Contacts of the helix formed by residues 800 - 810 (chain A) in PDB entry 5A31
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 GLY 800 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A LYS 3.7 1.7 - - - -
799A LEU* 1.3 78.1 - - - +
801A PRO* 1.4 54.1 - - - +
802A TYR 3.1 0.9 - - - +
803A VAL* 3.0 29.3 + - - +
804A ASP* 2.6 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 801 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A LEU* 2.7 28.7 - - + +
800A GLY* 1.4 68.3 - - - +
802A TYR* 1.3 59.5 + - + +
804A ASP* 2.1 36.5 - - - +
805A HIS* 3.3 10.4 + - - +
840A GLU* 5.8 2.2 - - + -
841A PRO* 3.8 26.2 - - + +
1897A PRO* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 802 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A PHE* 3.7 31.4 - + + -
764A PHE* 4.4 14.2 - + - -
767A HIS* 3.6 34.5 - + - -
794A ALA* 4.7 4.9 - - + -
799A LEU* 3.5 36.3 - - + -
800A GLY 3.1 1.0 - - - +
801A PRO* 1.3 79.5 - - + +
803A VAL* 1.3 65.7 + - - +
805A HIS* 3.3 7.0 + - - +
806A TYR* 3.2 29.9 + - + -
839A SER* 3.3 31.9 + - - -
840A GLU* 4.8 0.2 - - - -
841A PRO* 3.5 36.3 - - + +
842A PRO* 3.7 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 803 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A VAL* 5.0 13.0 - - + +
794A ALA* 4.1 22.2 - - + +
795A ARG* 4.1 31.4 - - + +
800A GLY* 3.0 24.7 + - - +
802A TYR* 1.3 76.8 - - - +
804A ASP* 1.3 65.3 + - + +
806A TYR* 3.1 14.2 + - - +
807A TYR* 3.0 19.1 + - + +
814A ALA* 5.0 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 804 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A GLY 2.6 6.7 + - - +
801A PRO* 2.1 45.0 - - - +
803A VAL* 1.3 79.1 - - - +
805A HIS* 1.3 54.9 + - - -
807A TYR* 3.2 13.4 + - + +
808A ARG* 2.9 39.0 + - - +
1871A TYR* 5.3 7.9 - - + +
1896A ALA* 3.7 27.1 - - + +
1897A PRO* 5.4 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 805 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A HIS* 4.3 6.1 - + - -
770A TYR* 4.3 3.1 - + - -
771A GLU* 3.5 24.7 + - - -
801A PRO 3.6 10.1 - - - +
802A TYR* 3.5 11.4 - - - +
803A VAL 3.2 0.6 - - - -
804A ASP* 1.3 82.3 + - - +
806A TYR* 1.3 74.7 + - - +
808A ARG* 3.1 20.5 + - + +
809A ASP* 3.1 48.5 + - - -
841A PRO* 4.6 16.8 - - + -
842A PRO 5.0 0.4 - - - -
843A SER* 3.3 29.3 + - - -
846A GLN* 6.1 0.7 - - + -
1812A TRP* 6.3 1.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 806 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A PHE* 3.9 10.2 - + - -
767A HIS* 2.4 36.3 + + - +
770A TYR* 3.2 43.5 - + - -
787A VAL* 4.3 14.6 - - + -
790A LEU* 3.2 36.0 - - + +
791A VAL* 3.9 29.6 - - + -
794A ALA* 4.8 1.8 - - + -
802A TYR* 3.2 29.4 + + + -
803A VAL* 3.1 7.1 + - - +
805A HIS* 1.3 78.7 - - - +
807A TYR* 1.3 56.4 + - - +
809A ASP* 3.6 3.7 - - - +
810A TYR* 2.7 38.2 + - - +
813A LEU 5.4 1.1 - - - +
814A ALA* 5.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 807 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A VAL* 3.0 11.2 + - + +
804A ASP* 3.2 19.7 + - + +
806A TYR* 1.3 74.8 - - - +
808A ARG* 1.3 77.6 + - - +
810A TYR 3.0 21.1 - - - +
811A PRO* 3.5 17.8 - - - +
814A ALA* 4.0 23.1 - - + +
1871A TYR* 5.0 15.3 - + - -
1882A LEU* 3.1 57.9 + - + +
1885A LEU* 3.8 22.9 - - + +
1886A ALA* 3.8 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 808 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A ASP* 2.9 23.2 + - - +
805A HIS* 3.1 23.1 + - + +
807A TYR* 1.3 89.0 - - - +
809A ASP* 1.3 65.9 + - - +
846A GLN* 6.0 2.4 - - - +
1808A THR* 3.0 19.9 + - - +
1812A TRP* 5.8 0.9 - - + +
1871A TYR* 3.8 17.6 + - - -
1886A ALA* 4.1 4.9 - - - +
1889A ALA* 3.7 27.5 + - + +
1890A VAL* 3.5 29.9 - - + +
1893A SER* 4.5 2.6 - - - +
1894A VAL 2.5 42.6 + - - +
1895A PRO* 3.7 8.6 - - - +
1896A ALA* 5.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 809 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TYR* 2.9 29.9 + - - +
774A LYS* 3.7 16.7 - - - -
805A HIS* 3.1 44.1 + - - +
806A TYR* 3.2 2.2 + - - +
808A ARG* 1.3 83.0 - - - +
810A TYR* 1.3 66.8 + - + +
843A SER* 5.1 0.3 + - - -
845A TYR* 5.7 0.3 - - - -
1807A GLU 2.6 24.3 - - - +
1808A THR* 2.6 7.7 + - - -
1809A SER* 4.4 4.4 + - - +
1812A TRP* 3.6 24.5 + - - -
1890A VAL* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A TYR* 3.6 25.1 - + - -
774A LYS* 4.5 5.5 + - - -
783A ILE* 3.2 34.7 - - + +
784A CYS* 4.3 31.4 - - + -
787A VAL* 4.5 21.5 - - + -
806A TYR 2.7 20.4 + - - +
807A TYR* 3.0 12.8 - - - +
809A ASP* 1.3 87.3 - - + +
811A PRO* 1.3 73.8 - - + +
812A THR 3.2 15.4 + - - +
813A LEU* 4.3 6.9 - - + +
1807A GLU* 3.8 32.2 + - + -
1809A SER* 5.0 6.7 + - - -
----------------------------------------------------------
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