Contacts of the helix formed by residues 765 - 770 (chain A) in PDB entry 2VWK
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 765 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ILE* 5.0 11.0 - - + +
734A GLU* 5.1 0.4 - - - -
763A VAL* 2.7 32.9 + - + +
764A GLY* 1.3 77.5 - - - +
766A GLY* 1.3 55.0 + - - +
767A ALA* 3.2 3.4 - - - -
768A TRP* 2.9 35.6 + - + +
769A LEU* 2.7 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 766 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A GLU* 3.4 34.6 + - - +
763A VAL 4.5 0.2 + - - -
764A GLY 3.7 1.2 - - - -
765A LEU* 1.3 74.9 - - - +
767A ALA* 1.3 55.3 + - - +
770A LYS* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 767 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A LEU 3.2 1.2 - - - -
766A GLY* 1.3 74.5 - - - +
768A TRP* 1.3 62.0 + - - +
770A LYS* 4.3 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 768 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A THR* 4.6 14.6 - - + -
709A ARG* 3.1 36.8 - - - +
710A ILE 5.3 3.8 + - - -
765A LEU* 2.9 34.2 + - + +
767A ALA* 1.3 79.2 - - - +
769A LEU* 1.3 81.8 + - + +
770A LYS 3.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 769 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A ILE* 4.0 48.2 - - + +
730A GLU* 4.1 28.5 - - + +
731A TYR* 4.2 16.4 - - + -
734A GLU* 3.8 20.6 - - + -
735A ASN* 3.2 28.3 + - - +
765A LEU* 2.7 35.3 + - + +
768A TRP* 1.3 85.5 - - + +
770A LYS* 1.3 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 770 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A GLU 3.8 8.7 + - - +
735A ASN* 4.7 0.2 - - - -
739A PRO* 5.0 3.4 - - + -
766A GLY 2.9 18.9 + - - +
767A ALA* 4.3 9.2 - - - +
768A TRP 3.3 10.1 - - - +
769A LEU* 1.3 79.9 - - - +
771A PRO* 1.3 76.8 - - + +
772A LYS* 3.5 2.4 + - - +
----------------------------------------------------------
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