Contacts of the helix formed by residues 499 - 514 (chain A) in PDB entry 3ZRH
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 ARG 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A LEU* 1.3 93.6 - - - +
500A GLU* 1.3 54.5 + - - +
501A GLU* 4.2 11.9 - - + +
502A GLN* 2.3 60.4 + - + +
503A TRP* 3.0 9.4 + - - -
505A GLU* 4.0 11.9 + - - -
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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
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478A TYR* 3.0 18.4 + - - -
482A LYS* 2.7 34.6 + - - -
498A LEU 3.6 4.4 + - - -
499A ARG* 1.3 68.9 - - - +
501A GLU* 1.3 64.9 + - - +
502A GLN 2.9 1.7 + - - -
503A TRP* 3.0 16.6 + - + -
504A GLN* 3.1 29.0 + - - +
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Residues in contact with GLU 501 (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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499A ARG* 4.2 12.3 - - + +
500A GLU* 1.3 77.9 - - - +
502A GLN* 1.3 56.9 + - - +
504A GLN* 3.3 21.4 - - - +
505A GLU* 3.8 9.2 - - - +
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Residues in contact with GLN 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A LEU* 4.3 12.7 - - + +
499A ARG* 2.3 75.8 + - + +
501A GLU* 1.3 68.4 - - - +
503A TRP* 1.3 64.6 + - - +
504A GLN 3.0 1.3 - - - -
505A GLU* 3.5 17.5 - - - +
506A ASP* 3.4 18.9 + - - +
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Residues in contact with TRP 503 (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 TYR* 3.0 24.2 - - + +
481A TRP* 3.6 27.1 - + - -
482A LYS* 3.5 36.1 - - + +
485A GLU* 3.8 36.6 - - + -
486A SER* 4.3 5.8 - - - -
496A PHE* 4.1 26.7 - + - -
498A LEU* 3.2 53.5 + - + +
499A ARG 3.0 12.5 + - - -
500A GLU* 3.0 13.0 + - + +
502A GLN* 1.3 77.6 - - - +
504A GLN* 1.3 64.8 + - - +
506A ASP* 3.4 3.9 + - + +
507A TRP* 2.9 23.0 + - - +
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Residues in contact with GLN 504 (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 TYR* 3.0 26.7 + - - -
500A GLU* 3.1 25.9 + - - +
501A GLU* 3.3 18.6 - - - +
502A GLN 3.0 0.2 - - - -
503A TRP* 1.3 74.9 - - - +
505A GLU* 1.3 57.9 + - + +
507A TRP* 3.0 8.4 + - - +
508A ALA* 2.8 27.1 + - - +
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Residues in contact with GLU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A ARG* 4.0 11.3 + - - -
501A GLU 3.8 11.9 - - - +
502A GLN* 3.5 26.4 - - - +
504A GLN* 1.3 71.0 - - - +
506A ASP* 1.3 76.7 + - - +
507A TRP 3.0 0.9 + - - -
508A ALA* 3.1 18.7 + - - +
509A PHE* 3.1 13.7 + - - +
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Residues in contact with ASP 506 (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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481A TRP* 3.6 23.5 - - + -
498A LEU* 5.8 3.8 - - + -
502A GLN 3.4 14.7 + - - +
503A TRP* 3.4 4.4 + - + +
504A GLN 3.4 0.4 - - - -
505A GLU* 1.3 84.6 + - - +
507A TRP* 1.3 57.7 + - - +
509A PHE* 3.8 5.7 + - - +
510A ILE* 3.0 27.7 + - - +
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Residues in contact with TRP 507 (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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470A LEU* 3.9 17.3 - - + -
474A SER* 2.7 34.1 + - - -
477A PHE* 3.8 12.6 - - + -
478A TYR* 3.4 52.9 - + + +
481A TRP* 3.6 37.9 - + + -
503A TRP 2.9 13.8 + - - +
504A GLN* 3.3 8.7 - - - +
506A ASP* 1.3 74.5 - - - +
508A ALA* 1.3 69.2 + - - +
509A PHE 2.9 3.8 + - - -
510A ILE* 3.4 27.9 + - + +
511A LEU* 3.2 45.0 + - + +
524A THR* 3.9 6.3 - - + -
1695A CL 4.0 10.3 - - + -
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Residues in contact with ALA 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 GLN 2.8 16.6 + - - +
505A GLU* 3.1 11.4 + - - +
507A TRP* 1.3 75.2 - - - +
509A PHE* 1.3 57.4 + - - +
511A LEU* 3.0 27.1 + - - +
512A SER* 3.2 8.3 + - - -
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Residues in contact with PHE 509 (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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505A GLU 3.1 13.1 + - - +
506A ASP* 4.0 7.2 - - - +
507A TRP 2.9 2.4 + - - -
508A ALA* 1.3 71.5 - - - +
510A ILE* 1.3 68.9 + - + +
511A LEU 2.7 4.5 - - - -
512A SER* 2.6 39.5 + - - -
513A LEU* 3.2 26.3 + - + -
516A GLN* 5.3 7.4 - - - -
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Residues in contact with ILE 510 (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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470A LEU* 5.4 0.7 - - + -
481A TRP* 4.7 12.6 - - + +
506A ASP 3.0 22.9 - - - +
507A TRP* 3.8 27.4 - - + +
509A PHE* 1.3 75.4 - - + +
511A LEU* 1.3 65.3 + - + +
513A LEU* 3.2 36.0 - - + +
522A GLU* 2.8 37.9 - - + +
524A THR* 3.5 22.2 - - + +
525A HIS* 3.5 13.5 + - + -
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Residues in contact with LEU 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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467A HIS* 4.1 16.3 + - - -
470A LEU* 3.5 31.7 - - + +
471A HIS* 4.7 13.5 - - + -
474A SER* 3.6 28.7 - - - +
507A TRP* 3.2 50.0 + - + +
508A ALA* 3.0 17.9 + - - +
509A PHE 2.7 5.1 + - - -
510A ILE* 1.3 79.2 - - + +
512A SER* 1.3 58.7 + - - +
513A LEU 3.5 0.2 + - - -
514A ALA* 3.9 8.7 + - - +
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Residues in contact with SER 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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467A HIS* 5.6 0.2 - - - -
508A ALA 3.2 8.9 + - - -
509A PHE* 2.6 42.8 + - - -
511A LEU* 1.3 71.2 - - - +
513A LEU* 1.3 63.9 + - - -
515A SER* 2.6 32.5 + - - -
516A GLN* 3.0 15.9 + - - +
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Residues in contact with LEU 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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463A ARG* 2.9 20.1 + - - -
509A PHE* 3.2 30.9 + - + +
510A ILE* 3.2 32.2 + - + +
512A SER* 1.3 75.5 + - - +
514A ALA* 1.3 56.4 + - - +
516A GLN* 3.1 17.0 - - - +
519A ALA* 4.1 16.3 - - + +
520A SER 3.3 24.2 - - - +
521A LEU* 4.0 8.3 - - + +
522A GLU* 4.0 24.0 - - + -
525A HIS* 3.9 10.5 - - + -
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Residues in contact with ALA 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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463A ARG* 3.0 34.8 + - + +
466A LEU* 4.5 5.2 - - + -
467A HIS* 3.6 39.7 - - + +
470A LEU* 4.9 2.7 - - + -
511A LEU 3.9 5.9 + - - +
512A SER 3.2 1.0 - - - -
513A LEU* 1.3 77.8 - - - +
515A SER* 1.3 56.7 + - - +
521A LEU* 4.3 3.4 - - - -
525A HIS* 3.6 25.9 + - + +
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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