Contacts of the helix formed by residues 793 - 801 (chain A) in PDB entry 4X52
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 TYR 793 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A THR* 3.5 22.9 - - - +
790A SER* 3.0 22.2 + - - +
792A ALA* 1.3 81.9 - - + +
794A VAL* 1.4 63.5 + - - +
795A GLU 3.4 2.2 - - - -
796A SER* 2.8 25.2 + - - +
797A ILE* 3.2 21.7 + - + +
806A LEU* 3.5 21.6 - - + +
833A TYR* 3.5 25.4 - + - -
793C TYR* 3.5 39.0 - + - -
796C SER* 3.6 21.2 + - - -
803C ASP* 2.6 31.0 + - - +
806C LEU* 4.2 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 794 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A TYR* 5.7 0.9 - - - +
730A LEU* 3.9 27.8 - - + -
790A SER 3.8 0.8 + - - +
791A ARG* 3.2 25.1 + - + +
792A ALA 3.5 0.2 - - - -
793A TYR* 1.4 76.8 - - - +
795A GLU* 1.4 59.2 + - - +
797A ILE* 3.4 1.7 + - - +
798A CYS* 3.0 41.0 + - - -
839A VAL* 3.5 32.8 - - + -
841A PHE* 3.8 17.4 - - + -
890A VAL* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 795 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LYS* 3.6 26.7 + - - -
728A TYR* 3.4 28.5 + - + +
791A ARG 4.9 0.2 + - - -
792A ALA 4.9 3.5 + - - +
793A TYR 3.4 0.6 - - - -
794A VAL* 1.4 80.3 - - - +
796A SER* 1.4 64.9 + - - +
798A CYS 3.4 1.2 + - - -
799A SER* 3.0 29.9 + - - +
795C GLU* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 796 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ALA 5.3 0.6 + - - -
793A TYR* 2.8 26.4 + - - +
795A GLU* 1.4 77.2 - - - +
797A ILE* 1.3 59.4 + - - +
799A SER* 4.2 3.6 - - - -
800A ASN* 2.8 38.2 + - - +
801A ASN 3.9 1.5 - - - +
806A LEU* 5.8 0.2 - - - +
901A GOL 3.3 20.3 + - - -
792C ALA* 3.8 23.2 + - - -
793C TYR* 3.6 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 797 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A LEU* 4.0 0.2 - - - +
787A TYR* 3.9 19.1 - - + +
789A THR* 3.8 17.0 - - + +
793A TYR* 3.2 23.4 + - + +
794A VAL 3.8 3.4 - - - +
796A SER* 1.3 83.2 + - - +
798A CYS* 1.3 62.4 + - - +
801A ASN* 2.9 34.7 + - - +
802A PHE* 3.6 35.0 - - + +
803A ASP* 5.2 2.5 - - + +
806A LEU* 5.4 3.8 - - + -
841A PHE* 3.5 39.3 - - + -
887A PRO* 3.7 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 798 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A TYR* 3.4 38.0 - - + +
730A LEU* 4.2 9.9 - - - -
762A ILE* 3.7 41.4 - - + +
764A ASN* 2.7 23.4 + - - +
767A LEU* 3.8 2.6 - - - +
794A VAL* 3.0 33.3 + - - +
795A GLU 4.0 0.2 - - - +
797A ILE* 1.3 77.7 - - - +
799A SER* 1.4 57.9 + - - +
841A PHE* 4.0 7.4 - - - -
887A PRO* 4.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 799 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A LYS* 6.0 0.4 - - - -
727A LYS* 3.7 29.5 + - - +
728A TYR* 3.7 18.4 - - - -
764A ASN* 3.2 17.8 + - - +
766A GLU* 4.8 1.7 - - - +
767A LEU* 4.2 5.2 - - - +
795A GLU* 3.0 21.3 + - - +
796A SER* 3.7 3.1 + - - -
798A CYS* 1.4 78.9 - - - +
800A ASN* 1.3 75.2 + - - +
801A ASN 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 800 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LYS* 3.2 25.5 + - - +
767A LEU* 4.2 5.6 - - - +
796A SER 2.8 17.6 + - - +
799A SER* 1.3 82.9 + - - +
801A ASN* 1.4 63.1 + - - +
882A LYS* 2.7 34.4 + - - +
901A GOL 2.8 43.3 + - - +
790C SER* 5.3 0.4 + - - -
792C ALA* 4.0 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A LEU* 3.6 26.7 + - + +
796A SER 3.9 2.6 - - - +
797A ILE* 2.9 30.3 + - - +
800A ASN* 1.4 85.0 - - - +
802A PHE* 1.3 89.4 + - - +
803A ASP* 3.8 2.9 + - - +
818A ILE* 6.3 0.4 - - - -
882A LYS* 3.0 46.8 + - + +
883A ASP* 5.2 0.8 + - - +
885A VAL* 3.0 18.3 + - - +
887A PRO* 3.7 14.5 - - - +
901A GOL 4.9 1.9 + - - -
----------------------------------------------------------
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