Contacts of the strand formed by residues 758 - 763 (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 GLY 758 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737F CYS* 3.8 5.9 - - - -
738F LEU 3.3 13.5 - - - -
740F ASN* 3.9 2.9 - - - -
741F VAL 3.8 7.6 - - - -
742F VAL* 5.0 5.4 - - - -
755F SER* 2.6 38.0 + - - -
756F GLU 3.5 0.2 - - - -
757F GLN* 1.3 80.5 - - - +
759F LEU* 1.3 65.8 + - - -
760F VAL 3.3 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 759 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736F LEU 3.7 1.0 - - - +
737F CYS* 3.4 0.9 - - - -
738F LEU* 2.7 52.1 + - + +
741F VAL* 2.8 22.5 + - + +
742F VAL* 4.0 13.7 - - - +
743F LYS* 4.7 1.1 - - - -
744F VAL* 3.4 43.5 - - + +
752F GLN* 3.4 19.7 - - - +
753F ALA 3.0 31.2 - - - +
754F GLU* 4.0 11.2 - - + +
758F GLY* 1.3 69.0 - - - -
760F VAL* 1.3 65.3 + - - +
761F VAL* 4.4 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 760 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735F THR* 3.2 32.5 - - + +
736F LEU 3.9 2.2 - - - -
737F CYS* 4.3 10.8 - - + +
752F GLN* 3.3 5.7 - - - +
753F ALA* 3.0 46.3 + - + +
754F GLU 4.9 0.9 - - - +
755F SER* 3.7 32.1 - - - +
758F GLY 3.8 1.1 - - - +
759F LEU* 1.3 73.0 - - - +
761F VAL* 1.3 62.4 + - - +
762F LYS* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 761 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735F THR* 3.7 5.3 - - - +
736F LEU* 2.9 48.4 + - + +
738F LEU* 4.2 24.2 - - + -
747F LEU* 4.3 14.1 - - + -
751F SER 3.5 14.8 - - - +
759F LEU* 4.3 9.4 - - + +
760F VAL* 1.3 81.9 - - - +
762F LYS* 1.3 63.1 + - - +
763F PRO* 3.7 3.6 - - - +
768F LEU* 3.6 39.5 - - + -
770F ILE* 5.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 762 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733F ASN* 3.7 28.1 - - - +
734F TRP* 2.8 39.6 + - - +
735F THR* 3.6 13.5 - - + +
751F SER* 3.1 39.7 + - - +
752F GLN* 5.0 0.4 - - - +
760F VAL* 4.4 1.8 + - + -
761F VAL* 1.3 77.6 - - - +
763F PRO* 1.3 83.9 + - - +
764F GLN* 3.4 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 763 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734F TRP* 3.5 61.5 - - + +
749F ASP 3.7 8.1 - - - +
750F GLY* 4.1 0.9 - - - -
761F VAL 3.7 7.4 - - - +
762F LYS* 1.3 102.8 + - + +
764F GLN* 1.3 63.1 + - - +
765F GLY 5.4 2.9 - - - +
768F LEU* 3.5 26.8 - - + -
----------------------------------------------------------
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