Contacts of the helix formed by residues 474 - 498 (chain A) in PDB entry 5OQN
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 ASN 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A LYS* 5.6 2.0 - - - -
472A SER* 2.3 29.5 + - - -
473A ILE* 1.3 88.7 - - + +
475A GLU* 1.3 63.4 + - - +
476A LYS* 3.6 28.9 - - - +
477A ASP* 2.9 31.3 + - - +
478A PHE* 3.2 1.9 + - - +
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Residues in contact with GLU 475 (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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469A LYS* 4.1 20.6 - - - +
474A ASN* 1.3 73.2 - - - +
476A LYS* 1.3 69.9 + - + +
478A PHE* 2.8 20.0 + - + +
479A VAL* 2.9 20.1 + - + +
588A LEU 4.4 0.7 - - - +
589A VAL* 3.1 18.0 - - + +
590A ASN* 2.7 34.7 + - - +
591A THR* 2.2 32.9 + - + +
596A ASN* 3.8 11.9 + - - +
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Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ASN* 3.5 17.1 - - - +
475A GLU* 1.3 76.7 - - + +
477A ASP* 1.3 65.2 + - - +
479A VAL* 3.3 3.9 + - - +
480A THR* 2.9 34.8 + - + +
595A GLU* 3.8 20.9 + - + +
596A ASN* 3.7 21.8 - - - +
597A ILE* 6.1 1.9 - - - +
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Residues in contact with ASP 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 5.6 1.7 + - - -
472A SER* 3.2 26.7 + - - +
473A ILE* 3.6 13.5 + - + +
474A ASN* 2.9 24.1 + - - +
476A LYS* 1.3 74.1 - - - +
478A PHE* 1.3 64.3 + - - +
480A THR* 2.4 26.6 + - - -
481A MET* 3.1 33.2 + - - +
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Residues in contact with PHE 478 (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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465A ILE* 3.5 28.9 - - + -
468A MET* 3.6 29.7 - - + +
469A LYS* 3.6 52.7 - - + +
472A SER* 3.0 22.5 + - - +
474A ASN 3.9 2.0 - - - +
475A GLU* 2.8 15.4 + - + +
477A ASP* 1.3 75.1 - - - +
479A VAL* 1.3 66.4 + - + +
481A MET* 3.6 4.4 + - - -
482A ALA* 3.2 18.6 + - + +
585A MET* 3.9 24.2 - - + -
588A LEU* 3.7 21.5 - - + -
589A VAL* 4.6 8.5 - - + -
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Residues in contact with VAL 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLU* 2.9 26.6 + - + +
476A LYS* 3.6 6.7 - - - +
478A PHE* 1.3 77.5 - - + +
480A THR* 1.3 64.0 + - + +
482A ALA* 3.1 3.5 + - - +
483A ILE* 2.8 43.0 + - + +
585A MET* 4.3 11.9 - - - -
589A VAL* 3.9 26.9 - - + -
596A ASN* 4.1 19.5 - - + +
598A LEU* 4.6 9.9 - - + -
599A ILE* 4.1 22.7 - - + -
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Residues in contact with THR 480 (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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476A LYS* 2.9 25.0 + - + +
477A ASP* 2.4 30.0 + - - -
479A VAL* 1.3 74.6 - - + +
481A MET* 1.3 64.3 + - - +
483A ILE* 3.3 2.3 + - - +
484A GLU* 2.9 24.8 + - - +
598A LEU* 3.6 29.2 - - + +
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Residues in contact with MET 481 (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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444A LEU* 3.7 33.7 - - + -
448A ARG* 3.2 55.9 - - - +
468A MET* 4.2 17.7 - - - -
472A SER* 5.3 3.4 - - - -
477A ASP* 3.1 43.2 + - - +
478A PHE* 4.1 4.9 - - - +
480A THR* 1.3 75.1 + - - +
482A ALA* 1.3 64.4 + - - +
484A GLU* 3.2 9.7 + - - +
485A ILE* 3.1 26.1 + - - +
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Residues in contact with ALA 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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465A ILE* 5.0 7.9 - - + -
