Contacts of the helix formed by residues 498 - 521 (chain A) in PDB entry 2ZJ4
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 MET 498 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A GLU 3.9 14.1 - - - +
390A LEU* 3.7 19.5 - - + +
392A GLU* 3.8 29.6 - - - +
492A CYS* 3.4 29.6 - - + +
495A ARG* 3.0 45.4 + - + +
497A SER* 1.3 88.8 + - - +
499A GLN* 1.3 60.2 + - - +
500A GLU 3.5 1.8 - - - -
501A ARG* 3.3 13.2 + - + +
502A ARG* 3.0 28.1 + - - +
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Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A CYS 3.4 20.2 + - - -
493A ASP 3.8 11.5 + - - +
494A ASP 5.6 0.2 - - - -
495A ARG 2.7 30.1 + - - +
496A ILE* 3.4 17.9 + - + +
497A SER 3.5 0.2 - - - -
498A MET* 1.3 79.4 - - - +
500A GLU* 1.3 66.2 + - - +
502A ARG* 3.4 31.3 + - - +
503A LYS* 3.1 23.6 + - - +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ILE 5.0 0.6 + - - -
497A SER 5.1 3.2 + - - +
498A MET 3.5 0.4 - - - -
499A GLN* 1.3 77.2 - - - +
501A ARG* 1.3 61.0 + - - +
503A LYS* 3.3 29.0 + - - +
504A GLU* 2.9 29.2 + - - +
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Residues in contact with ARG 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 4.6 0.4 - - - +
389A GLU* 2.8 43.9 + - - +
390A LEU* 4.2 11.4 - - + -
497A SER 5.4 1.3 + - - +
498A MET* 3.3 18.1 + - + +
500A GLU* 1.3 77.7 - - - +
502A ARG* 1.3 62.0 + - + +
504A GLU* 3.0 31.3 + - - +
505A ILE* 3.1 41.6 + - + +
546A TYR* 3.5 11.1 + - - -
640A VAL* 3.5 12.9 - - - +
641A ASP* 3.0 33.8 + - - -
642A CYS* 4.1 8.2 - - - +
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Residues in contact with ARG 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 2.9 29.7 + - - +
349A THR* 4.8 1.4 - - - +
350A VAL* 3.8 20.0 + - - +
390A LEU* 5.6 0.4 - - + -
489A LEU* 2.9 50.8 + - + +
490A MET* 4.4 0.4 - - - +
492A CYS* 3.2 45.1 - - - -
493A ASP* 3.5 17.8 - - - +
498A MET 3.0 23.3 + - - +
499A GLN* 3.6 25.9 + - - +
500A GLU 3.3 0.2 - - - -
501A ARG* 1.3 76.9 - - + +
503A LYS* 1.3 57.8 + - - +
505A ILE* 3.4 2.4 + - - +
506A MET* 2.8 39.1 + - - +
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Residues in contact with LYS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 3.1 54.6 - - + +
499A GLN 3.1 17.2 + - - +
500A GLU* 3.7 28.6 + - - +
501A ARG 3.2 0.2 - - - -
502A ARG* 1.3 74.9 - - - +
504A GLU* 1.3 65.4 + - - +
506A MET* 3.9 5.7 - - - +
507A LEU* 2.9 37.3 + - + +
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLU 2.9 13.6 + - - +
501A ARG* 3.0 44.5 + - - +
503A LYS* 1.3 77.2 - - - +
505A ILE* 1.3 62.7 + - - +
507A LEU* 3.4 7.5 + - - +
508A GLY 3.1 17.5 + - - -
640A VAL* 3.9 22.0 - - + +
641A ASP* 6.0 0.2 - - - -
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Residues in contact with ILE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 4.5 2.7 - - + -
390A LEU* 4.0 23.1 - - + -
485A VAL* 3.8 27.6 - - + -
489A LEU* 4.0 16.2 - - + -
501A ARG* 3.1 43.9 + - + +
502A ARG 3.7 6.3 - - - +
504A GLU* 1.3 75.9 - - - +
506A MET* 1.3 61.5 + - - +
508A GLY 3.2 1.6 + - - -
509A LEU* 3.1 22.9 + - + +
640A VAL* 4.4 7.4 - - + -
642A CYS* 3.8 29.2 - - - -
643A LEU* 3.7 9.8 - - + +
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Residues in contact with MET 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A VAL* 3.3 31.6 - - + -
344A ASN 4.0 2.5 - - - +
