Contacts of the helix formed by residues 808 - 821 (chain F) in PDB entry 4OQB
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 SER 808 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F VAL* 4.0 8.0 - - - +
805F ASP* 3.2 26.6 + - - +
806F ARG 3.8 0.3 - - - +
807F ASP* 1.3 82.1 - - - +
809F GLU* 1.3 65.8 + - - +
810F GLU* 3.3 22.1 + - - +
811F ALA* 3.4 18.9 + - - +
812F GLU* 3.5 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 809 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807F ASP 4.8 6.7 - - - +
808F SER* 1.3 73.7 + - - +
810F GLU* 1.3 64.1 + - - +
812F GLU* 3.3 38.6 + - - +
813F ILE* 3.6 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 810 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F VAL* 4.1 25.1 - - + +
808F SER* 3.3 18.1 + - - +
809F GLU* 1.3 75.9 - - - +
811F ALA* 1.3 65.3 + - - +
813F ILE* 3.2 29.8 + - + +
814F ILE* 3.4 19.9 + - - +
838F LYS* 4.9 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 811 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F VAL* 3.8 14.8 - - + -
805F ASP 3.2 27.6 - - - +
806F ARG 4.2 1.3 - - - +
808F SER 3.4 7.8 + - - +
809F GLU 3.3 0.4 - - - -
810F GLU* 1.3 80.7 - - - +
812F GLU* 1.3 63.2 + - - +
814F ILE* 3.4 10.2 + - - +
815F ARG* 3.2 44.5 + - - +
836F ILE* 5.0 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 812 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806F ARG 4.8 1.2 - - - +
807F ASP 5.3 2.5 - - - +
808F SER 3.7 12.3 - - - +
809F GLU* 3.3 30.2 + - - +
810F GLU 3.3 0.4 - - - -
811F ALA* 1.3 77.7 - - - +
813F ILE* 1.3 57.5 + - + +
815F ARG* 3.6 24.5 + - - +
816F LYS* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 813 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809F GLU 3.6 11.7 - - - +
810F GLU* 3.2 23.1 + - + +
811F ALA 3.2 0.6 - - - -
812F GLU* 1.3 75.7 - - + +
814F ILE* 1.3 57.2 + - + +
816F LYS* 3.3 9.8 + - + +
817F TYR* 2.8 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 814 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804F VAL* 5.8 1.1 - - + -
810F GLU* 3.4 20.6 + - - +
811F ALA* 3.4 8.4 + - - +
812F GLU 3.4 0.2 - - - -
813F ILE* 1.3 75.9 - - + +
815F ARG* 1.3 54.4 + - - +
817F TYR* 2.9 9.6 + - + +
818F VAL* 2.7 45.6 + - + +
836F ILE* 3.4 50.0 - - + -
859F LEU* 6.2 0.7 - - + -
861F TRP* 4.5 2.0 - - + -
921F LEU* 4.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 815 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806F ARG* 3.0 69.8 + - - +
811F ALA* 3.2 32.3 + - - +
812F GLU* 3.6 29.5 + - - +
814F ILE* 1.3 78.0 - - - +
816F LYS* 1.3 56.1 + - - +
818F VAL* 3.8 8.3 - - - +
819F LYS* 3.0 30.4 + - - +
833F VAL* 4.4 28.0 - - + +
836F ILE* 4.9 8.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 816 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812F GLU 3.0 19.9 + - - +
813F ILE* 3.3 9.6 - - + +
814F ILE 3.1 0.2 - - - -
815F ARG* 1.3 75.0 - - - +
817F TYR* 1.3 56.8 + - - +
819F LYS* 4.5 4.0 - - + -
820F ASN* 2.7 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 817 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813F ILE* 2.8 20.1 + - + +
814F ILE* 2.9 12.5 + - + +
816F LYS* 1.3 72.9 - - - +
818F VAL* 1.3 56.9 + - - +
820F ASN* 4.8 2.2 - - - -
821F THR* 2.6 45.4 + - + -
859F LEU* 3.0 30.5 + - + -
860F LEU* 3.9 3.5 - - - +
861F TRP* 3.2 36.3 - + + -
899F ASP* 3.2 34.8 + - + +
921F LEU* 3.6 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 818 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814F ILE* 2.7 26.9 + - + +
815F ARG 3.8 4.7 - - - +
817F TYR* 1.3 73.3 - - - +
819F LYS* 1.3 67.5 + - - +
820F ASN 3.4 0.5 + - - -
821F THR 3.7 3.3 + - - -
822F HIS* 4.0 6.6 + - - +
831F LEU* 4.1 25.7 - - + +
833F VAL* 3.7 33.2 - - + +
861F TRP* 3.4 26.0 - - + -
901F VAL* 3.4 31.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 819 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815F ARG 3.0 20.5 + - - +
816F LYS* 3.9 4.5 - - + +
818F VAL* 1.3 79.6 - - - +
820F ASN* 1.3 71.8 + - - +
822F HIS* 4.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 820 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816F LYS* 2.7 60.5 + - - +
817F TYR* 4.8 0.9 - - - -
819F LYS* 1.3 89.7 - - - +
821F THR* 1.3 65.3 + - + +
822F HIS* 3.2 10.3 + - - +
900F MET* 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 821 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817F TYR* 2.6 46.5 + - + +
818F VAL 4.1 3.8 - - - -
819F LYS 3.6 0.2 - - - -
820F ASN* 1.3 82.2 - - + +
822F HIS* 1.3 58.0 + - - +
861F TRP* 3.7 3.6 + - - -
899F ASP 3.8 10.3 - - - +
900F MET* 3.5 29.6 - - + +
901F VAL* 3.1 31.7 + - - +
902F SER 3.8 1.2 + - - -
----------------------------------------------------------
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