Contacts of the helix formed by residues 463 - 486 (chain A) in PDB entry 2P8Q
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 GLU 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A VAL* 3.2 43.3 - - + +
425A ARG* 2.5 31.0 + - - -
462A ALA* 1.3 75.9 - - - +
464A PRO* 1.3 67.4 - - + +
465A ARG* 4.6 7.9 - - + +
466A VAL* 2.8 27.0 + - - +
467A ALA 2.9 10.2 + - - -
516A ARG* 4.5 0.7 - - - +
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Residues in contact with PRO 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ALA 3.6 0.4 - - - -
463A GLU* 1.3 87.8 - - + +
465A ARG* 1.3 56.4 + - - +
467A ALA* 4.5 1.1 - - + +
468A SER* 3.0 34.7 + - - -
516A ARG* 3.7 10.1 - - - +
518A ASP* 3.5 26.2 - - - +
521A GLN* 3.8 33.7 - - + +
522A ASN* 3.2 22.1 - - - +
524A LEU* 4.3 14.7 - - + +
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Residues in contact with ARG 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP 5.8 0.4 + - - -
335A GLU 4.8 5.5 + - - -
337A ASP* 3.6 42.0 + - - +
422A VAL* 4.1 19.2 - - + +
423A VAL* 4.0 41.6 + - - +
426A ASP* 3.0 39.4 + - - +
463A GLU* 4.7 5.4 - - + -
464A PRO* 1.3 78.3 - - - +
466A VAL* 1.3 69.6 + - + +
468A SER* 4.4 2.9 - - - -
469A ASN* 3.4 20.3 + - - -
522A ASN* 3.5 25.0 - - - +
32B LYS* 5.7 1.6 - - - +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A MET* 5.1 3.8 - - + -
422A VAL* 4.0 25.4 - - + +
425A ARG* 4.0 25.6 - - + +
426A ASP* 3.8 26.9 - - - +
429A ALA* 4.1 1.1 - - + +
459A GLY* 4.4 2.2 - - - +
462A ALA* 3.8 20.0 - - + -
463A GLU* 2.8 15.1 + - - +
465A ARG* 1.3 77.9 - - + +
467A ALA* 1.3 64.4 + - - +
468A SER 3.2 1.3 - - - -
469A ASN* 3.2 6.2 + - - +
470A VAL* 3.1 36.6 + - + +
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLY 3.5 22.1 + - - +
460A LEU* 3.7 19.1 - - - +
462A ALA 3.8 0.7 - - - +
463A GLU 2.9 13.5 + - - +
464A PRO 4.2 2.2 - - - +
466A VAL* 1.3 77.4 - - - +
468A SER* 1.3 57.6 + - - +
470A VAL* 3.4 4.0 - - - +
471A CYS* 2.9 35.2 + - - -
513A THR* 5.0 0.9 - - + -
516A ARG* 3.8 13.9 - - - +
524A LEU* 4.4 11.7 - - + -
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A PRO 3.0 18.9 + - - -
465A ARG* 4.6 4.3 - - - -
466A VAL 3.2 0.2 - - - -
467A ALA* 1.3 79.5 - - - +
469A ASN* 1.3 63.0 + - - +
471A CYS* 3.4 6.2 + - - +
472A TRP* 3.3 15.4 + - - +
522A ASN* 3.3 21.3 + - - -
524A LEU* 4.5 8.0 - - - +
527A SER* 3.2 20.7 + - - -
34B LYS* 2.6 35.4 + - - -
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Residues in contact with ASN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ASP* 2.9 37.0 + - - -
429A ALA* 3.7 20.5 - - + +
430A TRP* 3.9 22.6 - - - +
465A ARG 3.4 12.6 + - - -
466A VAL 3.2 4.1 + - - +
468A SER* 1.3 76.2 + - - +
470A VAL* 1.3 60.8 + - - +
472A TRP* 3.3 11.1 + - + +
473A ALA* 2.8 27.5 + - - +
32B LYS* 4.9 7.6 - - - +
34B LYS* 3.5 24.8 + - - +
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A MET* 5.1 4.7 - - + -
429A ALA* 3.9 15.3 - - + -
455A CYS 5.6 0.2 - - - +
456A LEU* 3.2 44.0 - - + +
459A GLY* 4.1 14.1 - - - +
460A LEU* 3.6 17.9 - - + +
466A VAL* 3.1 24.8 + - + +
467A ALA* 3.4 10.3 - - - +
469A ASN* 1.3 74.4 - - - +
471A CYS* 1.3 58.6 + - - +
473A ALA* 3.1 8.1 + - - +
474A PHE* 2.8 30.8 + - + +