345A PHE* 3.3 17.4 - - + -
348A TYR* 3.5 51.4 - - + +
349A THR 3.4 22.4 - - - +
350A VAL* 3.9 11.9 - - + -
489A LEU* 3.9 17.5 - - + -
502A ARG* 2.8 32.7 + - - +
503A LYS 4.0 3.4 - - - +
505A ILE* 1.3 72.7 - - - +
507A LEU* 1.3 58.1 + - - +
509A LEU* 3.4 7.4 + - + +
510A LYS 3.0 23.6 + - - -
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 6.2 0.4 - - + -
348A TYR* 3.4 31.6 - - + +
503A LYS* 2.9 36.4 + - + +
504A GLU* 3.8 6.3 - - - +
506A MET* 1.3 76.9 - - - +
508A GLY* 1.3 60.9 + - - +
510A LYS* 3.5 35.2 + - + +
511A ARG* 3.2 53.4 + - - +
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Residues in contact with GLY 508 (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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504A GLU 3.1 11.3 + - - -
505A ILE 3.2 0.6 + - - -
507A LEU* 1.3 75.0 - - - +
509A LEU* 1.3 58.6 + - - +
511A ARG* 3.3 8.6 + - - +
512A LEU* 3.0 27.9 + - - +
515A LEU* 5.7 0.5 - - - +
639A SER* 4.5 8.1 + - - -
640A VAL* 4.0 11.2 - - - -
643A LEU* 3.5 20.4 - - - +
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Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET* 3.4 37.7 - - - +
343A VAL* 4.9 6.1 - - + -
345A PHE* 4.4 2.5 - - + -
482A VAL* 4.2 16.6 - - + -
485A VAL* 4.6 7.4 - - + -
486A MET* 4.7 11.0 - - + -
489A LEU* 4.1 24.2 - - + -
505A ILE* 3.1 19.1 + - + +
506A MET* 3.4 13.9 + - + +
508A GLY* 1.3 71.6 - - - +
510A LYS* 1.3 66.1 + - - +
512A LEU* 3.3 27.6 + - + +
513A PRO* 3.4 10.6 - - - +
643A LEU* 3.5 25.9 - - + +
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Residues in contact with LYS 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET* 5.2 0.2 - - - -
345A PHE* 3.6 44.5 + - + -
506A MET 3.0 14.4 + - - +
507A LEU* 3.5 35.4 - - + +
509A LEU* 1.3 76.2 - - - +
511A ARG* 1.3 77.1 + - - +
512A LEU 3.5 0.2 + - - -
513A PRO* 3.5 10.2 - - - +
514A ASP* 5.5 2.4 + - - +
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Residues in contact with ARG 511 (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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507A LEU* 3.2 55.0 + - - +
508A GLY* 3.3 11.0 + - - +
510A LYS* 1.3 91.8 - - - +
512A LEU* 1.3 63.9 + - - +
513A PRO* 3.5 1.1 - - - -
514A ASP* 3.4 12.8 + - + +
515A LEU* 3.2 35.4 + - + +
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Residues in contact with LEU 512 (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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335A VAL* 4.3 8.1 - - + -
482A VAL* 4.3 7.0 - - + -
508A GLY 3.0 11.8 + - - +
509A LEU* 3.3 25.8 + - + +
511A ARG* 1.3 77.4 - - - +
513A PRO* 1.3 65.6 - - + +
515A LEU* 3.0 6.4 + - + +
516A ILE* 2.9 42.5 + - + +
639A SER* 4.5 12.6 - - - +
643A LEU* 4.7 7.9 - - + +
646A ILE* 3.6 40.2 - - + -
647A LEU* 4.0 33.7 - - + -
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Residues in contact with PRO 513 (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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332A PRO* 3.8 29.4 - - + +
335A VAL* 4.4 10.3 - - + -
336A VAL* 3.7 26.7 - - + -
339A MET* 4.8 2.9 - - + -
509A LEU 3.4 14.1 - - - +
510A LYS 3.5 10.1 - - - +
511A ARG 3.5 0.7 - - - -
512A LEU* 1.3 91.7 - - + +
514A ASP* 1.3 64.8 + - - +
516A ILE* 3.3 7.5 + - + +
517A LYS* 3.1 29.7 + - - +
