Contacts of the strand formed by residues 422 - 430 (chain A) in PDB entry 2QR8
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 TYR 422 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PHE* 3.2 45.9 + + + +
419A THR* 3.3 25.8 - - - +
420A ASP 3.8 0.4 - - - -
421A GLY* 1.3 80.7 - - - +
423A GLU* 1.3 60.2 + - - +
424A VAL 3.9 1.4 + - - -
439A CYS* 3.8 17.5 - - + -
440A ILE 3.2 14.6 - - - -
441A HIS* 3.7 29.8 + + - -
442A LYS* 3.9 6.5 + - - +
448A PHE* 3.9 17.2 - + - -
480A LYS* 4.8 5.5 - - - +
481A ASP* 3.1 36.6 + - + +
483A TYR* 3.6 14.6 - + - -
492A VAL* 3.9 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TYR* 1.3 69.8 - - - +
424A VAL* 1.3 64.0 + - - +
425A LYS* 3.0 34.6 + - - +
439A CYS* 3.2 5.2 - - - -
440A ILE* 2.9 49.3 + - + +
442A LYS* 4.1 22.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A PHE* 3.5 31.9 - - + -
419A THR* 4.7 11.4 - - + -
422A TYR 3.9 0.4 + - - +
423A GLU* 1.3 75.8 - - - +
425A LYS* 1.3 82.5 + - - +
437A LYS* 3.5 35.4 - - + +
438A ARG 4.1 3.1 - - - +
439A CYS* 4.4 2.0 - - + -
450A VAL* 5.4 2.0 - - + -
452A ILE* 5.7 3.4 - - + -
490A TYR* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU* 3.0 41.0 + - - +
424A VAL* 1.3 94.1 + - - +
426A GLU* 1.3 68.1 + - + +
427A ASP* 5.1 0.5 - - - +
437A LYS* 4.3 4.2 + - - +
438A ARG* 2.9 52.8 + - - +
439A CYS* 4.4 1.3 - - - -
440A ILE* 3.3 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LYS* 1.3 80.3 - - + +
427A ASP* 1.3 74.2 + - - +
428A ILE* 4.9 3.6 - - - +
437A LYS* 3.3 2.5 - - - -
438A ARG* 2.9 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LYS 5.1 0.3 - - - +
426A GLU* 1.3 84.2 - - - +
428A ILE* 1.3 59.1 + - - +
429A GLY 4.3 0.4 - - - +
430A VAL* 3.9 29.7 - - + +
435A VAL* 4.0 3.6 - - - +
436A CYS 3.5 5.6 - - - +
437A LYS* 3.4 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU* 3.6 3.8 + - - +
427A ASP* 1.3 73.1 - - - +
429A GLY* 1.3 56.6 + - - +
436A CYS* 2.7 22.9 + - + +
437A LYS 3.8 6.7 - - - +
438A ARG* 3.8 26.7 - - + +
449A ALA* 4.0 9.9 - - + -
495A LEU* 3.4 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 3.5 4.0 - - - +
428A ILE* 1.3 80.5 - - - +
430A VAL* 1.3 61.3 + - - +
435A VAL* 3.8 0.2 - - - -
436A CYS* 2.7 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 3.9 29.4 - - + +
429A GLY* 1.3 80.0 - - - +
431A GLY* 1.3 65.5 + - - +
434A SER 4.1 3.6 - - - -
435A VAL* 4.0 26.9 - - + +
----------------------------------------------------------
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