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Residues in contact with CYS 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A LEU* 3.8 19.7 - - - -
467A ALA 2.9 23.8 + - - -
468A SER 3.5 8.7 - - - +
470A VAL* 1.3 76.2 - - - +
472A TRP* 1.3 63.5 + - - +
474A PHE* 3.1 11.7 + - - +
475A SER* 3.1 3.5 + - - -
510A LEU* 4.2 5.6 - - - -
513A THR* 4.4 2.0 - - - -
524A LEU* 4.4 9.9 - - - -
527A SER* 3.8 20.0 - - - +
528A ALA* 3.8 30.3 - - - -
531A SER* 3.0 25.1 + - - -
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Residues in contact with TRP 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TRP* 3.4 39.5 - + - -
433A GLY* 3.5 29.6 - - - -
434A ARG* 3.8 11.4 - - + -
437A GLU* 3.5 34.6 + - + -
468A SER 3.3 2.9 + - - +
469A ASN* 3.3 9.8 + - - +
471A CYS* 1.3 78.9 - - - +
473A ALA* 1.3 62.1 + - - +
475A SER* 2.8 25.9 + - - -
476A SER* 3.1 25.4 + - - -
527A SER* 5.4 1.5 - - - -
33B SER 4.0 9.4 - - - -
34B LYS* 3.3 52.2 - - + -
35B TYR* 3.5 30.1 - - + +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ALA 4.2 3.4 - - - +
432A VAL* 4.6 3.1 - - + +
433A GLY* 3.6 32.8 - - - +
436A CYS* 4.2 3.8 - - - +
456A LEU* 4.0 24.0 - - + -
469A ASN 2.8 14.2 + - - +
470A VAL* 3.4 8.7 - - - +
472A TRP* 1.3 76.9 - - - +
474A PHE* 1.3 57.6 + - - +
476A SER* 3.1 5.1 + - - -
477A LEU* 2.8 30.3 + - - +
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Residues in contact with PHE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LEU* 4.1 18.8 - - + -
456A LEU* 3.4 49.6 - - + +
457A ILE* 3.4 31.4 - - + -
460A LEU* 4.1 17.5 - - + -
470A VAL* 2.8 20.5 + - + +
471A CYS* 3.4 9.2 - - - +
473A ALA* 1.3 76.5 - - - +
475A SER* 1.3 57.6 + - - +
477A LEU* 3.2 10.7 + - + +
478A ALA* 2.8 30.0 + - - +
499A LEU* 5.2 3.1 - - + +
506A ILE* 3.8 35.7 - - + -
510A LEU* 5.4 2.7 - - + -
531A SER* 3.9 8.3 - - - +
535A ILE* 5.6 2.9 - - + +
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Residues in contact with SER 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A CYS 3.1 3.1 + - - -
472A TRP* 2.8 31.4 + - - -
474A PHE* 1.3 78.4 - - - +
476A SER* 1.3 61.4 + - - +
478A ALA* 3.3 8.1 + - - +
479A GLU* 3.0 31.6 + - - +
530A GLU* 5.3 4.3 - - - +
531A SER* 3.8 21.9 + - - -
534A GLU* 3.8 28.8 - - - +
535A ILE* 5.3 1.1 - - - +
35B TYR 5.6 0.7 + - - -
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A GLY 3.8 12.1 + - - -
436A CYS* 3.7 20.4 - - - +
437A GLU* 4.0 14.6 - - - +
472A TRP* 3.1 29.3 + - - -
473A ALA 3.1 7.8 + - - -
475A SER* 1.3 78.4 + - - +
477A LEU* 1.3 65.1 + - - +
479A GLU* 3.2 12.4 + - - +
480A ALA* 3.1 23.2 + - - +
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A CYS* 3.6 26.2 - - + +
440A PRO* 6.4 0.9 - - + -
443A ALA* 4.0 17.0 - - + -
444A ILE* 4.7 11.8 - - + +
449A LEU* 4.3 14.6 - - + -
452A LEU* 4.5 6.3 - - + -
453A LEU* 3.6 31.0 - - + -
456A LEU* 4.1 17.5 - - + -
473A ALA 2.8 13.9 + - - +
474A PHE* 3.2 14.6 + - + +
476A SER* 1.3 75.9 - - - +
478A ALA* 1.3 56.9 + - - +
480A ALA* 3.4 4.6 + - + +
481A ALA* 2.9 30.9 + - + +
499A LEU* 4.3 11.9 - - + -
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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
----------------------------------------------------------
474A PHE* 2.8 16.6 + - + +
475A SER* 3.5 9.2 - - - +
476A SER 3.2 0.2 - - - -
477A LEU* 1.3 75.1 - - - +
