Contacts of the helix formed by residues 772 - 800 (chain A) in PDB entry 4RNP
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 HIS 772 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A ALA* 3.8 27.6 - - - +
773A LYS* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A HIS* 3.8 25.8 - - - +
774A GLN* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A LYS* 3.8 28.9 - - - +
775A GLU* 3.8 27.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A GLN* 3.8 26.2 - - - +
776A SER* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775A GLU* 3.8 26.0 - - - +
777A GLY* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A SER* 3.8 28.9 - - - +
778A ILE* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A GLY* 3.8 28.0 - - - +
779A ALA* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778A ILE* 3.8 29.2 - - - +
780A PRO* 3.8 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A ALA* 3.8 25.6 - - - -
781A ASN* 3.8 28.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A PRO* 3.8 25.4 - - - -
782A PHE* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781A ASN* 3.8 28.7 - - - +
783A VAL* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A PHE* 3.8 24.9 - - - +
784A HIS* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A VAL* 3.8 26.0 - - - +
785A SER* 3.8 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A HIS* 3.8 28.7 - - - +
786A GLN* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A SER* 3.8 27.1 - - - +
787A ASP* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A GLN* 3.8 24.9 - - - +
788A GLY* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ARG* 4.3 23.8 - - - +
787A ASP* 3.8 29.4 - - - +
789A SER* 3.8 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A GLY* 3.8 29.2 - - - +
790A HIS* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 790 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A SER* 3.8 29.2 - - - +
791A LEU* 3.8 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A HIS* 3.8 26.5 - - - +
792A ARG* 3.8 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 792 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A LEU* 3.8 28.7 - - - +
793A LYS* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 793 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ARG* 3.8 28.0 - - - +
794A THR* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A LYS* 3.8 25.4 - - - +
795A VAL* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A THR* 3.8 29.2 - - - +
796A VAL* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795A VAL* 3.8 27.8 - - - +
797A TRP* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A VAL* 3.8 29.6 - - - +
798A ALA* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A TRP* 3.8 24.0 - - - +
799A HIS* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A ALA* 3.8 29.2 - - - +
800A GLU* 3.8 28.3 - - - +
803A GLY* 4.4 21.3 - - - +
804A ILE* 4.6 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A HIS* 3.8 26.2 - - - +
801A LYS* 3.8 29.4 - - - +
----------------------------------------------------------
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