Contacts of the strand formed by residues 440 - 444 (chain A) in PDB entry 5KVI
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 ALA 440 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLY* 4.9 0.7 - - - -
421A PHE 3.8 1.8 - - - -
423A VAL* 4.6 10.8 - - + -
427A LEU* 5.4 1.6 - - + -
435A VAL* 3.8 36.5 - - + +
436A ALA* 4.1 3.8 - - - +
437A GLY 3.2 16.1 + - - +
438A ASP 4.2 1.2 - - - +
439A ALA* 1.3 78.0 - - - +
441A CYS* 1.3 58.9 + - - +
442A PHE* 3.7 12.0 + - + +
451A ARG* 3.7 19.4 - - - +
452A VAL 4.8 0.5 + - - -
457A HIS* 4.5 7.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 3.3 41.7 - - + -
418A PHE* 4.1 5.8 - - - -
419A GLY 3.4 20.6 - - - +
421A PHE 2.8 18.1 + - - +
422A ALA* 3.7 1.0 - - - -
423A VAL* 3.3 12.3 + - - -
439A ALA 3.8 1.2 + - - -
440A ALA* 1.3 69.2 - - - +
442A PHE* 1.3 53.5 + - - +
449A ARG* 2.8 40.7 + - - -
450A ARG 3.4 17.9 - - - -
451A ARG* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL* 3.8 18.8 - - + -
424A ASN 5.6 0.4 - - - +
427A LEU* 4.3 14.1 - - + -
440A ALA* 3.9 9.4 - - + -
441A CYS* 1.3 75.3 - - - +
443A TYR* 1.3 63.0 + - - +
444A ASP* 3.5 33.8 + - + -
449A ARG* 3.3 6.7 - - - -
450A ARG* 2.9 60.9 + - + +
452A VAL* 4.1 23.1 - - + -
457A HIS* 3.3 38.4 - + - -
476A TYR* 3.8 25.1 - + + -
478A HIS 5.1 2.9 - - - -
480A SER* 5.4 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL* 4.8 3.8 + - - +
424A ASN 5.3 2.5 + - - -
425A ALA* 5.5 12.5 - - + +
442A PHE* 1.3 79.0 - - - +
444A ASP* 1.3 71.6 + - - +
445A ILE* 3.4 8.1 + - - -
448A GLY* 3.6 23.1 - - - -
449A ARG* 3.8 39.0 - - + +
476A TYR* 4.1 11.6 - - - +
477A TRP* 5.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 3.5 18.5 + - + -
443A TYR* 1.3 77.4 - - - +
445A ILE* 1.3 72.6 + - - +
446A LYS* 2.7 32.6 + - - +
447A LEU* 2.8 15.1 + - - +
448A GLY* 2.8 41.1 + - - +
450A ARG* 3.2 43.3 + - + -
476A TYR* 5.6 0.4 - - - -
478A HIS 4.5 7.3 - - - +
479A GLN* 5.0 8.1 - - - +
480A SER 5.2 0.9 + - - -
----------------------------------------------------------
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