468A MET* 3.6 18.9 - - + +
478A PHE* 3.2 15.0 + - + +
479A VAL 3.1 0.6 + - - -
481A MET* 1.3 78.4 - - - +
483A ILE* 1.3 63.7 + - - +
485A ILE* 2.9 11.3 + - - +
486A ILE* 2.9 28.9 + - + +
585A MET* 3.4 33.0 - - + -
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Residues in contact with ILE 483 (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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479A VAL* 2.8 40.5 + - + +
480A THR 3.7 4.3 - - - +
482A ALA* 1.3 70.7 - - - +
484A GLU* 1.3 57.9 + - - +
486A ILE* 3.0 7.4 + - + +
487A ASN* 2.8 52.6 + - - +
585A MET* 3.7 18.4 - - + -
598A LEU* 4.1 35.0 - - + +
599A ILE* 4.8 2.0 - - - +
602A LEU* 3.6 38.4 - - + -
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Residues in contact with GLU 484 (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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448A ARG* 3.7 22.5 + - - -
480A THR 2.9 12.3 + - - +
481A MET* 3.4 10.1 - - - +
483A ILE* 1.3 78.9 - - - +
485A ILE* 1.3 60.5 + - + +
487A ASN* 3.9 4.3 - - - +
488A ASP* 2.7 49.8 + - - +
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Residues in contact with ILE 485 (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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448A ARG* 4.2 28.5 - - + +
451A LEU* 3.7 40.2 - - + +
452A ALA* 3.7 33.9 - - + +
468A MET* 4.2 9.9 - - - -
481A MET 3.4 14.4 - - - +
482A ALA* 2.9 8.8 + - - +
484A GLU* 1.3 76.8 - - + +
486A ILE* 1.3 63.7 + - + +
488A ASP* 3.8 8.4 - - + +
489A ILE* 3.2 28.4 + - + +
581A ARG* 4.7 5.2 - - - +
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Residues in contact with ILE 486 (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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482A ALA* 2.9 23.5 + - + +
483A ILE* 3.0 8.9 + - + +
485A ILE* 1.3 79.2 - - + +
487A ASN* 1.3 65.5 + - - +
489A ILE* 3.4 4.3 + - - +
490A ARG* 3.0 21.4 + - + +
578A CYS* 3.6 33.5 - - + +
581A ARG* 4.3 19.7 - - + +
582A SER* 4.1 32.3 - - - +
585A MET* 4.2 16.8 - - + -
602A LEU* 4.1 25.1 - - + -
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Residues in contact with ASN 487 (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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483A ILE* 2.8 46.1 + - - +
484A GLU* 4.0 4.7 - - - +
486A ILE* 1.3 75.5 - - - +
488A ASP* 1.3 54.5 + - - +
490A ARG* 3.0 24.1 + - - +
491A ASP* 2.6 52.8 + - - +
602A LEU* 5.5 10.2 - - - +
605A THR* 5.5 7.9 + - - +
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Residues in contact with ASP 488 (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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452A ALA* 6.4 2.7 - - + -
484A GLU* 2.7 49.4 + - - +
485A ILE* 3.8 8.2 + - - +
487A ASN* 1.3 76.2 - - - +
489A ILE* 1.3 58.9 + - + +
491A ASP* 4.5 6.0 - - - +
492A ASP* 2.6 45.5 + - - +
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Residues in contact with ILE 489 (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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451A LEU 3.9 12.1 - - - +
452A ALA* 3.9 18.6 - - + +
453A LEU 4.6 1.3 - - - +
454A THR* 4.0 22.9 - - + -
485A ILE* 3.2 22.5 + - + +
486A ILE* 3.9 3.8 - - - +
488A ASP* 1.3 77.6 - - + +
490A ARG* 1.3 63.3 + - - +
492A ASP* 3.8 10.8 + - - +
493A ASP* 3.9 6.9 + - - +
574A THR* 3.4 24.6 - - + +
577A LEU* 5.1 11.0 - - + -
578A CYS* 4.6 5.6 - - - -
581A ARG* 3.8 36.1 - - - +
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Residues in contact with ARG 490 (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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486A ILE* 3.0 16.5 + - - +
