Contacts of the helix formed by residues 737 - 746 (chain E) in PDB entry 6V3O
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 ARG 737 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735E GLU* 2.9 15.7 + - - +
736E ALA* 1.3 81.9 - - + +
738E PHE* 1.3 63.4 + - - +
739E VAL 3.5 1.3 - - - -
740E GLU* 3.5 39.5 + - + +
741E TYR* 3.1 21.7 + - - +
850E ALA* 5.6 2.4 - - - +
852E GLU* 3.0 41.8 + - - +
853E LEU* 3.6 33.0 - - + +
856E PHE* 5.0 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 738 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731E VAL* 3.3 42.6 - - + +
732E VAL* 3.6 26.2 - - + +
735E GLU* 3.3 18.1 + - - +
736E ALA 3.3 1.8 - - - -
737E ARG* 1.3 74.1 - - - +
739E VAL* 1.3 67.9 + - + +
741E TYR* 3.0 9.7 + + - +
742E PHE* 2.7 30.9 + - + +
769E ILE* 3.9 16.2 - - + -
777E TRP* 3.8 33.4 - + - -
781E TRP* 4.1 21.8 - + - -
788E LEU* 4.4 10.3 - - + -
856E PHE* 4.0 14.4 - + + -
860E LEU* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 739 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732E VAL 5.3 2.2 - - - +
736E ALA 4.7 2.7 + - - +
737E ARG 3.5 0.4 - - - -
738E PHE* 1.3 78.3 - - + +
740E GLU* 1.3 57.1 + - - +
742E PHE* 3.1 10.8 + - + +
743E ARG* 2.8 52.6 + - + +
768E GLY* 4.0 22.2 - - - -
769E ILE* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 740 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736E ALA 5.4 0.4 + - - -
737E ARG* 3.6 43.2 + - - +
738E PHE 3.2 0.6 - - - -
739E VAL* 1.3 79.9 - - - +
741E TYR* 1.3 55.1 + - - +
743E ARG* 3.5 5.2 + - - +
744E SER* 2.7 34.7 + - - +
850E ALA* 4.9 5.4 - - - +
853E LEU* 3.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 741 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737E ARG 3.1 13.2 + - - +
738E PHE* 3.0 10.8 + + - +
740E GLU* 1.3 75.1 - - - +
742E PHE* 1.3 59.6 + - - +
744E SER* 3.2 3.7 + - - -
745E ALA* 2.9 35.7 + - + +
781E TRP* 3.9 23.6 - + - -
786E PHE* 5.1 5.9 - + - -
845E ASP* 2.4 33.5 + - - -
849E VAL* 3.9 23.8 - - + -
853E LEU* 4.1 21.7 - - + +
854E LYS* 5.5 0.2 - - - -
856E PHE* 3.8 28.3 - + + -
857E GLY* 3.3 23.6 + - - -
860E LEU* 3.7 21.5 - - + +
861E ARG* 4.0 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 742 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738E PHE* 2.7 25.1 + - + +
739E VAL* 3.1 8.0 + - + +
741E TYR* 1.3 75.1 - - - +
743E ARG* 1.3 72.3 - - + +
744E SER 3.3 0.7 + - - -
746E THR* 2.7 47.8 + - + -
748E GLU* 3.6 30.5 - - + -
769E ILE* 3.9 18.8 - - + -
772E LEU* 3.8 23.1 - - + -
776E PRO 4.7 1.1 - - - -
777E TRP* 4.0 14.4 - + - -
780E SER* 3.8 14.6 - - - -
781E TRP* 3.4 47.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 743 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739E VAL* 2.8 34.7 + - + +
740E GLU* 4.2 4.9 - - - +
742E PHE* 1.3 84.1 - - + +
744E SER* 1.3 57.4 + - - +
746E THR* 3.8 4.2 - - - +
748E GLU* 3.8 30.7 + - - +
749E THR* 3.3 38.6 + - - +
753E ARG* 6.0 0.8 - - - +
762E LYS* 3.6 32.1 - - - +
772E LEU* 4.6 3.4 - - - +
913E ARG* 3.4 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 744 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740E GLU* 2.7 26.7 + - - +
741E TYR* 3.2 3.5 + - - -
742E PHE 3.2 0.4 - - - -
743E ARG* 1.3 78.3 - - - +
745E ALA* 1.3 62.8 + - - +
746E THR 3.3 2.5 + - - -
848E LEU* 3.3 32.8 - - - +
849E VAL* 4.0 13.5 - - - -
850E ALA 5.3 1.8 + - - -
853E LEU* 5.3 3.2 - - - +
913E ARG* 2.8 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741E TYR* 2.9 36.3 + - + +
744E SER* 1.3 75.4 - - - +
746E THR* 1.3 64.2 + - + +
781E TRP* 4.7 5.6 - - + -
784E THR* 3.4 18.4 + - - +
844E TYR* 3.7 18.8 - - - +
845E ASP* 3.3 25.4 - - - +
849E VAL* 4.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 746 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742E PHE* 2.7 36.0 + - + +
743E ARG 3.8 6.1 - - - +
744E SER 3.3 0.4 - - - -
745E ALA* 1.3 81.6 - - - +
747E PRO* 1.3 71.0 - - - +
748E GLU* 3.1 14.7 + - - +
780E SER* 3.6 16.2 - - - +
781E TRP* 3.6 40.2 - - + -
784E THR* 4.0 3.4 - - + -
844E TYR* 5.3 0.2 - - - -
909E LEU* 4.9 3.1 - - - -
913E ARG* 3.0 20.7 + - - -
----------------------------------------------------------
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