Contacts of the strand formed by residues 507 - 510 (chain v) in PDB entry 6FF7
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 507 (chain v).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460v TRP* 5.4 4.7 - - - -
505v THR* 5.0 3.6 - - - -
506v LEU* 1.3 79.6 + - - +
508v CYS* 1.3 62.9 + - - +
517v VAL 4.7 0.4 - - - -
518v GLN* 3.2 7.2 - - - +
519v VAL* 2.9 43.0 + - - +
547v CYS* 4.2 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 508 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460v TRP* 4.6 22.3 - - + +
461v THR 4.9 4.9 - - - +
462v VAL* 4.7 14.4 - - + -
475v ILE* 5.4 10.3 - - + -
507v SER* 1.3 78.1 - - - +
509v SER* 1.3 65.1 + - - +
516v LEU* 6.1 2.9 - - + -
517v VAL 3.6 7.0 - - - +
518v GLN* 4.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 509 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461v THR 5.6 0.9 - - - -
462v VAL* 4.8 9.6 - - - +
508v CYS* 1.3 78.7 - - - +
510v LEU* 1.3 63.2 + - - +
511v LEU* 3.9 1.8 - - - -
516v LEU* 3.2 9.9 - - - +
517v VAL* 2.9 38.1 + - - -
549v VAL* 4.6 19.7 - - - -
550v ASN 4.8 10.1 - - - -
551v GLN* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 510 (chain v).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462v VAL* 4.9 3.6 - - + +
463v ARG* 4.3 27.1 - - + +
464v ARG 5.3 4.5 - - - +
465v HIS 6.0 3.6 - - - +
509v SER* 1.3 73.8 - - - +
511v LEU* 1.3 61.3 + - - +
512v GLY 3.9 6.1 - - - +
513v ASP 5.8 1.3 - - - +
514v ASP 6.2 1.1 - - - -
515v ALA 3.8 7.6 - - - +
516v LEU* 4.4 2.7 - - + +
550v ASN 5.5 0.2 - - - -
551v GLN* 3.6 20.3 - - - +
----------------------------------------------------------
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