Contacts of the helix formed by residues 764 - 781 (chain A) in PDB entry 4K6J
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 ASP 764 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A ASN* 3.0 36.3 + - - +
763A LYS* 1.3 77.6 - - - +
765A MET* 1.3 65.1 + - - +
766A ASN 3.3 0.4 - - - -
767A LYS* 3.8 26.9 - - - +
768A ILE* 3.5 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 765 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A ASN* 4.7 9.0 - - - +
675A CYS* 5.1 6.3 - - + -
715A ASN* 3.3 48.5 - - + +
718A LEU* 5.7 7.0 - - - -
719A CYS* 6.0 1.8 - - - -
761A ASN* 3.0 36.3 - - + +
762A GLU* 2.9 12.0 + - + +
764A ASP* 1.3 81.3 + - - +
766A ASN* 1.3 59.1 + - - +
768A ILE* 3.3 28.8 + - + +
769A LYS* 2.8 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A GLU* 3.1 29.5 + - - +
763A LYS* 4.1 11.6 - - - +
765A MET* 1.3 80.1 - - - +
767A LYS* 1.3 60.2 + - + +
769A LYS* 3.6 19.9 + - - +
770A GLU* 2.8 31.0 + - - +
786A LEU* 5.1 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A LYS 3.5 13.2 - - - +
764A ASP* 3.8 28.5 - - - +
765A MET 3.3 0.2 - - - -
766A ASN* 1.3 77.3 - - - +
768A ILE* 1.3 58.8 + - + +
770A GLU* 3.6 6.4 + - - +
771A LYS* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A CYS* 4.9 4.0 - - + -
676A LEU* 4.1 27.6 - - + -
679A ILE* 4.1 26.9 - - + -
718A LEU* 5.2 5.6 - - + -
719A CYS* 4.6 11.7 - - - -
764A ASP 3.5 15.1 + - - +
765A MET* 3.3 32.2 + - + +
766A ASN 3.2 0.4 - - - -
767A LYS* 1.3 77.9 - - + +
769A LYS* 1.3 60.4 + - - +
771A LYS* 3.2 6.4 + - - +
772A ILE* 2.9 44.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A LEU* 4.0 18.4 - - + -
765A MET* 2.8 29.2 + - - +
766A ASN* 3.6 21.6 + - - +
768A ILE* 1.3 75.5 - - - +
770A GLU* 1.3 56.6 + - - +
772A ILE* 3.2 3.8 + - - +
773A ARG* 2.9 28.9 + - - +
786A LEU* 3.9 23.0 + - + +
789A ILE* 3.4 44.0 - - + +
790A THR* 5.5 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A ASN 2.8 20.6 + - - +
767A LYS* 3.9 7.4 - - - +
769A LYS* 1.3 73.1 - - - +
771A LYS* 1.3 62.8 + - - +
773A ARG* 3.3 24.9 + - - +
774A ARG* 3.1 42.5 + - - +
786A LEU* 3.3 31.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 771 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 4.0 21.5 - - + -
683A THR* 3.3 35.1 - - - +
767A LYS 3.1 18.4 + - - +
768A ILE* 3.4 7.9 - - - +
769A LYS 3.2 0.2 - - - -
770A GLU* 1.3 77.0 - - - +
772A ILE* 1.3 61.6 + - - +
774A ARG* 3.5 34.3 + - + +
775A LEU* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 3.9 19.3 - - + -
682A ALA* 6.5 0.2 - - + -
718A LEU* 4.1 22.4 - - + +
719A CYS* 4.8 0.7 - - - -
722A ALA* 3.8 25.4 - - + -
726A ILE* 5.9 1.3 - - + -
768A ILE* 2.9 34.2 + - + +
769A LYS 3.2 6.9 + - - +
771A LYS* 1.3 75.4 - - + +
773A ARG* 1.3 65.3 + - - +
775A LEU* 3.2 14.6 + - + +
776A CYS* 2.9 31.3 + - - -
789A ILE* 3.8 13.0 - - + -
794A LEU* 3.8 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A LYS 2.9 13.2 + - - +
770A GLU* 3.4 31.3 + - - +
772A ILE* 1.3 78.0 - - - +
774A ARG* 1.3 61.7 + - - +
776A CYS* 3.2 7.2 + - - +
777A GLU* 3.1 42.0 + - - +
784A LEU 3.0 31.6 + - - +
785A ASP* 4.3 11.1 + - - +
786A LEU* 3.4 34.9 - - + +
789A ILE* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLU* 3.1 40.4 + - - +
771A LYS* 3.7 42.2 - - + +
772A ILE 3.3 0.2 - - - -
773A ARG* 1.3 77.3 - - + +
775A LEU* 1.3 62.1 + - + +
777A GLU* 3.5 17.1 + - - +
778A THR* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A ILE* 4.7 3.4 - - + +
682A ALA* 4.0 7.2 - - + +
683A THR* 3.9 39.7 - - + +
686A ALA* 3.8 28.0 - - + -
726A ILE* 3.7 28.9 - - + -
771A LYS* 3.2 31.0 + - + +
772A ILE* 3.2 16.5 + - + +
774A ARG* 1.3 76.1 - - - +
776A CYS* 1.3 58.2 + - - +
778A THR* 4.4 3.8 - - - -
779A VAL* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ALA* 6.1 0.9 - - - -
725A TYR* 3.7 35.7 - - + -
726A ILE* 5.4 4.9 - - - -
772A ILE* 2.9 37.0 + - - -
773A ARG* 3.2 10.7 + - - +
775A LEU* 1.3 78.3 - - - +
777A GLU* 1.3 57.2 + - - +
780A HIS* 2.9 35.7 + - - +
782A LYS* 3.4 14.3 + - + +
784A LEU* 4.3 13.0 - - + -
794A LEU* 4.1 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A ARG* 3.1 37.4 + - + +
774A ARG* 3.7 19.8 - - - +
775A LEU 3.3 0.2 - - - -
776A CYS* 1.3 76.3 - - - +
778A THR* 1.3 58.6 + - - +
781A ASN* 2.8 27.9 + - - +
782A LYS 3.4 19.3 - - - +
783A HIS* 3.2 42.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA* 4.7 15.7 - - + +
774A ARG* 3.0 17.9 + - - +
775A LEU* 3.7 8.2 - - - -
777A GLU* 1.3 80.6 - - - +
779A VAL* 1.3 69.2 + - + +
781A ASN 4.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A ALA* 3.7 37.0 - - + +
691A ARG* 4.0 11.4 + - - +
726A ILE* 3.7 22.7 - - + +
729A ARG* 3.3 42.8 + - + +
775A LEU* 2.9 22.3 + - - +
778A THR* 1.3 80.8 - - + +
780A HIS* 1.3 79.4 + - + +
781A ASN 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A TYR* 2.8 75.9 + + - +
726A ILE* 3.7 6.7 + - + -
729A ARG* 3.6 43.9 + - - +
776A CYS* 2.9 15.3 + - - +
779A VAL* 1.3 90.5 - - + +
781A ASN* 1.3 72.4 + - - +
782A LYS* 3.2 6.7 + - + +
801A SER* 3.9 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLU 2.8 18.6 + - - -
778A THR 4.5 0.6 + - - -
779A VAL 3.7 1.0 - - - -
780A HIS* 1.3 81.6 - - - +
782A LYS* 1.3 58.2 + - - +
783A HIS* 3.5 25.9 + - - -
----------------------------------------------------------
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