Contacts of the helix formed by residues 469 - 492 (chain A) in PDB entry 3Q7I
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 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.7 5.2 - - - -
162A TYR* 3.5 10.3 - - - -
467A GLU* 3.6 25.7 + - - +
468A LEU* 1.3 74.4 - - - +
470A PRO* 1.4 78.0 - - - +
471A TYR* 3.5 8.6 + - - +
472A SER* 3.0 25.7 + - - -
473A LEU* 2.9 23.6 + - - +
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Residues in contact with PRO 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.6 26.7 - - + -
162A TYR* 3.7 29.6 - - + -
280A ASN* 3.4 50.0 - - + +
283A LYS* 4.0 9.0 - - + -
284A LEU* 3.3 19.3 - - - +
469A SER* 1.4 86.9 - - - +
471A TYR* 1.3 62.5 + - - +
474A GLY 3.0 18.4 + - - -
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Residues in contact with TYR 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 2.6 36.6 + - - -
283A LYS* 3.3 26.3 + - + +
286A ALA* 3.6 15.9 + - + -
287A GLY* 3.2 38.4 - - - -
290A SER* 3.3 11.2 - - - -
469A SER* 3.2 7.5 + - - +
470A PRO* 1.3 80.4 - - - +
472A SER* 1.3 61.6 + - - +
474A GLY 3.2 1.9 + - - -
475A ALA* 3.0 18.5 + - - +
605A IPA 3.5 27.8 - - + -
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Residues in contact with SER 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.4 1.4 - - - +
465A LEU* 3.7 14.8 - - - +
466A ASP* 4.5 3.8 - - - -
467A GLU 2.6 28.2 + - - -
468A LEU* 3.5 2.6 - - - -
469A SER* 3.0 27.7 + - - -
471A TYR* 1.3 76.6 - - - +
473A LEU* 1.3 55.2 + - - +
475A ALA* 3.4 2.9 + - - +
476A LEU* 2.9 28.8 + - - +
605A IPA 3.3 27.8 - - - -
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 4.5 5.6 - - - -
155A VAL* 4.0 23.6 - - + -
158A ALA* 3.6 24.7 - - + -
159A LEU* 3.8 20.6 - - + -
284A LEU* 4.4 2.0 - - + -
333A LEU* 4.1 25.6 - - + -
336A PHE* 4.6 1.6 - - + -
468A LEU* 4.1 14.1 - - + -
469A SER 2.9 17.7 + - - +
470A PRO 3.8 2.2 - - - +
472A SER* 1.3 75.5 + - - +
474A GLY* 1.3 65.2 + - - +
476A LEU* 3.2 11.4 + - + +
477A ILE* 3.0 42.4 + - + +
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Residues in contact with GLY 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TRP* 3.7 9.7 - - - -
284A LEU* 3.5 32.9 - - - +
288A ALA* 3.5 12.1 - - - +
470A PRO 3.0 12.1 + - - -
471A TYR 3.2 1.3 + - - -
473A LEU* 1.3 77.5 - - - +
475A ALA* 1.3 60.2 + - - +
477A ILE 3.5 0.2 + - - -
478A ALA* 3.1 24.6 + - - +
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Residues in contact with ALA 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.8 6.5 - - + -
287A GLY 3.4 21.1 - - - +
288A ALA* 4.3 0.4 - - - +
291A VAL* 3.5 24.3 - - + +
471A TYR 3.0 11.2 + - - +
472A SER 3.5 8.3 - - - +
473A LEU 3.3 0.2 - - - -
474A GLY* 1.3 73.3 - - - +
476A LEU* 1.3 62.5 + - - +
478A ALA 3.2 1.6 + - - -
479A LEU* 3.0 21.4 + - - +
605A IPA 3.6 25.8 - - + -
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Residues in contact with LEU 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.3 1.1 - - - +
333A LEU* 4.6 9.0 - - + -
336A PHE* 3.8 26.2 - - + -
395A ILE* 4.1 31.2 - - + -
463A ILE* 4.4 17.7 - - + -
465A LEU* 4.2 19.5 - - + -
468A LEU* 5.0 0.4 - - + -
472A SER 2.9 17.4 + - - +
473A LEU* 3.2 14.1 + - + +
475A ALA* 1.3 76.3 - - - +
477A ILE* 1.3 62.2 + - - +
479A LEU* 3.3 20.7 + - + +
480A TYR* 3.5 34.9 - - + -
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Residues in contact with ILE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 3.8 21.5 - - + -
155A VAL* 4.2 11.2 - - + -
264A LEU* 4.4 4.0 - - + -
