Contacts of the helix formed by residues 900 - 906 (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 MET 900 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820F ASN 5.0 0.7 - - - +
821F THR* 3.5 42.8 - - + +
822F HIS 4.4 7.2 - - - +
823F ALA* 4.8 15.3 - - + -
861F TRP* 3.4 8.0 - - - +
898F ALA* 4.0 3.4 - - + +
899F ASP* 1.3 95.3 - - - +
901F VAL* 1.3 64.7 + - - +
902F SER* 3.4 4.6 + - - +
903F LYS* 3.6 16.1 + - + +
904F SER* 3.5 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 901 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818F VAL* 3.4 38.1 - - + +
821F THR* 3.1 16.5 + - - +
822F HIS* 4.6 3.1 - - - +
831F LEU* 4.9 14.4 - - + -
861F TRP* 3.3 54.1 - - + +
900F MET* 1.3 73.2 - - - +
902F SER* 1.3 58.0 + - - +
904F SER 3.5 0.2 + - - -
905F ALA* 2.8 38.6 + - + +
919F ILE* 3.4 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 902 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821F THR 3.8 0.8 + - - -
822F HIS* 3.9 17.6 - - - -
823F ALA* 3.5 26.5 - - - -
826F HIS* 3.1 30.1 - - - +
829F TYR* 2.9 17.0 + - - -
831F LEU* 5.0 0.9 - - - -
900F MET* 3.3 0.8 - - - -
901F VAL* 1.3 80.2 - - - +
903F LYS* 1.3 59.6 + - - +
905F ALA* 3.0 11.6 + - - -
906F ASN* 2.6 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 903 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823F ALA* 5.2 0.2 - - - +
826F HIS* 3.9 18.5 + - + -
898F ALA* 4.3 19.7 - - + +
899F ASP* 6.1 0.2 - - - +
900F MET* 3.6 19.7 + - + +
902F SER* 1.3 78.9 - - - +
904F SER* 1.3 61.0 + - - +
906F ASN* 3.7 13.4 + - - +
907F TYR* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 904 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861F TRP* 3.2 36.9 + - - +
862F HIS* 3.7 1.4 + - - -
863F GLY* 3.4 27.9 - - - +
897F PHE* 5.0 0.3 - - - -
898F ALA* 3.5 14.4 + - - +
900F MET 3.5 1.8 + - - -
901F VAL 3.5 2.0 + - - -
902F SER 3.2 0.4 - - - -
903F LYS* 1.3 76.6 - - - +
905F ALA* 1.3 63.9 + - - +
906F ASN 3.2 0.7 - - - -
907F TYR* 3.1 20.9 + - - +
908F CYS 4.1 0.2 + - - -
919F ILE* 3.6 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 905 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829F TYR* 3.9 17.6 - - + +
831F LEU* 4.5 16.2 - - + -
901F VAL* 2.8 23.6 + - + +
902F SER* 3.0 9.6 + - - +
904F SER* 1.3 72.6 - - - +
906F ASN* 1.3 61.4 + - - +
907F TYR 3.2 0.4 - - - -
908F CYS* 3.2 27.0 + - - +
909F HIS 4.4 1.0 + - - -
910F THR* 4.9 4.0 + - - -
919F ILE* 3.4 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 906 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826F HIS* 3.8 22.3 + - - +
829F TYR* 2.6 28.2 + - - -
902F SER 2.6 30.3 + - - -
903F LYS* 3.8 11.6 + - - +
904F SER 3.2 1.0 - - - -
905F ALA* 1.3 76.9 - - - +
907F TYR* 1.3 64.7 + - + +
908F CYS 3.2 1.6 + - - -
909F HIS* 3.5 21.0 + - - -
----------------------------------------------------------
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