Contacts of the strand formed by residues 763 - 767 (chain C) in PDB entry 5J67
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 LEU 763 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722C LEU 4.7 2.5 - - - +
723C PHE* 3.7 35.7 - - + +
726C MET* 5.3 1.1 - - + -
727C LEU* 4.4 17.5 - - + -
751C ASN* 4.2 16.0 + - - +
759C LEU* 4.0 16.8 - - + +
760C ALA* 3.5 34.8 - - + +
761C ASP 3.3 1.0 - - - +
762C GLY* 1.3 78.4 - - - +
764C LEU* 1.3 60.5 + - - +
765C VAL* 3.7 26.0 + - + +
815C VAL* 4.6 5.6 - - + -
816C LYS 3.5 9.2 - - - +
817C LEU* 4.1 10.1 - - + +
820C ILE* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 764 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762C GLY 4.2 0.4 + - - -
763C LEU* 1.3 69.0 - - - +
765C VAL* 1.3 65.0 + - - +
766C ILE* 3.8 32.7 + - + +
814C ARG 3.5 5.4 - - - +
815C VAL* 3.6 0.6 - - - -
816C LYS* 2.7 47.6 + - + +
818C SER* 5.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 765 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723C PHE* 3.9 21.1 - - + -
753C ILE* 3.7 25.6 - - + +
759C LEU* 3.5 26.4 - - + +
763C LEU* 3.7 18.5 + - + -
764C LEU* 1.3 76.0 - - - +
766C ILE* 1.3 64.0 + - - +
767C PRO* 3.8 6.1 - - - +
813C TYR* 3.6 37.2 - - + -
814C ARG 3.7 2.9 - - - -
815C VAL* 4.4 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 766 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764C LEU* 3.8 30.1 - - + +
765C VAL* 1.3 77.8 - - - +
767C PRO* 1.4 73.8 - - + +
768C LEU* 3.4 1.1 + - - +
813C TYR* 4.4 1.8 - - - -
814C ARG* 2.9 41.3 + - + +
816C LYS* 3.5 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 767 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753C ILE* 5.7 3.8 - - + -
754C LYS* 4.4 12.8 - - - +
765C VAL* 3.8 7.2 - - + +
766C ILE* 1.4 93.3 - - + +
768C LEU* 1.3 68.0 + - - +
769C PRO* 3.9 0.7 - - - +
773C GLN* 4.8 2.9 - - - +
812C LEU 3.7 10.1 - - - +
813C TYR* 3.8 27.8 - - + -
----------------------------------------------------------
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