Contacts of the strand formed by residues 504 - 510 (chain B) in PDB entry 2VKX
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 504 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B SER* 4.4 3.5 + - - -
503B PRO* 1.3 78.2 + - - +
505B ILE* 1.3 63.9 + - - +
506B ASP* 3.4 7.4 + - - +
519B PHE* 2.9 7.8 - - - +
520B ASP* 2.8 49.8 + - - +
588B SER* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 5.5 0.9 - - - +
654A GLY* 3.2 23.3 - - - +
504B SER* 1.3 75.2 - - - +
506B ASP* 1.3 61.0 + - - +
507B GLN 3.6 2.9 - - - +
508B VAL* 3.5 29.6 - - + -
517B VAL* 3.8 6.1 - - + -
518B GLN 3.5 12.1 - - - +
519B PHE* 4.0 0.2 - - - -
574B VAL* 3.8 30.1 - - + +
575B ARG* 4.1 6.7 - - - -
576B LEU* 4.2 22.9 - - + -
588B SER* 4.1 19.6 + - - +
589B ALA 4.5 2.9 - - - +
591B SER* 3.9 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 5.5 1.3 - - - -
653A SER* 2.7 39.9 + - - +
654A GLY* 3.9 8.7 + - - -
504B SER* 3.7 8.8 - - - +
505B ILE* 1.3 78.3 - - - +
507B GLN* 1.3 69.4 + - + +
518B GLN* 3.0 14.7 + - - +
519B PHE* 3.2 25.6 + - - +
520B ASP* 3.3 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 5.5 2.5 - - - +
626A ASP* 4.0 10.8 + - - +
630A PRO* 3.6 12.8 - - + +
631A ILE* 2.8 58.1 + - - +
653A SER* 3.2 7.4 + - - -
505B ILE* 3.6 1.0 - - - +
506B ASP* 1.3 89.7 + - + +
508B VAL* 1.3 73.2 + - - +
509B GLU* 4.2 1.3 - - + +
516B GLN 4.2 0.9 - - - +
517B VAL* 3.4 0.7 - - - -
518B GLN* 2.7 67.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS* 4.2 23.0 - - + +
624A GLN 4.6 2.4 - - - +
626A ASP* 5.2 2.4 - - - +
505B ILE* 3.5 21.1 - - + -
507B GLN* 1.3 84.2 + - - +
509B GLU* 1.3 60.9 + - - +
510B PRO* 3.2 12.0 - - - +
515B ALA* 4.5 9.6 - - + -
516B GLN 3.3 6.5 - - - +
517B VAL* 4.4 11.9 - - + -
574B VAL* 4.4 10.5 - - + -
591B SER* 4.2 12.3 - - - +
592B GLU 5.9 0.2 - - - +
593B PHE* 3.5 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A GLN 4.0 0.5 - - - +
625A ASP* 2.6 27.0 - - - +
626A ASP* 2.9 47.2 + - - +
628A GLY* 4.7 3.8 + - - -
507B GLN* 5.2 1.3 - - + +
508B VAL* 1.3 70.6 - - - +
510B PRO* 1.3 70.0 - - - +
511B TYR* 3.5 38.4 + - + +
515B ALA* 3.2 4.7 - - - -
516B GLN* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS 4.3 3.6 - - - +
624A GLN* 3.8 17.0 - - - +
625A ASP* 3.8 13.6 - - - +
508B VAL* 3.2 12.3 - - + +
509B GLU* 1.3 95.3 - - - +
511B TYR* 1.3 57.7 + - - +
514B THR 4.1 3.4 - - - +
515B ALA* 4.3 2.9 - - + -
593B PHE* 3.8 23.1 - - + -
594B LYS 3.4 28.9 - - - +
595B THR* 4.1 3.4 - - + -
596B GLN* 2.8 30.7 + - + +
----------------------------------------------------------
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