Contacts of the helix formed by residues 723 - 733 (chain A) in PDB entry 2RC4
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 723 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A SER* 3.7 17.7 - - - -
713A ILE* 3.7 38.4 - - - -
716A LEU* 3.0 25.9 - - + +
722A ILE* 1.3 66.5 - - - +
724A PRO* 1.3 68.1 - - + +
725A GLN 2.4 19.1 - - - +
726A ASP* 3.4 7.2 - - - -
727A ILE* 3.1 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 724 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ILE* 3.4 24.7 - - + -
723A CYS* 1.3 93.2 - - + +
725A GLN* 1.3 65.0 + - - +
727A ILE* 3.7 3.1 - - + +
728A THR* 2.8 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A TYR* 5.7 0.2 - - - +
678A SER* 3.4 21.9 + - - +
681A LYS* 3.3 40.4 - - - +
695A TRP* 3.8 41.3 - - + +
721A GLY 5.0 0.4 - - - -
722A ILE* 2.8 26.0 + - + +
723A CYS 2.4 19.4 - - - +
724A PRO* 1.3 74.8 - - - +
726A ASP* 1.3 60.2 + - + +
727A ILE 2.2 22.6 + - - -
728A THR* 3.7 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A TRP* 4.7 5.9 - - + -
699A ILE* 3.6 32.0 - - + +
712A SER* 4.1 12.7 + - - +
715A LYS* 5.6 4.7 - - - +
716A LEU* 5.1 1.4 - - - +
719A LEU* 5.7 0.4 - - + -
721A GLY* 2.7 31.4 - - - +
722A ILE 2.8 14.4 - - - +
723A CYS* 3.4 4.7 - - - -
725A GLN* 1.3 73.6 - - + +
727A ILE* 1.3 73.8 + - - +
728A THR 3.5 0.2 - - - -
729A SER* 2.9 25.8 + - - -
730A THR* 2.6 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A SER* 3.7 21.3 - - - +
723A CYS* 3.1 33.4 - - + +
724A PRO* 3.7 2.9 - - + +
725A GLN 2.2 19.4 + - - -
726A ASP* 1.3 73.8 + - - +
728A THR* 1.3 57.3 + - + +
729A SER 3.0 1.1 - - - -
730A THR* 2.8 9.7 + - - +
731A LEU* 2.6 35.0 + - + +
736A MET* 4.1 23.8 - - + +
738A ASP* 5.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A MET* 5.0 3.7 - - - +
695A TRP* 4.8 5.5 - - - -
724A PRO* 2.8 28.5 - - + +
725A GLN* 3.7 21.8 + - - +
727A ILE* 1.3 77.9 - - + +
729A SER* 1.3 62.2 + - - +
731A LEU* 3.5 9.3 + - - +
732A HIS* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A MET* 3.7 17.9 - - - -
695A TRP* 3.5 31.5 - - - +
696A LYS 5.0 0.4 - - - -
699A ILE* 5.2 0.9 - - - -
726A ASP* 2.9 31.0 + - - -
728A THR* 1.3 78.5 + - - +
730A THR* 1.3 50.6 + - - +
732A HIS* 2.7 19.6 + - - +
733A HIS* 2.7 39.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A ILE* 4.4 17.0 - - + -
700A LEU* 6.5 0.2 - - + -
726A ASP* 2.6 29.9 + - - +
727A ILE* 2.8 17.7 + - - +
729A SER* 1.3 71.7 - - - +
731A LEU* 1.3 55.6 + - - +
733A HIS* 2.9 36.6 + - + +
735A ARG* 3.5 28.3 - - + +
736A MET* 2.8 25.8 + - - +
737A LEU 5.1 0.6 + - - -
748A ARG 5.4 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
727A ILE* 2.6 20.8 + - + +
728A THR* 3.6 11.4 - - - +
730A THR* 1.3 67.8 - - - +
732A HIS* 1.3 59.8 + - - +
733A HIS 3.1 12.0 + - - +
736A MET* 3.3 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A MET* 4.1 36.5 - - + +
728A THR 2.9 12.7 + - - +
729A SER 2.7 16.8 + - - +
731A LEU* 1.3 72.0 - - - +
733A HIS* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 733 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A MET* 3.7 11.3 - - + +
696A LYS* 4.2 24.0 - - + +
699A ILE* 5.0 5.6 - - + -
700A LEU* 4.8 14.6 - - + +
729A SER* 2.7 44.6 + - - -
730A THR* 2.9 32.8 + - + +
731A LEU 3.5 7.3 - - - +
732A HIS* 1.3 93.0 - - + +
734A LEU* 1.3 69.8 + - - +
735A ARG* 3.2 15.3 + - + +
736A MET* 4.5 2.4 + - - +
750A GLU* 5.8 0.7 - - - +
----------------------------------------------------------
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