Contacts of the helix formed by residues 737 - 746 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G GLU* 2.7 39.1 + - - +
736G ALA* 1.3 76.3 - - + +
738G PHE* 1.3 62.0 + - - +
739G VAL 3.5 0.7 - - - -
740G GLU* 3.4 14.0 + - - +
741G TYR* 3.1 22.4 + - - +
852G GLU 4.3 8.9 + - - -
853G LEU* 3.8 35.3 - - + +
855G PRO* 6.4 0.4 - - - +
856G PHE* 4.0 33.5 - - + +
859G GLN* 5.1 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 738 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731G VAL* 3.3 42.4 - - + +
732G VAL* 3.8 25.8 - - + +
735G GLU* 3.2 16.8 + - + +
736G ALA 3.2 3.0 - - - -
737G ARG* 1.3 74.8 - - - +
739G VAL* 1.3 69.2 + - - +
741G TYR* 3.0 8.4 + + - +
742G PHE* 2.8 28.7 + - + +
769G ILE* 4.1 20.9 - - + -
777G TRP* 3.7 33.4 - + - -
781G TRP* 4.2 21.1 - + - -
788G LEU* 4.5 9.9 - - + -
856G PHE* 4.1 14.6 - + - -
860G LEU* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 739 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G GLU 4.9 0.4 + - - -
736G ALA 3.9 15.9 - - - +
738G PHE* 1.3 80.8 - - - +
740G GLU* 1.3 68.7 + - + +
742G PHE* 3.3 5.3 + - + +
743G ARG* 3.0 46.4 + - + +
768G GLY* 5.4 9.9 - - - -
769G ILE* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 740 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737G ARG* 3.4 16.1 + - - +
738G PHE 3.1 0.6 - - - -
739G VAL* 1.3 86.1 - - + +
741G TYR* 1.3 59.9 + - - +
743G ARG* 3.4 5.5 + - - +
744G SER* 2.9 26.6 + - - +
850G ALA* 4.9 7.6 - - - +
852G GLU* 4.0 12.4 - - - +
853G LEU* 3.6 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 741 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737G ARG 3.1 12.6 + - - +
738G PHE* 3.0 10.6 + + - +
740G GLU* 1.3 75.3 - - - +
742G PHE* 1.3 60.0 + - - +
744G SER* 2.9 6.5 + - - -
745G ALA* 2.9 34.0 + - + +
781G TRP* 3.9 23.1 - + - -
786G PHE* 5.2 4.7 - - - -
845G ASP* 2.8 40.1 + - - -
849G VAL* 3.9 26.0 - - + -
853G LEU* 4.2 17.8 - - + +
856G PHE* 3.9 24.7 - + + -
857G GLY* 3.4 22.1 + - - -
860G LEU* 3.6 21.5 - - + +
861G ARG* 4.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 742 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738G PHE* 2.8 28.0 + - + +
739G VAL* 3.6 6.1 - - + +
741G TYR* 1.3 73.9 - - - +
743G ARG* 1.3 70.2 + - + +
744G SER 3.2 0.9 + - - -
745G ALA 4.7 0.2 - - - +
746G THR* 2.8 45.5 + - - -
748G GLU* 3.7 27.4 - - + -
769G ILE* 4.3 16.4 - - + -
772G LEU* 3.7 24.9 - - + -
776G PRO 4.8 1.8 - - - -
777G TRP* 4.1 16.8 - + - -
780G SER* 3.8 11.4 - - - -
781G TRP* 3.3 53.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 743 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739G VAL* 3.0 37.6 + - + +
740G GLU* 4.1 5.6 - - - +
741G TYR 3.3 0.4 - - - -
742G PHE* 1.3 84.4 - - + +
744G SER* 1.3 56.5 + - - +
746G THR* 3.6 4.3 - - - +
748G GLU* 4.2 24.3 + - - +
749G THR* 3.2 35.4 + - - +
762G LYS* 3.5 36.6 - - - +
765G PRO 5.6 0.2 + - - -
769G ILE* 6.3 1.4 - - - +
772G LEU* 5.7 4.8 - - - +
913G ARG* 3.4 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 744 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740G GLU* 2.9 19.0 + - - +
741G TYR* 2.9 13.0 + - - -
743G ARG* 1.3 76.2 - - - +
745G ALA* 1.3 60.3 + - - +
746G THR 3.2 3.2 + - - +
848G LEU* 3.2 33.0 - - - +
849G VAL* 3.8 12.5 - - - +
850G ALA 5.2 1.2 + - - -
853G LEU* 5.8 1.0 - - - +
909G LEU* 5.7 0.3 - - - +
913G ARG* 2.7 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741G TYR* 2.9 33.2 + - + +
744G SER* 1.3 76.0 - - - +
746G THR* 1.3 62.7 + - + +
781G TRP* 4.7 5.1 - - + -
784G THR* 3.4 17.7 + - - +
844G TYR* 3.7 21.8 - - - +
845G ASP* 3.7 22.7 - - - +
849G VAL* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 746 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742G PHE* 2.8 35.4 + - + +
743G ARG 3.6 5.4 - - - +
744G SER 4.5 0.2 - - - -
745G ALA* 1.3 82.2 - - - +
747G PRO* 1.3 70.5 - - - +
748G GLU* 3.1 14.1 + - - +
780G SER* 3.5 15.9 - - - +
781G TRP* 3.6 39.5 - - + -
784G THR* 3.8 3.4 - - + -
844G TYR* 5.2 0.7 - - - -
909G LEU* 4.8 4.0 - - - -
913G ARG* 2.9 21.9 + - - -
----------------------------------------------------------
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