265A TRP* 3.6 28.9 - - + -
284A LEU* 4.7 2.2 - - + -
336A PHE* 4.1 16.6 - - + -
339A TYR* 3.9 24.5 - - + +
340A LEU* 5.0 2.5 - - + -
473A LEU* 3.0 38.3 + - + +
474A GLY* 4.0 3.6 - - - +
476A LEU* 1.3 75.3 - - - +
478A ALA* 1.3 59.5 + - - +
480A TYR* 3.1 8.3 + - - +
481A GLU* 2.9 33.1 + - + +
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 4.0 11.4 - - - +
265A TRP* 4.6 0.4 - - - -
288A ALA* 3.9 19.5 - - + +
291A VAL* 3.7 21.3 - - + -
292A ASP* 4.4 1.3 - - - +
474A GLY 3.1 18.8 + - - +
475A ALA 3.2 4.2 + - - +
477A ILE* 1.3 74.7 - - - +
479A LEU* 1.3 65.1 + - - +
481A GLU* 3.2 11.9 + - - +
482A HIS* 3.0 27.9 + - - -
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 5.6 2.5 - - + -
39A ILE* 4.4 30.1 - - + -
291A VAL* 3.7 24.4 - - + +
294A HIS* 5.0 2.9 - - + -
304A ILE* 3.8 35.7 - - + -
305A PRO* 3.8 20.5 - - + +
308A MET* 4.1 15.3 - - + +
463A ILE* 4.8 7.9 - - + -
475A ALA 3.0 19.3 + - - +
476A LEU* 3.5 18.8 - - + +
477A ILE 3.2 0.4 - - - -
478A ALA* 1.3 76.3 - - - +
480A TYR* 1.3 58.5 + - + +
482A HIS 3.4 1.0 + - - -
483A LYS* 2.9 26.2 + - - +
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Residues in contact with TYR 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A MET* 3.4 24.9 - - + -
326A LEU* 3.6 19.1 - - + +
336A PHE* 4.2 8.7 - + - -
340A LEU* 3.5 40.4 - - + -
367A LEU* 6.1 4.3 - - + -
393A ASP* 2.7 28.9 + - - -
395A ILE* 3.6 2.9 - - + +
463A ILE* 3.5 15.7 - - + +
476A LEU* 3.5 36.6 - - + -
477A ILE 3.1 7.4 + - - +
479A LEU* 1.3 78.5 - - + +
481A GLU* 1.3 66.1 + - - +
483A LYS* 3.5 20.4 - - + +
484A ILE* 3.0 34.9 + - + +
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Residues in contact with GLU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 3.6 9.0 + - - +
92A ARG* 2.8 34.2 + - - +
261A ARG 5.8 0.2 - - - +
262A TYR* 3.6 41.6 - - + -
265A TRP* 2.9 33.6 + - - -
339A TYR* 4.2 6.0 + - + +
340A LEU* 5.4 1.7 - - + +
343A ALA* 5.9 3.8 - - + -
477A ILE* 2.9 24.3 + - + +
478A ALA* 3.2 7.3 + - - +
480A TYR* 1.3 76.4 - - - +
482A HIS* 1.3 68.1 + - - +
484A ILE* 3.4 7.8 + - + +
485A PHE* 3.2 20.8 + - - +
496A TYR* 4.8 1.7 + - - -
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Residues in contact with HIS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 4.6 8.4 - - - -
73A PHE* 4.6 1.3 - + - -
88A HIS* 4.9 5.3 + - - -
89A THR* 3.8 20.0 - - + -
92A ARG* 3.9 7.5 + - - -
291A VAL* 4.1 11.4 - - + -
292A ASP* 2.7 30.9 + - - -
295A PHE* 3.4 46.6 - + + -
305A PRO* 3.5 21.8 - - + -
478A ALA 3.0 18.0 + - - +
481A GLU* 1.3 78.4 + - + +
483A LYS* 1.3 65.0 + - - +
485A PHE* 3.3 8.5 + - - +
486A VAL* 2.9 27.0 + - - +
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Residues in contact with LYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PRO* 3.8 13.1 - - - +
308A MET* 3.7 32.7 - - + +
309A ALA* 3.5 17.3 - - - +
312A ALA* 3.5 23.8 - - - +
324A GLN* 3.0 28.1 + - - +
344A ASP* 5.1 4.5 + - - +
367A LEU* 5.7 3.2 - - - +
393A ASP* 4.5 8.1 + - - -
479A LEU 2.9 15.3 + - - +
480A TYR* 3.2 29.2 + - + +
482A HIS* 1.3 75.3 - - - +
484A ILE* 1.3 65.2 + - + +
486A VAL 3.2 1.2 + - - -
487A GLN* 3.0 36.6 + - - +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 3.5 21.1 - - - +
340A LEU* 5.0 2.5 - - + +
343A ALA* 3.6 16.6 - - + +
344A ASP* 3.6 43.3 - - + +
347A SER* 3.6 21.8 - - - -
348A ASN* 3.1 21.9 + - - +
480A TYR* 3.0 27.0 + - + +
481A GLU* 3.6 6.5 - - - +
483A LYS* 1.3 79.5 - - + +
485A PHE* 1.3 64.5 + - - +
487A GLN* 3.3 6.5 + - - +
488A GLY 3.0 18.0 + - - -
495A SER* 3.9 3.9 + - - +
