Contacts of the helix formed by residues 737 - 746 (chain A) in PDB entry 1JQO
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A GLU* 2.6 17.3 + - - +
736A ALA* 1.3 78.8 - - + +
738A PHE* 1.3 62.3 + - - -
739A VAL* 3.5 1.1 - - - -
740A GLU* 3.0 45.8 + - + +
741A TYR* 3.1 22.2 + - - +
850A ALA* 5.2 0.8 - - - +
852A GLU* 3.2 37.8 + - - +
853A LEU* 3.6 26.6 - - + +
856A PHE* 4.9 2.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A VAL* 3.2 29.8 - - + +
732A VAL* 3.3 38.4 - - + +
735A GLU* 3.4 16.6 + - + +
736A ALA 2.9 4.9 + - - -
737A ARG* 1.3 76.4 - - - +
739A VAL* 1.3 56.6 - - + +
741A TYR* 3.0 12.7 + + - +
742A PHE* 2.7 44.9 + + + +
777A TRP* 3.9 28.3 - + - -
781A TRP* 4.2 12.1 - + - -
788A LEU* 4.0 19.7 - - + -
856A PHE* 3.8 25.6 - + - -
860A LEU* 5.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A VAL 5.9 0.4 - - - +
736A ALA 3.9 12.5 + - - +
737A ARG* 5.5 0.2 - - - -
738A PHE* 1.3 87.1 - - + +
740A GLU* 1.3 71.4 + - + +
742A PHE* 3.3 13.6 - - + +
743A ARG* 2.9 49.2 + - + +
770A THR* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A ARG* 3.0 56.5 + - - +
738A PHE 3.1 0.4 - - - -
739A VAL* 1.3 89.5 - - + +
741A TYR* 1.3 61.7 + - - +
743A ARG* 3.5 4.3 + - - +
744A SER* 3.3 21.9 + - - -
850A ALA* 4.8 4.3 - - - +
853A LEU* 3.5 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A ARG 3.1 5.5 + - - +
738A PHE* 3.0 11.6 + + - +
740A GLU* 1.3 79.1 - - - +
742A PHE* 1.3 65.9 + - - +
744A SER* 3.2 4.6 + - - -
745A ALA* 3.0 27.7 + - + +
781A TRP* 4.2 21.2 - + - -
786A PHE* 5.0 7.4 - - - -
845A ASP* 2.6 29.7 + - - -
849A VAL* 3.4 42.8 - - + -
853A LEU* 3.5 24.2 - - + +
856A PHE* 3.9 22.4 - + + -
857A GLY* 3.4 20.8 + - - -
860A LEU* 3.6 20.9 - - + +
861A ARG* 5.0 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A PHE* 2.7 27.2 + + + +
739A VAL* 3.0 17.9 + - + +
741A TYR* 1.3 74.4 - - - +
743A ARG* 1.3 80.9 + - + +
744A SER 2.9 8.6 + - - -
746A THR* 2.6 33.6 + - - +
748A GLU* 3.3 39.9 - - + -
777A TRP* 3.3 40.4 - + - -
780A SER* 3.8 11.4 - - - -
781A TRP* 3.1 39.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A VAL* 2.9 30.3 + - - +
740A GLU* 3.8 3.8 - - - +
742A PHE* 1.3 90.1 - - + +
744A SER* 1.3 58.7 + - - +
746A THR* 4.2 7.9 - - - +
748A GLU* 2.4 47.2 + - - +
749A THR* 4.4 16.5 + - - +
769A ILE* 2.9 56.9 - - - +
770A THR* 4.0 5.1 - - - +
913A ARG* 3.8 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A GLU* 3.3 18.4 - - - -
741A TYR* 3.5 7.2 - - - -
742A PHE 2.9 1.2 - - - -
743A ARG* 1.3 80.4 - - - +
745A ALA* 1.3 60.5 + - - +
746A THR 3.1 6.7 + - - -
848A LEU* 3.1 35.0 + - - +
849A VAL* 3.7 8.1 + - - -
850A ALA 4.7 1.2 + - - -
853A LEU* 6.1 0.7 - - - -
913A ARG* 2.6 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A TYR* 3.0 21.7 + - + +
744A SER* 1.3 75.2 - - - +
746A THR* 1.3 67.8 + - + +
781A TRP* 5.2 4.7 - - + -
784A THR* 3.5 7.7 + - - +
841A ALA 5.5 0.4 - - - +
844A TYR* 3.5 26.3 - - + +
845A ASP* 3.7 13.0 - - - +
848A LEU* 4.3 7.9 - - - -
849A VAL* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A PHE* 2.6 24.6 + - - +
743A ARG* 4.2 7.6 - - - +
744A SER 3.1 1.8 - - - +
745A ALA* 1.3 87.4 - - - +
747A PRO* 1.3 68.3 - - - +
748A GLU* 3.1 11.5 + - - +
749A THR* 4.7 1.7 + - - -
780A SER* 3.3 35.5 - - - +
781A TRP* 3.8 32.5 - - + -
784A THR* 4.2 5.2 - - - -
844A TYR* 5.2 0.7 - - - -
909A LEU* 4.7 2.7 - - - -
913A ARG* 3.3 19.6 + - - -
----------------------------------------------------------
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