Contacts of the helix formed by residues 727 - 740 (chain A) in PDB entry 2DQM
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 CYS 727 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ASP* 2.9 33.6 + - - +
700A VAL* 4.3 6.3 - - - -
701A SER* 4.2 20.2 - - - -
720A ALA* 4.1 11.4 - - - -
725A LEU* 3.1 4.7 + - - -
726A PRO* 1.3 72.1 - - - +
728A ARG* 1.3 67.7 + - - +
729A ASP 3.5 0.7 - - - -
730A ALA* 3.2 11.5 + - + +
731A LEU* 3.0 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ALA* 3.7 26.0 - - + +
721A VAL* 3.9 37.0 + - + +
724A GLN* 4.2 25.3 + - - +
725A LEU 2.9 18.6 + - - +
726A PRO 3.2 0.4 - - - -
727A CYS* 1.3 79.6 - - - +
729A ASP* 1.3 93.5 + - - +
731A LEU* 3.2 1.8 + - - +
732A MET* 2.9 32.6 + - + +
756A SER* 4.8 3.3 + - - -
758A ALA* 4.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A PRO 4.3 5.1 + - - +
727A CYS 3.5 0.6 - - - -
728A ARG* 1.3 114.7 + - - +
730A ALA* 1.3 63.0 + - - +
732A MET* 3.5 5.5 + - - +
733A GLN* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A PRO 5.2 0.8 + - - +
727A CYS* 3.2 13.9 + - + +
729A ASP* 1.3 77.4 - - - +
731A LEU* 1.3 61.6 + - + +
733A GLN* 3.3 5.6 + - - +
734A GLU* 3.0 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A VAL* 4.5 4.5 - - + -
701A SER* 4.3 7.2 - - - -
704A PHE* 3.5 48.2 - - + -
705A HIS* 3.7 23.6 - - + +
717A LEU* 3.5 17.3 - - + -
720A ALA* 4.1 13.5 - - + -
727A CYS* 3.0 46.4 + - + +
728A ARG 3.8 2.2 - - - +
730A ALA* 1.3 77.2 - - + +
732A MET* 1.3 63.3 + - - +
734A GLU* 3.2 9.7 + - - +
735A TYR* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A LEU* 3.6 31.6 - - + -
721A VAL* 3.9 12.8 - - + -
728A ARG* 2.9 34.5 + - + +
729A ASP* 3.9 6.3 - - - +
731A LEU* 1.3 76.2 - - - +
733A GLN* 1.3 61.5 - - - +
735A TYR* 3.5 1.6 + - - -
736A ASP* 3.1 12.1 + - - +
749A TRP* 2.9 50.2 + - + +
752A LEU* 4.3 10.1 - - + -
753A GLN* 3.4 42.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A ASP 3.1 18.1 + - - +
730A ALA* 3.8 5.6 - - - +
732A MET* 1.3 73.7 - - - +
734A GLU* 1.3 62.0 + - + +
736A ASP* 3.3 18.0 + - - +
737A ASP* 2.9 67.1 + - - +
749A TRP* 5.7 1.0 - - - -
772A ARG* 4.8 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A PHE* 3.8 12.0 - - + -
705A HIS* 2.8 36.2 + - - -
730A ALA* 3.0 36.1 + - - +
731A LEU* 3.2 8.2 + - - +
733A GLN* 1.3 76.8 - - + +
735A TYR* 1.3 61.2 + - - +
737A ASP* 3.5 8.2 + - - +
738A LYS* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A PHE* 4.4 17.0 - + + -
710A MET* 3.6 29.5 - - + +
713A ALA* 6.1 0.7 - - + -
714A LEU* 4.7 5.6 - - + -
717A LEU* 3.6 23.3 - - + -
731A LEU 3.0 16.8 + - - +
732A MET 3.6 5.2 - - - +
733A GLN 3.2 0.2 - - - -
734A GLU* 1.3 75.1 - - - +
736A ASP* 1.3 58.7 + - - +
738A LYS* 3.2 1.8 + - - -
739A TRP* 2.8 40.7 + + - +
745A VAL* 2.7 47.9 + - + +
746A MET* 4.2 8.1 - - - -
748A LYS* 3.6 14.9 - - + +
749A TRP* 3.3 35.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A MET 3.1 11.8 + - - +
733A GLN* 3.4 23.1 + - - +
735A TYR* 1.3 79.1 - - - +
737A ASP* 1.3 57.8 + - - +
740A HIS* 2.8 39.8 + - - +
746A MET* 3.9 11.3 - - - +
749A TRP* 3.7 17.0 - - + +
771A HIS* 2.9 29.2 + - - -
772A ARG* 2.9 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A GLN* 2.9 51.0 + - - +
734A GLU* 3.9 7.4 - - - +
736A ASP* 1.3 76.0 - - - +
738A LYS* 1.3 60.5 + - - +
740A HIS* 3.4 15.1 + - - -
741A GLN* 4.6 0.9 - - - +
772A ARG* 3.6 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASP* 5.8 3.0 - - - +
734A GLU 3.1 18.7 + - - +
735A TYR* 3.8 3.6 - - - +
737A ASP* 1.3 79.1 - - - +
739A TRP* 1.3 100.1 + - + +
740A HIS 3.8 0.2 - - - -
741A GLN* 3.0 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 3.9 7.6 - - - -
281A ASP* 3.2 50.3 - - + -
282A THR* 3.7 17.7 - - + -
710A MET* 4.0 10.9 - - + +
735A TYR* 2.8 41.4 + + + +
738A LYS* 1.3 117.1 - - + +
740A HIS* 1.3 58.2 + - - +
741A GLN* 3.0 11.0 - - - +
742A ASN* 2.8 24.3 + - + +
745A VAL* 3.4 33.9 - - + -
746A MET* 3.3 15.9 - - - +
902A SO4 3.8 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A ASP* 2.8 23.2 + - - +
737A ASP* 3.4 24.7 + - - -
739A TRP* 1.3 70.3 - - - +
741A GLN* 1.3 79.6 + - + +
742A ASN 3.2 2.1 + - - -
743A GLY 4.9 0.3 + - - -
746A MET* 3.7 8.0 - - - +
772A ARG* 3.3 55.4 + - - +
773A SER* 2.7 33.1 + - - +
----------------------------------------------------------
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