487A ASN* 3.2 25.3 - - - +
489A ILE* 1.3 80.4 - - - +
491A ASP* 1.3 75.2 + - - +
492A ASP 3.4 0.3 + - - -
493A ASP* 3.5 10.0 + - - +
494A ILE* 3.5 37.3 + - + +
568A LYS 5.2 1.4 + - - -
569A GLU* 4.0 18.0 + - - -
570A ALA* 4.1 8.6 - - + +
574A THR* 4.0 10.3 - - + -
578A CYS* 4.2 9.3 - - - -
602A LEU* 6.4 2.0 - - - -
605A THR* 4.2 22.3 - - - +
606A LEU* 3.2 34.4 - - + +
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Residues in contact with ASP 491 (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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487A ASN* 2.6 38.5 + - - +
488A ASP* 4.0 7.0 + - - +
490A ARG* 1.3 95.7 + - - +
492A ASP* 1.3 68.7 + - - +
493A ASP 3.1 0.2 - - - -
494A ILE* 4.5 7.0 - - - +
495A GLU* 3.0 40.5 + - + +
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Residues in contact with ASP 492 (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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488A ASP* 2.6 37.7 + - - +
489A ILE* 4.1 8.0 - - - +
490A ARG 3.3 0.4 - - - -
491A ASP* 1.3 78.0 - - - +
493A ASP* 1.3 59.7 + - - +
495A GLU* 4.8 4.5 - - - +
496A LYS* 3.4 25.1 + - - +
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Residues in contact with ASP 493 (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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489A ILE 3.9 4.8 + - - +
490A ARG 3.5 8.1 + - - +
491A ASP 3.1 0.6 - - - -
492A ASP* 1.3 79.3 - - - +
494A ILE* 1.3 65.4 + - - +
496A LYS* 3.4 21.8 + - - +
497A GLN* 3.4 28.0 + - - +
570A ALA* 4.5 4.7 - - + -
571A SER* 2.7 43.7 + - - -
574A THR* 3.8 14.5 + - - +
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Residues in contact with ILE 494 (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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490A ARG* 3.5 54.3 + - + +
491A ASP* 3.2 9.5 + - - +
493A ASP* 1.3 77.4 - - - +
495A GLU* 1.3 66.0 + - + +
497A GLN* 3.1 21.1 + - - +
498A GLU* 3.2 16.2 + - - +
568A LYS* 4.0 38.8 - - + +
569A GLU* 4.2 7.2 - - - +
570A ALA* 3.9 24.5 - - - +
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Residues in contact with GLU 495 (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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491A ASP* 3.0 27.3 + - + +
492A ASP* 4.8 4.3 - - - +
494A ILE* 1.3 80.0 - - + +
496A LYS* 1.3 61.0 + - - +
497A GLN 3.3 0.2 - - - -
498A GLU* 3.3 29.3 - - + +
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Residues in contact with LYS 496 (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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492A ASP 3.4 20.5 + - - +
493A ASP* 3.4 17.6 + - - +
494A ILE 3.1 1.0 - - - -
495A GLU* 1.3 77.9 - - - +
497A GLN* 1.3 62.7 + - + +
498A GLU 3.3 0.7 - - - -
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Residues in contact with GLN 497 (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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493A ASP* 3.6 31.2 + - - +
494A ILE* 3.1 11.6 + - - +
496A LYS* 1.3 79.0 - - + +
498A GLU* 1.3 65.7 + - - +
567A GLU* 3.6 31.4 + - + +
569A GLU 3.9 12.9 + - - +
571A SER* 5.2 6.1 - - - +
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Residues in contact with GLU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ILE* 3.2 20.1 + - - +
495A GLU* 3.3 27.5 - - + +
496A LYS 3.3 2.9 - - - -
497A GLN* 1.3 83.8 - - - +
568A LYS* 4.1 30.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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