Contacts of the helix formed by residues 473 - 492 (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 CYS 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 4.0 6.5 - - + -
371A ALA 3.2 44.6 - - - -
372A CYS* 3.3 17.5 - - - -
469A SER 2.8 19.0 + - - +
470A LEU 3.5 2.9 - - - -
472A ASP* 1.3 79.5 - - - +
474A SER* 1.3 67.2 + - - +
475A HIS* 3.4 3.1 - - - -
476A TRP* 3.0 30.4 + - + -
477A PHE* 3.3 25.1 + - + -
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Residues in contact with SER 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A LEU 2.9 16.2 + - - -
471A HIS 3.5 11.3 + - - -
472A ASP 3.5 1.0 - - - -
473A CYS* 1.3 77.0 - - - +
475A HIS* 1.3 59.1 + - - +
477A PHE 3.2 0.7 + - - -
478A TYR* 2.8 28.6 + - - +
507A TRP* 2.7 35.8 + - - +
511A LEU* 3.6 11.5 - - - +
1695A CL 4.0 6.8 - - - +
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Residues in contact with HIS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP 4.9 1.8 - - - -
472A ASP 5.9 1.1 + - - -
473A CYS* 3.1 1.8 + - - -
474A SER* 1.3 77.9 - - - +
476A TRP* 1.3 125.7 + + - +
478A TYR* 3.7 10.2 - - + +
479A THR* 3.2 29.7 + - - -
1695A CL 4.7 3.4 - - - -
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Residues in contact with TRP 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP* 3.0 46.3 + - + -
370A PHE* 3.6 37.1 - + + -
472A ASP 5.2 1.3 + - - -
473A CYS* 3.0 23.5 + - + +
475A HIS* 1.3 112.3 - + - +
477A PHE* 1.3 63.2 + - + +
479A THR* 3.7 4.7 + - - -
480A ARG* 3.4 23.4 + - - +
566A LEU* 4.1 18.6 - - + +
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Residues in contact with PHE 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 4.1 12.6 - + - -
372A CYS* 4.6 5.4 - - - -
469A SER 4.5 4.5 - - - -
470A LEU* 3.8 13.5 - - + -
473A CYS* 3.3 35.5 + - + -
474A SER 3.2 2.9 + - - +
476A TRP* 1.3 73.9 - - - +
478A TYR* 1.3 66.8 + - - +
480A ARG* 3.1 5.0 + - - +
481A TRP* 2.9 24.6 + - - +
507A TRP* 3.8 19.1 - - + -
524A THR* 4.6 5.4 - - + +
527A PHE* 3.8 26.5 - + - -
528A VAL* 3.6 39.9 - - + -
531A HIS* 4.1 12.1 - - - -
566A LEU* 3.5 26.7 - - + -
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Residues in contact with TYR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER 2.8 18.1 + - - +
475A HIS* 3.7 9.9 - - + +
477A PHE* 1.3 75.8 - - - +
479A THR* 1.3 64.0 + - - +
481A TRP* 3.2 11.3 + + - +
482A LYS* 3.0 55.0 + - + +
500A GLU* 3.0 16.6 + - - -
503A TRP* 3.0 24.9 - - + +
504A GLN* 3.0 28.9 + - - -
507A TRP* 3.4 50.8 - + + +
1695A CL 4.2 11.4 - - + -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A HIS* 3.2 17.3 + - - -
476A TRP* 4.0 4.7 - - - -
478A TYR* 1.3 86.8 - - - +
480A ARG* 1.3 69.0 + - - +
482A LYS* 3.6 11.1 + - - +
483A ASP* 3.4 33.0 + - - +
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Residues in contact with ARG 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 TRP 3.4 18.2 - - - +
477A PHE* 3.1 7.9 + - - +
479A THR* 1.3 82.9 - - - +
481A TRP* 1.3 59.4 + - - +
483A ASP* 3.5 8.7 + - - +
484A TRP* 3.0 26.3 + - - +
527A PHE* 4.0 20.4 - - + -
565A LEU* 3.4 20.0 + - - +
566A LEU* 3.6 29.7 - - + +
631A PHE* 3.1 44.4 + - + +
633A SER* 3.8 16.0 + - - +
636A GLU* 2.9 27.8 + - - -
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Residues in contact with TRP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A PHE 2.9 16.5 + - - +
478A TYR* 3.4 13.2 - + - +
480A ARG* 1.3 76.0 - - - +
482A LYS* 1.3 75.8 + - - +
484A TRP* 2.8 15.4 + + - +
485A GLU* 2.8 59.0 + - + +
503A TRP* 3.6 38.4 - + - -
506A ASP* 3.6 36.6 - - + -
507A TRP* 3.6 36.8 - + + -
510A ILE* 4.7 8.7 - - + +
522A GLU* 4.8 5.5 + - - -
524A THR* 3.4 23.1 - - + +
631A PHE* 4.1 9.8 - + + -
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Residues in contact with LYS 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TYR* 3.0 41.6 + - + +
479A THR* 3.8 12.9 + - - +
481A TRP* 1.3 84.3 - - + +
