Contacts of the strand formed by residues 430 - 437 (chain B) in PDB entry 2VRW
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 430 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B TYR* 3.5 31.1 + - + +
425B PHE 3.8 1.9 - - - +
426B LEU* 3.8 0.5 - - - +
427B LEU* 3.1 32.6 + - - +
428B ASP 3.5 2.4 + - - -
429B LYS* 1.3 82.6 - - - +
431B LEU* 1.3 60.4 + - - +
432B LEU* 3.9 11.2 + - + -
446B SER* 4.8 1.8 - - - -
447B VAL 3.1 19.5 - - - +
448B ASN* 4.5 1.6 - - - -
449B LEU* 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU* 5.2 1.6 - - + -
424B ALA* 3.8 17.3 - - + -
425B PHE 3.7 3.6 - - - +
426B LEU* 4.0 12.3 - - + -
430B ALA* 1.3 71.0 - - - +
432B LEU* 1.3 61.0 + - - +
433B ILE* 3.6 27.8 + - + -
445B ALA 3.6 2.1 - - - +
446B SER* 3.6 0.2 - - - -
447B VAL* 2.8 44.3 + - + +
449B LEU* 4.3 2.8 - - + +
473B LEU* 3.8 23.1 - - + -
484B LEU* 4.1 15.9 - - + -
495B TRP* 3.7 29.2 - - + -
499B PHE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.7 8.5 - - + -
393B LEU* 4.0 15.5 - - + -
397B LEU* 3.4 34.3 - - + -
400B TYR* 4.1 14.1 - - + +
423B TYR 3.8 0.3 - - - +
424B ALA* 3.3 5.2 - - - -
425B PHE* 2.9 38.8 + - + +
427B LEU* 3.9 15.7 - - + -
430B ALA* 4.1 13.0 - - + +
431B LEU* 1.3 73.4 - - - +
433B ILE* 1.3 63.6 + - - +
434B CYS* 3.6 7.5 + - - -
443B LEU* 3.8 13.9 - - + -
445B ALA 3.6 2.7 - - - -
446B SER* 3.7 27.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.6 37.2 - - + -
422B ARG* 3.7 23.8 - - + +
423B TYR 4.1 2.0 - - - -
424B ALA* 4.7 2.7 - - + +
431B LEU* 3.9 21.1 - - + -
432B LEU* 1.3 69.6 - - - +
434B CYS* 1.3 55.3 + - - +
443B LEU* 3.7 1.6 - - - +
444B LYS* 2.8 35.2 + - + -
445B ALA* 2.8 25.8 + - + +
447B VAL* 3.7 25.8 - - + -
482B TYR* 4.1 22.9 - - + -
484B LEU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.3 8.7 - - - -
422B ARG* 3.2 12.9 - - - -
423B TYR* 2.8 41.4 + - - +
425B PHE* 4.0 20.2 - - + -
432B LEU* 3.9 11.7 - - - -
433B ILE* 1.3 79.4 - - - +
435B LYS* 1.3 58.5 + - - +
441B TYR* 3.7 22.0 - - + -
442B ASP 3.1 9.9 - - - +
443B LEU* 3.9 23.8 - - - -
444B LYS* 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B THR* 6.0 1.6 - - - +
421B ASP 4.9 2.7 - - - +
422B ARG* 3.6 29.1 - - - +
423B TYR 4.8 0.4 - - - +
434B CYS* 1.3 73.2 - - - +
436B ARG* 1.3 76.7 + - - +
437B ARG* 3.2 3.3 + - + +
441B TYR* 4.4 1.3 - - - -
442B ASP* 2.9 33.2 + - + +
444B LYS* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLU* 4.0 18.4 + - - +
422B ARG* 5.7 0.8 - - - +
423B TYR* 3.5 37.5 - - + +
434B CYS 4.1 1.4 + - - -
435B LYS* 1.3 80.6 - - - +
437B ARG* 1.3 59.8 + - - +
438B GLY 3.5 27.1 + - - +
439B ASP* 5.6 2.8 + - - +
440B SER 3.6 9.9 - - - +
441B TYR* 3.1 37.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLU* 4.3 17.4 - - - +
435B LYS* 3.2 4.7 + - + +
436B ARG* 1.3 72.7 - - - +
438B GLY* 1.3 62.8 + - - +
439B ASP 3.3 0.5 + - - -
440B SER* 2.9 30.8 + - - +
442B ASP* 2.8 55.5 + - + +
----------------------------------------------------------
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