Contacts of the strand formed by residues 765 - 770 (chain A) in PDB entry 3PT6
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 CYS 765 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A GLY 4.4 2.0 - - - -
764A ASP* 1.3 77.3 - - - +
766A VAL* 1.3 60.4 + - - +
779A LEU* 6.3 0.7 - - + -
780A ALA 3.1 9.6 - - - +
781A ARG* 3.9 22.2 - - - -
800A PHE* 3.4 32.5 - - + -
834A LYS* 3.5 8.0 - - - +
835A VAL* 2.8 44.1 + - + +
837A VAL* 3.9 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A ASP 4.3 0.4 + - - -
765A CYS* 1.3 75.4 - - - +
767A SER* 1.3 63.7 + - - +
768A VAL* 4.9 4.1 - - + +
779A LEU* 3.5 2.6 - - - +
780A ALA* 2.9 33.9 + - + +
782A VAL* 4.6 12.8 - - + +
795A PHE* 5.6 3.1 - - + -
831A ILE* 4.0 30.5 - - + -
833A SER 3.3 11.7 - - - +
834A LYS* 4.2 3.6 - - + +
835A VAL* 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A VAL* 1.3 72.1 - - - +
768A VAL* 1.3 70.0 + - - +
777A LEU* 3.9 18.5 - - - +
778A TYR 3.2 11.4 - - - -
779A LEU* 4.4 7.6 - - - +
831A ILE* 3.9 1.6 - - - -
832A HIS* 3.0 31.4 + - - +
833A SER* 2.8 36.0 + - - +
835A VAL* 4.3 16.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LYS* 4.4 13.5 - - + -
727A LYS 5.2 0.9 - - - +
766A VAL* 4.9 5.6 - - + +
767A SER* 1.3 82.0 - - - +
769A ILE* 1.3 78.9 + - - +
770A PRO* 3.6 0.2 - - - +
777A LEU* 3.3 9.9 - - - +
778A TYR* 2.9 50.2 + - + -
780A ALA* 6.0 2.5 - - + -
795A PHE* 5.3 6.1 - - + -
799A TRP* 4.7 16.2 - - + -
826A MET* 5.1 7.6 - - - -
830A TYR* 3.9 26.7 - - + +
831A ILE* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LYS* 3.3 7.4 - - - +
727A LYS* 2.7 66.6 + - + +
729A GLN* 3.6 18.4 - - + +
768A VAL* 1.3 82.3 - - - +
770A PRO* 1.3 69.4 - - + +
777A LEU* 4.2 19.1 - - + -
778A TYR* 4.7 0.2 - - - -
830A TYR 4.9 0.9 - - - +
832A HIS* 3.1 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LYS 3.9 4.9 - - - +
727A LYS* 4.1 5.7 - - - +
768A VAL 3.6 6.1 - - - +
769A ILE* 1.3 99.5 - - + +
771A ASP* 1.3 67.8 + - - +
772A ASP 3.2 16.9 - - - +
773A SER* 5.1 0.3 - - - -
775A LYS* 4.1 20.9 - - + +
776A PRO 3.8 20.6 - - - +
777A LEU* 4.2 10.3 - - + -
778A TYR* 3.8 35.9 - - + +
----------------------------------------------------------
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