479A GLU* 1.3 65.1 + - - +
481A ALA* 3.5 1.9 + - - +
482A TYR* 2.9 24.9 + - - +
497A TYR* 4.2 0.7 - - - -
499A LEU* 3.7 14.5 - - + +
534A GLU 4.9 0.2 - - - +
535A ILE* 3.1 42.6 - - + -
538A ASN* 3.8 7.4 - - + +
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Residues in contact with GLU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A SER* 3.0 22.8 + - - +
476A SER* 3.2 10.1 + - - +
478A ALA* 1.3 74.7 - - - +
480A ALA* 1.3 58.8 + - - +
482A TYR* 3.3 3.6 + - - +
483A GLU* 2.9 44.6 + - + +
534A GLU* 3.2 26.4 - - + +
538A ASN* 3.5 29.6 - - - +
35B TYR* 5.2 11.9 - - - -
46B ARG* 6.0 0.2 + - - -
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Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A CYS 4.3 3.8 - - - +
440A PRO* 3.3 37.7 - - + -
444A ILE* 3.4 10.7 - - + +
476A SER 3.1 13.1 + - - +
477A LEU* 3.7 5.6 - - + +
479A GLU* 1.3 75.5 - - - +
481A ALA* 1.3 67.1 + - - +
483A GLU* 3.1 10.6 + - - +
484A ALA* 2.8 25.6 + - - +
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Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ILE* 3.4 12.6 - - + +
477A LEU* 2.9 19.0 + - + +
478A ALA 3.8 2.5 - - - +
480A ALA* 1.3 74.8 - - - +
482A TYR* 1.3 63.5 + - - +
484A ALA* 3.4 3.2 + - - +
485A ALA* 3.1 24.3 + - - +
497A TYR* 3.7 16.7 - - + +
498A CYS* 3.5 29.5 - - - -
499A LEU* 3.9 12.1 - - + -
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Residues in contact with TYR 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A ALA 2.9 18.7 + - - +
479A GLU 3.4 4.3 - - - +
481A ALA* 1.3 76.2 - - - +
483A GLU* 1.3 68.3 + - + +
485A ALA* 3.2 13.3 + - - +
486A ASP* 2.9 32.6 + - - +
492A GLU 5.3 0.2 + - - -
493A GLU* 3.8 14.4 + - - +
494A PRO* 3.4 33.3 - - + +
497A TYR* 3.6 10.0 - + - -
537A LYS 4.7 2.9 - - - -
538A ASN* 3.6 26.9 - - + +
539A SER 3.3 42.2 - - - -
540A ALA 4.6 0.2 - - - -
594A LYS* 4.3 5.6 + - - -
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Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A GLU* 2.9 36.6 + - - +
480A ALA* 3.6 6.4 + - - +
482A TYR* 1.3 77.3 - - + +
484A ALA* 1.3 66.1 + - - +
486A ASP* 2.9 20.6 + - - +
487A VAL* 3.1 22.2 + - + +
538A ASN* 5.8 1.1 - - - +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ILE* 4.3 18.4 - - + -
480A ALA 2.8 19.5 + - - +
481A ALA* 3.5 8.7 - - - +
483A GLU* 1.3 72.5 - - - +
485A ALA* 1.3 62.8 - - - +
486A ASP 3.4 0.3 + - - -
487A VAL* 3.6 19.0 - - - +
498A CYS* 6.3 0.2 - - - -
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ALA 3.1 12.8 + - - +
482A TYR 3.6 8.7 - - - +
483A GLU 3.2 0.2 - - - -
484A ALA* 1.3 78.5 - - - +
486A ASP* 1.3 58.4 + - - +
487A VAL 3.7 0.4 - - - -
489A ASP 3.9 15.4 + - - -
490A ASP 4.7 3.1 + - - -
494A PRO* 4.1 12.8 - - + +
496A THR 3.9 9.9 - - - +
497A TYR* 3.7 24.2 - - + -
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Residues in contact with ASP 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A TYR* 2.9 41.1 + - - +
483A GLU* 2.9 14.8 + - - +
485A ALA* 1.3 79.7 - - - +
487A VAL* 1.3 64.1 + - - +
488A ALA* 3.8 5.4 - - - +
489A ASP 4.7 0.4 - - - +
490A ASP 5.3 8.5 - - - +
492A GLU 5.2 4.3 - - - +
493A GLU* 5.3 0.7 - - - -
494A PRO* 3.8 27.4 - - + +
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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