Contacts of the helix formed by residues 764 - 773 (chain F) in PDB entry 2VE8
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 SER 764 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C VAL* 5.6 4.6 + - - -
762F ARG* 3.4 4.5 + - - +
763F ALA* 1.3 79.9 - - - +
765F ILE* 1.3 65.4 + - - +
766F SER* 3.6 7.5 + - - -
767F ALA* 3.0 27.0 + - - +
768F VAL* 3.2 22.5 + - - +
783F ILE* 4.3 6.4 - - - +
801F ARG* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 765 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764F SER* 1.3 73.2 - - - +
766F SER* 1.3 53.6 + - - +
768F VAL* 3.2 5.3 + - - +
769F GLN* 2.8 36.6 + - - +
776F TYR* 3.9 33.7 - - + +
779F ALA* 3.8 19.5 - - + -
780F ALA* 3.5 36.8 - - + +
783F ILE* 4.2 20.4 - - + +
801F ARG* 6.1 0.2 - - - +
797H THR* 3.3 37.7 - - - +
798H ASN* 4.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 766 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C PRO* 3.6 9.3 - - - +
807C ALA* 2.6 41.1 + - - +
808C PRO 4.1 9.2 - - - -
809C VAL* 4.2 4.1 - - - +
764F SER* 3.2 8.6 + - - -
765F ILE* 1.3 82.6 - - - +
767F ALA* 1.3 63.0 + - - +
769F GLN* 3.7 3.0 - - - +
770F ARG* 2.8 52.2 + - - +
798H ASN* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 767 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C VAL* 5.7 0.2 - - - +
756F PHE* 3.5 22.0 - - + -
762F ARG* 3.6 49.9 + - + +
764F SER* 3.0 22.3 + - - +
766F SER* 1.3 77.6 - - - +
768F VAL* 1.3 62.7 + - - +
770F ARG* 3.7 2.9 - - - +
771F LYS* 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 768 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753F ALA* 4.4 4.0 - - + -
756F PHE* 4.2 11.0 - - + -
757F VAL* 3.7 29.2 - - + -
764F SER 3.2 12.0 + - - +
765F ILE* 3.2 7.9 + - - +
767F ALA* 1.3 75.0 - - - +
769F GLN* 1.3 65.4 + - - +
771F LYS 3.4 0.2 + - - -
772F LEU* 3.0 34.2 + - + +
774F ILE* 4.2 12.1 - - + -
779F ALA* 3.9 20.9 - - + +
782F MET* 4.2 15.3 - - + -
783F ILE* 4.0 12.6 - - + -
786F MET* 4.9 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 769 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C ILE 3.9 19.0 + - - -
806C PRO* 3.5 32.9 - - + +
807C ALA 4.6 0.2 + - - -
765F ILE* 2.8 24.9 + - + +
766F SER* 3.7 6.2 - - - +
767F ALA 3.3 0.2 - - - -
768F VAL* 1.3 73.3 - - - +
770F ARG* 1.3 55.0 + - - +
773F LYS* 2.8 34.1 + - - -
774F ILE* 3.3 29.3 + - - +
775F GLY* 3.9 2.1 - - - +
776F TYR* 3.3 39.0 - - - +
779F ALA* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 770 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806C PRO* 3.7 27.5 + - + +
807C ALA 2.9 25.3 + - - -
808C PRO* 3.9 8.9 - - - +
809C VAL* 3.4 24.7 - - - +
762F ARG* 4.7 4.3 - - - +
766F SER* 2.8 38.2 + - - +
767F ALA* 3.7 6.1 - - - +
769F GLN* 1.3 76.3 - - - +
771F LYS* 1.4 64.1 + - - +
773F LYS* 3.8 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 771 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A ASP* 2.9 37.5 + - - +
785A ALA* 5.9 2.0 - - - +
788A MET* 5.5 8.9 - - - +
752F GLU* 4.3 20.8 - - - +
755F ARG* 6.1 0.4 - - - +
756F PHE* 3.6 33.0 - - + -
767F ALA 3.0 16.7 + - - +
770F ARG* 1.4 76.3 - - - +
772F LEU* 1.3 84.0 + - + +
773F LYS* 3.8 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 772 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749F LEU* 4.2 24.1 - - + +
752F GLU* 3.1 44.9 - - + +
753F ALA* 4.1 28.7 - - + +
756F PHE* 4.8 1.6 - - + -
768F VAL* 3.0 24.4 + - + +
771F LYS* 1.3 97.4 - - + +
773F LYS* 1.3 75.2 + - - +
774F ILE* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 773 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A MET* 5.9 2.0 + - - +
769F GLN 2.8 15.2 + - - +
770F ARG 3.8 13.9 - - - +
771F LYS 3.8 15.9 - - - -
772F LEU* 1.3 82.8 - - - +
774F ILE* 1.3 58.1 + - - +
----------------------------------------------------------
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