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Residues in contact with ASP 514 (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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510A LYS 5.5 1.6 - - - +
511A ARG* 3.4 12.9 + - + +
512A LEU 3.4 0.6 - - - -
513A PRO* 1.3 80.0 - - - +
515A LEU* 1.3 66.8 + - + +
517A LYS* 3.5 24.5 + - - +
518A GLU* 3.3 20.6 + - - +
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Residues in contact with LEU 515 (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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511A ARG* 3.2 28.7 + - + +
512A LEU* 3.0 11.0 + - - +
514A ASP* 1.3 78.7 - - + +
516A ILE* 1.3 60.0 + - - +
518A GLU* 3.3 25.0 + - - +
519A VAL* 3.1 23.0 + - - +
637A PRO* 3.6 18.5 - - + +
638A HIS 3.4 25.8 - - - +
639A SER* 4.4 8.3 - - - +
647A LEU* 3.8 26.9 - - + -
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Residues in contact with ILE 516 (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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331A GLN* 4.0 14.8 - - + +
332A PRO* 3.6 26.5 - - + -
335A VAL* 3.8 29.8 - - + -
478A THR* 6.1 0.4 - - + -
512A LEU* 2.9 33.1 + - + +
513A PRO* 3.7 6.5 - - + +
515A LEU* 1.3 74.2 - - - +
517A LYS* 1.3 64.3 + - - +
519A VAL* 3.2 5.5 + - - +
520A LEU* 2.9 27.1 + - + +
646A ILE* 4.1 10.5 - - + -
647A LEU* 3.6 19.7 - - + -
650A ILE* 3.8 22.2 - - + -
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Residues in contact with LYS 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A PRO* 3.6 26.7 - - + -
513A PRO* 3.1 19.7 + - - +
514A ASP* 3.7 25.4 + - - +
515A LEU 3.4 0.2 - - - -
516A ILE* 1.3 75.1 - - - +
518A GLU* 1.3 60.2 + - - +
520A LEU* 3.3 13.0 + - + +
521A SER* 3.3 20.3 + - - -
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Residues in contact with GLU 518 (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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514A ASP 3.3 8.6 + - - +
515A LEU* 3.4 26.3 - - - +
516A ILE 3.2 0.4 - - - -
517A LYS* 1.3 75.8 - - - +
519A VAL* 1.3 63.4 + - - +
521A SER* 2.7 27.3 + - - +
522A MET* 4.0 4.9 + - - +
621A LYS* 2.9 34.9 - - + +
637A PRO* 3.7 15.1 - - + +
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Residues in contact with VAL 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A LEU 3.1 15.5 + - - +
516A ILE* 3.7 7.2 - - - +
518A GLU* 1.3 74.6 - - - +
520A LEU* 1.3 61.4 + - - +
522A MET* 2.9 37.5 + - + +
523A ASP 4.3 0.3 + - - -
636A VAL* 4.3 5.2 - - + -
637A PRO* 3.3 29.4 - - + -
647A LEU* 3.9 21.8 - - + +
650A ILE* 3.8 28.3 - - + -
651A PRO* 3.9 26.5 - - + -
654A LEU* 4.8 3.6 - - + +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.8 33.7 - - + +
329A PHE* 3.9 53.8 - - + +
332A PRO* 3.9 26.0 - - + -
516A ILE* 2.9 22.9 + - + +
517A LYS* 3.3 10.0 + - + +
519A VAL* 1.3 76.1 - - - +
521A SER* 1.3 59.4 + - - +
522A MET 3.1 0.4 - - - -
523A ASP* 3.2 23.1 + - - +
650A ILE* 4.1 14.6 - - + -
654A LEU* 4.6 5.8 - - + -
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A LYS 3.3 11.3 + - - -
518A GLU* 2.7 24.3 + - - +
519A VAL 3.1 0.2 - - - -
520A LEU* 1.3 77.1 - - - +
522A MET* 1.3 57.9 + - - +
523A ASP* 3.3 2.7 + - - -
524A ASP* 4.7 3.8 + - - +
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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) + - + + + + + -
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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