Contacts of the helix formed by residues 727 - 739 (chain A) in PDB entry 2RD0
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 THR 727 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A GLU* 1.3 86.7 - - + +
728A GLN* 1.3 68.2 + - - +
729A LYS* 4.1 6.6 + - - +
730A VAL* 2.9 24.6 + - - +
731A GLN* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A THR* 1.3 70.5 - - - +
729A LYS* 1.3 55.9 + - - +
731A GLN* 3.8 7.6 + - - -
732A MET* 2.8 63.3 + - - +
771A ILE* 3.0 17.1 + - - +
773A SER* 2.8 44.7 + - - +
777A ARG* 4.1 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A THR* 3.1 7.2 + - - +
728A GLN* 1.3 79.9 - - - +
730A VAL* 1.3 64.3 + - + +
732A MET* 3.5 5.3 + - - +
733A LYS* 3.0 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A LYS* 5.6 6.7 - - + -
726A GLU* 4.0 32.8 - - + +
727A THR* 2.9 29.3 + - - +
729A LYS* 1.3 76.9 - - + +
731A GLN* 1.3 61.1 + - - +
733A LYS* 2.9 30.7 - - + +
734A PHE* 3.0 7.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A LEU* 3.8 29.8 + - + +
724A LYS* 3.1 34.4 + - + +
725A ASP* 5.6 0.2 + - - -
726A GLU* 4.3 3.8 - - + +
727A THR* 2.8 31.1 + - - +
728A GLN 3.5 6.3 + - - +
730A VAL* 1.3 70.8 - - - +
732A MET* 1.3 54.4 + - - +
734A PHE* 2.7 14.3 + - - +
735A LEU* 2.6 32.1 + - - +
771A ILE* 3.6 14.6 - - + +
777A ARG* 2.8 49.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
728A GLN* 2.8 39.9 + - - +
729A LYS* 3.8 4.7 - - - +
731A GLN* 1.3 72.9 - - - +
733A LYS* 1.3 66.8 + - - +
735A LEU* 3.8 13.7 - - + -
736A VAL* 3.0 38.6 + - + +
769A CYS 3.4 22.7 - - - +
770A ARG* 3.7 11.0 - - + -
771A ILE* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A LYS* 3.0 17.9 + - + +
730A VAL* 2.9 21.3 + - + +
732A MET* 1.3 79.9 - - - +
734A PHE* 1.3 59.1 + - - +
736A VAL* 3.2 7.8 + - - +
737A GLU* 3.1 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 734 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 4.4 7.4 - - + -
715A LEU* 3.8 22.2 - - + -
718A ILE* 3.6 40.6 - - + -
719A LEU* 3.5 20.9 - - + -
724A LYS* 3.7 28.7 - - - -
730A VAL* 3.0 6.4 + - + +
731A GLN* 2.7 16.7 + - - +
733A LYS* 1.3 75.4 - - - +
735A LEU* 1.3 61.8 + - - -
736A VAL 3.1 0.9 + - - -
737A GLU* 3.3 8.8 + - + +
738A GLN* 3.1 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 735 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 3.8 30.3 - - + -
719A LEU* 4.3 2.7 - - + -
731A GLN 2.6 15.3 + - - +
732A MET* 3.0 21.7 + - + +
734A PHE* 1.3 79.0 - - - +
736A VAL* 1.3 61.7 + - + +
738A GLN* 3.6 3.6 + - - +
739A MET* 3.1 46.0 + - - +
769A CYS* 4.2 7.6 - - + +
770A ARG* 4.0 10.8 - - - +
771A ILE* 3.6 35.4 - - + +
779A LEU* 3.6 25.4 - - + -
781A LEU* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 736 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732A MET* 3.0 33.0 + - + +
733A LYS* 4.0 7.9 - - - +
735A LEU* 1.3 80.1 - - + +
737A GLU* 1.3 68.6 + - + +
738A GLN 3.1 1.8 - - - -
739A MET* 3.4 6.8 + - - +
740A ARG* 3.2 60.7 + - - +
766A LEU* 4.3 18.6 - - + +
769A CYS 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 737 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A LYS* 3.1 35.3 + - + +
734A PHE* 3.8 8.8 - - + +
736A VAL* 1.3 75.7 - - - +
738A GLN* 1.3 65.0 + - - +
740A ARG* 3.2 21.3 + - - +
741A ARG* 3.6 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 738 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.5 21.0 - - + +
38A ARG* 3.2 14.7 + - - -
715A LEU* 4.6 9.4 - - + -
718A ILE* 5.8 0.7 - - + -
734A PHE* 3.1 49.9 + - + +
735A LEU 3.8 4.0 - - - +
737A GLU* 1.3 77.6 - - - +
739A MET* 1.3 57.6 + - - +
740A ARG 2.9 9.9 + - - -
741A ARG* 2.8 56.1 + - - +
744A PHE* 3.4 34.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A LEU* 5.9 1.8 - - + -
715A LEU* 4.2 10.8 - - + -
735A LEU* 3.1 44.9 + - - +
736A VAL* 3.4 6.0 + - - +
738A GLN* 1.3 74.5 - - - +
740A ARG* 1.3 59.1 + - - +
741A ARG 3.4 0.2 - - - -
744A PHE* 3.8 25.0 - - + +
745A MET* 3.0 34.3 - - + +
748A LEU* 5.1 9.0 - - + -
764A LEU* 4.1 19.1 - - + -
766A LEU* 4.0 28.6 - - + +
769A CYS* 4.3 7.2 - - - -
779A LEU* 5.8 1.1 - - + -
781A LEU* 3.9 26.0 - - + -
----------------------------------------------------------
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