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Residues in contact with PHE 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.9 1.3 - - + -
68A LYS* 3.5 28.3 - - + -
69A ILE* 4.0 15.9 - - + -
72A MET* 3.8 28.9 - - + -
78A ILE* 3.9 13.7 - - + -
295A PHE* 3.6 36.8 - + - -
481A GLU 3.2 12.9 + - - +
482A HIS* 3.3 9.4 + - - +
484A ILE* 1.3 77.2 - - - +
486A VAL* 1.3 62.5 + - - +
488A GLY* 3.2 3.1 + - - -
489A VAL* 3.0 40.4 + - + +
495A SER* 4.6 3.0 + - - -
496A TYR* 3.2 35.0 + + - +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.8 32.3 - - + -
295A PHE* 3.6 29.8 - - + -
305A PRO 4.4 0.9 - - - +
306A VAL* 4.0 23.6 - - + +
309A ALA* 3.4 24.5 - - + -
310A LEU 5.2 0.2 - - - +
482A HIS 2.9 21.0 + - - +
485A PHE* 1.3 74.3 - - - +
487A GLN* 1.3 65.1 + - - +
489A VAL* 3.1 2.8 + - - +
490A LEU* 2.9 34.9 + - + +
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA* 3.6 15.3 - - + -
312A ALA* 3.4 23.4 - - - +
313A SER* 2.9 29.5 + - - +
316A SER* 5.1 0.2 + - - -
324A GLN* 4.9 4.8 + - - +
344A ASP* 4.6 12.7 + - - -
348A ASN* 3.8 14.4 - - - +
483A LYS* 3.0 39.9 + - - +
484A ILE* 3.8 7.5 - - - +
485A PHE 3.3 0.2 - - - -
486A VAL* 1.3 76.0 - - - +
488A GLY* 1.3 62.7 + - - +
490A LEU* 3.3 5.6 + - - +
491A TRP* 3.0 48.1 + - + -
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Residues in contact with GLY 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 3.8 3.4 - - - +
484A ILE 3.0 10.9 + - - -
485A PHE 3.2 1.5 + - - -
487A GLN* 1.3 76.5 - - - +
489A VAL* 1.3 61.0 - - - +
491A TRP 3.3 1.0 + - - -
492A ASP 3.0 18.5 + - - -
493A ILE* 3.1 32.0 + - - +
495A SER* 3.5 22.4 - - - -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 4.8 3.6 - - - +
64A SER* 3.6 24.7 + - - +
65A LEU* 3.8 33.2 - - + +
68A LYS* 3.9 19.1 - - + -
485A PHE* 3.0 43.7 + - + +
486A VAL 3.6 7.0 - - - +
488A GLY* 1.3 75.0 - - - +
490A LEU* 1.3 66.5 + - + +
492A ASP* 3.0 16.2 + - - +
493A ILE 5.2 0.7 - - - -
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 21.3 - - + +
3A PHE* 3.6 38.0 + - + +
60A ALA* 4.2 14.4 - - + -
63A SER* 3.6 33.9 - - - +
65A LEU* 4.9 5.8 - - + -
309A ALA* 5.1 1.1 - - + -
310A LEU* 3.8 31.0 - - + -
313A SER* 5.1 6.7 - - - +
361A TYR* 5.2 0.7 + - - -
486A VAL* 2.9 35.6 + - + +
487A GLN* 3.9 5.8 - - - +
489A VAL* 1.3 77.6 - - - +
491A TRP* 1.3 62.6 + - + +
492A ASP* 3.6 1.0 + - - +
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Residues in contact with TRP 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 4.5 14.9 - + + -
4A CYS* 5.6 4.5 - - + +
313A SER* 3.5 25.9 + - - -
316A SER* 3.9 17.9 - - - -
317A CYS* 6.2 1.0 - - - +
348A ASN* 4.0 9.6 - - + -
359A VAL* 4.7 0.3 - - - +
361A TYR* 2.5 50.0 + + + -
362A GLN 3.8 11.7 + - - -
363A THR* 3.4 31.6 - - + -
364A GLY* 3.5 21.1 - - - -
365A VAL* 5.0 2.0 - - + -
487A GLN* 3.0 48.7 + - + +
488A GLY 3.3 3.8 + - - +
489A VAL 3.2 0.2 - - - -
490A LEU* 1.3 78.4 - - + +
492A ASP* 1.3 64.0 + - - +
493A ILE* 3.3 27.3 + - + +
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Residues in contact with ASP 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1A ASN 5.8 0.2 + - - -
0A ALA* 3.4 32.0 + - + +
1A MET 5.5 2.5 - - - +
353A ASN* 3.1 23.4 + - + +
354A ILE* 2.9 41.7 + - - +
355A ALA* 5.4 0.7 + - - +
361A TYR* 4.2 6.1 - - - +
488A GLY 3.0 4.4 + - - -
489A VAL* 3.0 14.2 + - - +
490A LEU 3.3 2.4 - - - +
491A TRP* 1.3 79.2 - - - +
493A ILE* 1.3 59.0 + - - +
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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