Contacts of the strand formed by residues 659 - 662 (chain A) in PDB entry 1WXR
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 ASP 659 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLY 3.2 5.8 + - - +
602A ARG* 3.5 25.0 + - + +
603A LEU 3.2 20.4 + - - +
658A THR* 1.3 76.9 + - - +
660A PHE* 1.3 61.0 + - - +
678A SER* 3.5 18.3 + - - +
680A THR* 5.1 0.9 + - - -
685A ARG* 2.6 43.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU* 3.2 35.0 - - + +
605A LEU* 3.7 28.5 - - + -
653A LEU* 3.5 24.0 - - + -
655A LEU* 3.6 31.4 - - + -
658A THR* 3.7 1.2 + - - +
659A ASP* 1.3 77.5 - - - +
661A GLY* 1.3 75.1 + - - +
662A LEU* 4.2 3.1 - - + -
668A LEU* 3.7 25.8 - - + -
672A ILE* 4.7 1.1 - - + -
678A SER 2.8 13.1 + - - +
679A VAL* 3.5 18.8 - - + -
680A THR* 2.9 29.3 + - - -
681A LEU* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU 2.8 13.1 + - - +
604A THR* 3.1 9.7 + - - +
605A LEU 2.8 26.9 + - - +
659A ASP 4.0 0.4 + - - -
660A PHE* 1.3 83.0 - - - +
662A LEU* 1.3 61.3 + - - -
663A GLY 4.0 0.2 - - - -
680A THR 3.5 3.6 - - - -
683A ASP* 3.2 24.7 - - - -
685A ARG* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU* 3.5 18.2 - - + +
648A PHE* 5.0 0.7 - - + -
660A PHE* 4.2 6.1 - - + -
661A GLY* 1.3 73.0 - - - -
663A GLY* 1.3 58.3 + - - +
666A ALA* 3.8 23.8 - - + -
667A THR 4.5 0.9 - - - -
668A LEU* 3.7 29.2 - - + +
680A THR 2.8 12.4 + - - +
681A LEU* 4.1 18.2 - - + -
682A GLY* 2.9 12.8 + - - -
683A ASP* 2.8 23.8 + - - -
714A SER* 3.8 12.1 + - - -
715A VAL 3.7 21.5 - - - +
716A PHE* 4.6 2.0 - - + -
732A ASP* 3.6 21.8 - - - +
----------------------------------------------------------
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