Contacts of the strand formed by residues 710 - 718 (chain F) in PDB entry 1XSK
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 VAL 710 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575F ARG* 3.8 25.8 - - - +
702F GLU* 3.4 31.6 - - + +
703F VAL 3.6 5.4 - - - +
704F PRO* 4.3 1.6 - - - -
709F SER* 1.3 75.6 + - - +
711F ILE* 1.3 63.0 + - - +
712F PHE 3.8 13.2 - - - +
713F THR* 3.3 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 711 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683F HIS* 3.4 57.2 - - + +
703F VAL 2.7 20.2 + - - +
704F PRO 3.9 11.9 - - - +
705F ALA* 3.7 22.2 - - + +
709F SER 3.3 1.0 + - - -
710F VAL* 1.3 75.4 - - - +
712F PHE* 1.3 59.5 + - + +
729F GLY* 3.6 5.1 - - - -
730F GLU* 3.0 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 712 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683F HIS* 4.8 0.7 - - + -
688F PHE* 3.6 36.1 - + - -
701F CYS 3.9 0.5 - - - +
702F GLU* 3.6 2.3 - - - -
703F VAL* 2.8 39.5 + - + +
710F VAL* 3.6 2.3 - - - +
711F ILE* 1.3 81.4 - - + +
713F THR* 1.3 61.5 + - - +
714F LEU* 3.9 14.8 - - + -
727F GLY* 4.2 12.3 - - - -
728F ALA* 3.0 37.9 - - - -
729F GLY 3.7 12.1 - - - -
730F GLU 3.2 15.5 - - - +
731F ALA* 3.3 30.3 - - + -
734F TRP* 3.8 25.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 713 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700F VAL* 3.8 26.9 - - + -
701F CYS 3.5 4.9 - - - +
702F GLU* 3.9 10.7 + - + +
710F VAL* 3.3 22.0 - - - +
712F PHE* 1.3 72.7 - - - +
714F LEU* 1.3 61.1 + - - +
715F LYS* 3.9 18.3 + - - +
726F THR 3.8 4.7 - - - +
728F ALA* 2.7 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 714 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F LEU* 3.0 33.0 - - + +
688F PHE* 3.7 43.5 - - + -
700F VAL* 3.8 0.3 - - - -
701F CYS 2.9 31.5 + - - +
712F PHE* 3.9 16.4 - - + -
713F THR* 1.3 72.9 - - - +
715F LYS* 1.3 65.3 + - - +
716F ALA* 6.1 0.4 - - + -
725F VAL* 3.5 29.4 - - + -
726F THR 3.5 10.8 - - - +
727F GLY* 4.2 3.8 - - - -
734F TRP* 4.1 21.1 - - + -
736F LEU* 4.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 715 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F LEU* 4.5 1.8 - - - -
698F GLU* 3.3 28.2 + - - +
699F ALA 3.7 3.6 - - - +
700F VAL* 4.0 20.7 - - + +
713F THR* 4.1 21.8 - - + +
714F LEU* 1.3 78.1 - - - +
716F ALA* 1.3 62.1 + - - +
717F ALA 4.1 0.7 - - - +
724F THR 3.6 0.8 - - - +
725F VAL* 3.3 9.9 - - - +
726F THR* 2.9 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 716 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668F LEU* 4.5 6.5 - - + -
690F LEU* 4.0 17.9 - - + -
693F LEU* 3.1 26.1 - - + +
698F GLU* 3.4 2.0 - - - +
699F ALA 3.0 34.4 + - - +
714F LEU* 6.1 0.2 - - + -
715F LYS* 1.3 75.1 - - - +
717F ALA* 1.3 60.3 + - - +
723F ILE* 4.1 11.4 - - + -
724F THR 3.4 5.6 - - - -
725F VAL* 4.7 7.2 - - + -
736F LEU* 6.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 717 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697F HIS 3.5 5.8 - - - +
698F GLU* 3.9 22.0 - - + +
715F LYS 4.1 0.4 - - - -
716F ALA* 1.3 73.7 - - - +
718F ARG* 1.3 59.7 + - - +
719F THR* 3.6 4.3 + - - +
723F ILE* 3.4 1.9 - - - -
724F THR* 2.7 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 718 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693F LEU* 3.0 41.3 + - + -
694F GLN* 3.8 2.9 - - - +
695F ASP* 3.4 33.4 - - - +
696F GLY* 2.7 34.2 + - - -
697F HIS 3.1 8.9 + - - -
716F ALA 4.0 1.0 + - - -
717F ALA* 1.3 71.0 - - - +
719F THR* 1.3 58.4 + - - +
720F GLY 3.9 15.3 + - - +
721F ASN* 3.6 16.8 + - - +
722F THR 3.4 6.5 - - - +
723F ILE* 3.5 26.5 - - + -
772F LEU* 3.6 27.3 - - - +
----------------------------------------------------------
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