Contacts of the strand formed by residues 710 - 718 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575C ARG* 4.0 17.5 - - - +
702C GLU* 3.3 37.2 - - + +
703C VAL 3.8 4.5 - - - +
704C PRO* 4.4 1.6 - - - -
708C GLY 5.1 1.1 - - - +
709C SER* 1.3 78.7 + - - +
711C ILE* 1.3 61.2 + - - +
712C PHE 3.6 14.6 - - - +
713C THR* 3.4 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 711 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C HIS* 3.5 53.2 - - + +
703C VAL 2.8 20.5 + - - +
704C PRO 3.7 14.6 - - - +
705C ALA* 4.1 21.1 - - + -
709C SER* 3.5 1.4 + - - -
710C VAL* 1.3 75.0 - - - +
712C PHE* 1.3 59.9 + - + +
729C GLY* 3.3 5.6 - - - -
730C GLU* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 712 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683C HIS* 4.9 0.7 - - + -
688C PHE* 3.9 30.3 - + - -
701C CYS 4.0 0.2 - - - +
702C GLU* 3.5 2.9 - - - -
703C VAL* 2.8 39.9 + - + +
710C VAL* 3.6 2.7 - - - +
711C ILE* 1.3 84.6 - - + +
713C THR* 1.3 75.6 + - - +
714C LEU* 4.0 14.8 - - + -
727C GLY* 4.0 13.0 - - - -
728C ALA 3.1 33.2 - - - -
729C GLY 3.4 17.7 - - - -
730C GLU 3.6 10.8 - - - +
731C ALA* 3.4 31.9 - - + -
734C TRP* 4.0 15.0 - + - -
766C ASN* 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 713 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700C VAL* 4.0 20.6 - - + -
701C CYS 3.4 10.3 - - - +
702C GLU* 4.0 11.0 + - + +
710C VAL* 3.4 17.7 - - - +
712C PHE* 1.3 79.9 - - - +
714C LEU* 1.3 63.4 + - - +
715C LYS* 4.3 18.2 - - + -
726C THR 4.6 0.2 - - - -
727C GLY* 3.0 4.5 - - - -
728C ALA* 2.7 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 714 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C LEU* 3.3 28.4 - - + +
688C PHE* 4.4 16.8 - - + -
700C VAL* 4.2 0.2 - - - +
701C CYS 3.0 32.2 + - - +
712C PHE* 4.0 13.2 - - + -
713C THR* 1.3 76.2 - - - +
715C LYS* 1.3 70.1 + - - +
716C ALA* 5.2 1.1 - - + -
725C VAL* 3.6 26.7 - - + -
726C THR 3.4 7.9 - - - +
727C GLY* 3.9 11.7 - - - +
734C TRP* 3.6 36.8 - - + -
736C LEU* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 715 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698C GLU* 3.1 33.1 + - + +
699C ALA 3.4 6.3 - - - +
700C VAL* 4.2 17.9 - - + +
713C THR* 4.3 17.3 - - + -
714C LEU* 1.3 83.0 - - - +
716C ALA* 1.3 60.5 + - - +
717C ALA* 4.0 1.3 - - + +
724C THR 3.3 2.6 - - - +
725C VAL* 3.3 9.4 - - - +
726C THR* 2.8 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 716 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C LEU* 4.3 9.4 - - + +
690C LEU* 3.8 33.0 - - + -
693C LEU* 2.9 20.1 - - + +
698C GLU* 3.6 0.8 - - - -
699C ALA 3.0 30.2 + - - +
714C LEU* 5.2 0.9 - - + -
715C LYS* 1.3 72.9 - - - +
717C ALA* 1.3 60.3 + - - +
723C ILE* 4.2 6.7 - - + -
724C THR 3.6 4.7 - - - -
725C VAL* 4.8 7.6 - - + -
736C LEU* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 717 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C LEU* 4.1 1.3 - - - -
697C HIS 3.4 7.9 - - - +
698C GLU* 3.6 24.0 - - + +
715C LYS* 4.0 1.5 - - + -
716C ALA* 1.3 72.9 - - - +
718C ARG* 1.3 61.2 + - - +
719C THR* 3.8 4.8 + - - +
722C THR 3.6 1.7 - - - +
723C ILE* 3.3 1.5 - - - +
724C THR* 3.0 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 718 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693C LEU* 3.1 41.8 + - + +
694C GLN* 3.7 10.1 - - - +
695C ASP* 3.7 27.2 - - - +
696C GLY* 2.6 36.0 + - - -
697C HIS 3.0 10.3 + - - +
717C ALA* 1.3 71.2 - - - +
719C THR* 1.3 60.0 + - - +
720C GLY 3.8 13.5 + - - +
721C ASN* 3.6 24.4 + - - +
722C THR 3.3 11.7 - - - +
723C ILE* 3.9 17.5 - - + +
772C LEU* 4.6 11.5 - - - +
----------------------------------------------------------
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