483A ASP* 1.3 68.2 + - - +
485A GLU* 3.4 3.5 + - - +
486A SER* 3.1 27.3 + - - +
500A GLU* 2.7 26.6 + - - -
503A TRP* 3.5 51.9 - - + +
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Residues in contact with ASP 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A THR* 3.4 24.2 + - - +
480A ARG* 3.9 9.3 - - - +
481A TRP 3.2 0.4 - - - -
482A LYS* 1.3 81.7 - - - +
484A TRP* 1.3 56.3 + - - +
486A SER* 3.7 6.7 - - - +
487A TRP* 2.7 34.1 + - - +
632A LEU 4.7 14.1 - - - +
633A SER* 4.5 16.1 - - - -
634A ALA* 4.9 5.9 + - + +
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Residues in contact with TRP 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ARG 3.0 14.6 + - - +
481A TRP* 2.8 19.3 + + - +
483A ASP* 1.3 76.8 - - - +
485A GLU* 1.3 98.3 + - + +
487A TRP* 2.9 65.3 - + - +
488A TYR* 3.2 0.7 + - - +
522A GLU* 5.9 2.2 - - - -
523A GLN* 2.8 49.6 - - + +
524A THR* 6.0 0.2 - - - -
557A ARG* 3.5 30.5 - - - -
628A HIS* 4.9 0.7 - + - -
630A HIS* 3.2 23.0 + - - +
631A PHE* 3.6 41.5 - + + +
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Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A TRP* 2.8 56.3 + - + +
482A LYS 3.5 8.3 - - - +
484A TRP* 1.3 93.2 - - + +
486A SER* 1.3 61.1 + - - +
488A TYR* 3.3 12.8 + - - +
489A SER* 3.5 13.3 + - - -
496A PHE* 4.4 4.9 - - + -
503A TRP* 3.8 19.3 - - + -
557A ARG* 3.8 15.5 + - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LYS* 3.1 18.6 + - - +
483A ASP* 3.8 6.5 - - - -
485A GLU* 1.3 72.2 - - - +
487A TRP* 1.3 60.7 + - - +
489A SER* 3.5 8.9 + - - -
490A GLN* 2.5 47.1 + - - +
496A PHE* 3.8 20.5 - - - -
503A TRP* 4.3 7.4 - - - -
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Residues in contact with TRP 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASP 2.7 18.6 + - - +
484A TRP* 2.9 72.9 - + + +
486A SER* 1.3 70.9 - - - +
488A TYR* 1.3 81.0 + + + +
490A GLN* 2.9 23.9 - - - +
491A SER* 3.4 9.0 + - - -
555A TYR* 6.4 0.9 - + - -
557A ARG* 3.9 35.0 - - + -
628A HIS* 3.3 44.5 + + + -
630A HIS* 4.3 5.2 - + - -
637A LEU* 6.0 7.4 - - + -
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Residues in contact with TYR 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A TRP 3.2 2.0 + - - -
485A GLU* 3.6 7.2 - - - +
486A SER 3.2 0.8 - - - -
487A TRP* 1.3 89.0 - + + +
489A SER* 1.3 57.3 + - - +
490A GLN 2.6 4.4 + - - -
491A SER* 2.1 49.7 + - - -
492A PHE* 3.1 39.3 - + - -
555A TYR* 3.7 30.8 + + - +
557A ARG* 3.0 70.7 - - + +
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Residues in contact with SER 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLU 3.5 3.0 + - - -
486A SER 3.6 4.7 + - - -
488A TYR* 1.3 82.3 - - - +
490A GLN* 1.3 62.0 + - - +
491A SER 3.1 1.0 + - - -
492A PHE* 3.5 18.0 + - - +
494A LEU* 3.2 30.8 + - - +
496A PHE* 3.2 51.4 - - - -
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Residues in contact with GLN 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 SER* 2.5 40.8 + - - +
487A TRP* 2.9 14.6 - - - +
488A TYR 2.6 5.5 + - - -
489A SER* 1.3 77.8 + - - +
491A SER* 1.3 58.6 + - - -
493A GLY* 3.3 13.9 + - - -
494A LEU 4.0 11.9 - - - +
495A HIS* 5.3 8.9 - - - -
496A PHE* 5.8 3.8 + - - -
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A TRP* 4.2 9.9 - - - -
488A TYR* 2.1 54.3 + - - -
490A GLN* 1.3 70.3 - - - +
492A PHE* 1.3 69.4 + - - -
493A GLY 3.2 5.7 + - - -
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Residues in contact with PHE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A TYR* 3.1 59.0 - + - -
489A SER* 3.5 11.6 + - - +
490A GLN 3.3 0.4 - - - -
491A SER* 1.3 86.5 - - - +
493A GLY* 1.3 57.7 + - - +
494A LEU* 3.1 12.9 + - + +
555A TYR* 5.5 7.4 - + + -
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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
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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