Contacts of the helix formed by residues 763 - 770 (chain D) in PDB entry 3V53
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 763 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760D SER 5.0 5.2 - - - +
761D ILE* 3.1 16.4 - - - +
762D VAL* 1.3 74.3 - - - +
764D SER* 1.3 69.1 + - - +
765D ILE* 2.9 32.3 + - + +
766D LEU* 3.0 26.2 + - - +
767D MET* 3.0 13.6 + - - +
799D MET* 4.1 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 764 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763D ASP* 1.3 73.7 - - - +
765D ILE* 1.3 63.1 + - - +
767D MET* 3.4 10.3 + - - +
768D GLU* 2.9 28.8 + - - +
799D MET* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 765 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A ILE* 5.8 4.3 - - + +
781A GLU* 4.7 36.8 - - + +
763D ASP* 2.9 20.1 + - + +
764D SER* 1.3 81.1 - - - +
766D LEU* 1.3 60.9 + - - +
768D GLU* 3.0 6.9 + - + +
769D ARG* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 766 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761D ILE* 3.5 23.1 - - + +
762D VAL* 4.0 14.1 - - + -
763D ASP* 3.0 20.2 + - - +
765D ILE* 1.3 78.6 - - - +
767D MET* 1.3 56.9 + - - +
769D ARG* 5.2 1.8 - - - -
770D ARG* 2.9 34.2 + - + +
771D ILE* 3.1 32.2 + - + -
830D LEU* 5.1 2.0 - - + -
833D GLU* 4.1 38.4 - - + +
834D THR* 4.9 7.6 - - - +
837D LYS* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 767 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762D VAL* 4.1 2.9 - - + -
763D ASP 3.0 13.9 + - - +
764D SER* 3.5 10.1 - - - +
766D LEU* 1.3 77.9 - - - +
768D GLU* 1.3 59.4 + - - +
771D ILE* 3.6 38.1 - - + -
772D ARG* 3.0 36.6 + - + +
773D PRO* 3.6 0.5 - - - +
775D ILE* 4.8 0.2 - - + -
795D CYS* 3.7 45.8 - - + +
798D VAL* 4.0 14.8 - - + -
799D MET* 3.3 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 768 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764D SER* 2.9 17.6 + - - +
765D ILE* 3.0 7.8 + - + +
767D MET* 1.3 79.7 - - - +
769D ARG* 1.3 62.1 + - - +
772D ARG* 5.2 3.2 - - - +
773D PRO* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 769 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765D ILE* 2.9 19.3 + - + +
766D LEU* 4.7 1.8 - - - +
768D GLU* 1.3 79.3 - - - +
770D ARG* 1.3 64.7 + - + +
773D PRO* 3.4 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 770 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734D LYS* 3.9 15.6 - - - +
766D LEU* 2.9 22.0 + - + +
768D GLU 3.6 0.2 - - - -
769D ARG* 1.3 87.0 - - + +
771D ILE* 1.3 60.3 + - + +
772D ARG 3.8 0.7 - - - -
773D PRO* 3.8 5.4 - - - +
774D TRP* 3.4 40.8 + - - +
829D LEU* 3.6 25.1 - - + +
833D GLU* 2.8 45.5 + - + +
----------------------------------------------------------
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