Contacts of the helix formed by residues 460 - 473 (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 SER 460 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ASP* 5.8 1.4 + - - -
457A ASP* 3.2 19.4 + - - -
458A LYS 2.9 2.8 - - - -
459A ASP* 1.3 77.7 - - - +
461A VAL* 1.3 64.8 + - - +
462A LEU 3.4 2.2 - - - -
463A ARG* 3.3 20.0 + - - +
464A LYS* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 4.4 25.6 - - + +
359A ILE* 4.5 20.2 - - + -
360A ALA* 4.4 16.2 - - + -
363A LEU* 3.7 20.4 - - + -
449A LEU* 5.6 2.9 - - + -
457A ASP* 3.3 7.7 + - - +
458A LYS 3.4 9.1 + - - +
459A ASP 3.0 6.0 + - - +
460A SER* 1.3 78.9 - - - +
462A LEU* 1.3 66.5 + - + +
464A LYS* 3.5 14.2 + - + +
465A ALA* 3.2 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE* 5.9 4.5 - - + -
363A LEU* 5.0 6.3 - - + -
375A LEU* 5.1 9.0 - - + -
445A LEU* 3.4 27.4 - - + +
448A VAL* 4.1 18.6 - - + -
449A LEU* 4.0 30.1 - - + -
457A ASP* 2.9 21.7 + - - +
461A VAL* 1.3 76.5 - - + +
463A ARG* 1.3 58.5 + - - +
465A ALA* 3.1 9.1 + - + +
466A LEU* 2.9 26.9 + - - +
529A LEU* 4.1 16.6 - - + -
532A ILE* 4.1 27.1 - - + -
533A LEU* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 463 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ASP* 2.6 44.9 + - - -
445A LEU* 3.6 26.3 - - + +
457A ASP* 3.1 17.9 + - - +
460A SER* 3.7 19.7 - - - +
461A VAL 3.2 0.2 - - - -
462A LEU* 1.3 76.1 - - - +
464A LYS* 1.3 57.4 + - + +
466A LEU* 3.0 6.9 + - + +
467A HIS* 2.8 28.1 + - - +
513A LEU 2.9 17.2 + - - -
514A ALA* 3.0 23.5 + - - +
515A SER 4.9 1.0 + - - -
516A GLN 2.7 28.6 + - - -
517A PRO* 4.1 11.1 - - - +
518A GLY 3.7 6.8 - - - +
519A ALA 4.1 6.3 + - - +
521A LEU* 3.7 17.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 464 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ASP* 3.3 26.0 + - - +
460A SER* 2.8 22.2 + - - +
461A VAL* 4.0 14.8 - - + +
463A ARG* 1.3 76.3 - - + +
465A ALA* 1.3 57.9 + - - +
467A HIS* 3.6 7.1 - - + +
468A ASP* 2.8 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 4.0 20.2 - - + -
373A TYR* 3.9 37.7 - - + -
461A VAL 3.2 11.4 + - - +
462A LEU* 3.1 12.1 + - + +
464A LYS* 1.3 76.2 - - - +
466A LEU* 1.3 57.8 + - - +
468A ASP* 3.8 0.8 - - - -
469A SER* 2.8 35.0 + - - -
532A ILE* 4.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU* 4.2 22.0 - - + -
462A LEU 2.9 12.9 + - - +
463A ARG* 3.0 9.4 + - + +
465A ALA* 1.3 75.8 - - - +
467A HIS* 1.3 64.1 + - - +
469A SER* 3.3 2.1 + - - -
470A LEU* 3.0 23.0 + - + +
514A ALA* 4.5 4.0 - - + -
521A LEU* 4.2 15.3 - - + -
525A HIS* 3.7 45.5 - - + +
528A VAL* 3.5 33.2 - - + -
529A LEU* 4.3 18.8 - - + -
532A ILE* 3.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ARG 2.8 14.6 + - - +
464A LYS* 3.6 7.6 - - - +
466A LEU* 1.3 79.7 - - - +
468A ASP* 1.3 86.2 + - - +
470A LEU* 3.3 3.3 + - - +
471A HIS* 3.0 35.2 + + + +
511A LEU 4.1 11.7 + - - +
512A SER* 5.6 0.4 - - - -
514A ALA* 3.6 26.2 - - + +
515A SER* 3.2 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN* 5.1 0.2 - - - -
373A TYR* 3.8 29.4 + - + +
464A LYS* 2.8 32.7 + - - +
467A HIS* 1.3 88.7 + - - +
469A SER* 1.3 61.2 + - - +
471A HIS* 3.7 4.5 - - - +
472A ASP* 2.8 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 469 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ALA 4.6 4.9 - - - -
372A CYS* 3.8 9.9 - - - -
373A TYR* 2.8 37.0 + - - +
465A ALA 2.8 22.6 + - - -
466A LEU* 3.6 4.7 - - - -
468A ASP* 1.3 77.8 - - - +
470A LEU* 1.3 57.1 - - - +
473A CYS* 2.8 36.8 + - - +
477A PHE* 4.8 1.6 - - - -
528A VAL* 3.9 18.6 - - - -
532A ILE* 3.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A LEU* 3.0 11.6 + - + +
467A HIS* 3.6 8.1 - - - +
469A SER* 1.3 77.7 - - - +
471A HIS* 1.3 59.9 + - - +
473A CYS 3.5 0.5 - - - -
474A SER* 2.9 32.2 + - - -
477A PHE* 3.8 24.0 - - + -
507A TRP* 3.9 24.7 - - + -
510A ILE* 5.0 1.1 - - + +
511A LEU* 3.5 25.2 - - + +
514A ALA* 4.9 4.0 - - + -
524A THR* 4.3 6.5 - - + -
525A HIS* 3.4 40.2 - - + +
528A VAL* 3.9 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A HIS* 3.0 31.1 + + + +
468A ASP* 3.8 6.3 - - - +
469A SER 3.2 0.2 - - - -
470A LEU* 1.3 79.5 - - - +
472A ASP* 1.3 87.4 + - - +
473A CYS 3.4 0.3 + - - -
474A SER* 3.5 13.2 + - - -
511A LEU* 4.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLN* 2.9 34.8 + - - +
369A ASP 5.8 0.3 - - - +
371A ALA* 4.1 15.2 + - + +
468A ASP* 2.8 28.2 + - - +
471A HIS* 1.3 104.8 + - - +
473A CYS* 1.3 62.3 + - - +
474A SER 3.5 0.2 - - - -
475A HIS* 5.9 0.7 + - - -
476A TRP* 5.2 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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 + - + -
----------------------------------------------------------
Back to top of page
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