Contacts of the helix formed by residues 868 - 876 (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 ASN 868 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766F ASP* 4.5 1.6 - - - +
767F ASN* 3.2 31.3 + - - +
770F ASP* 3.0 33.2 - - - +
864F SER* 2.7 28.7 + - - +
865F ARG* 2.9 13.2 + - - +
867F THR* 1.3 80.6 + - - +
869F PHE* 1.3 57.4 + - - +
870F ALA 3.1 3.1 - - - -
871F GLY* 2.8 21.0 + - - -
872F ILE* 2.9 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 869 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676F ILE* 4.0 19.3 - - + +
862F HIS 4.8 0.4 - - - -
864F SER* 3.3 36.8 - - - -
865F ARG 3.3 13.7 + - - -
866F THR* 3.9 9.6 - - - +
867F THR 3.4 1.4 - - - -
868F ASN* 1.3 75.6 - - - +
870F ALA* 1.3 61.3 + - - +
872F ILE* 3.8 15.7 - - + -
873F LEU* 3.4 42.6 + - + +
918F LEU* 3.5 48.2 - - + -
919F ILE* 4.0 4.7 - - - -
920F LEU* 3.7 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 870 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676F ILE* 3.4 30.5 - - - +
677F PHE* 4.8 8.9 - - + -
770F ASP 5.1 0.2 - - - +
773F VAL* 5.6 1.3 - - - -
774F ALA* 3.9 29.6 - - + -
777F LEU* 5.0 6.1 - - + +
797F LEU* 3.9 21.6 - - - +
867F THR 3.8 10.4 + - - +
868F ASN 3.1 0.6 + - - -
869F PHE* 1.3 78.5 - - - +
871F GLY* 1.3 59.2 + - - +
874F SER* 3.5 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 871 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770F ASP* 5.2 6.6 + - - -
773F VAL* 4.4 18.6 - - - +
867F THR 4.7 0.2 + - - -
868F ASN 2.8 7.7 + - - -
870F ALA* 1.3 79.6 - - - +
872F ILE* 1.3 58.7 + - - +
873F LEU 3.3 1.8 - - - -
874F SER* 3.0 7.9 + - - -
875F GLN* 3.0 28.7 + - - +
878F ARG* 3.3 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 872 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841F ARG* 4.1 2.9 - - - -
862F HIS* 5.5 0.2 - - - +
864F SER* 3.9 14.1 - - - +
868F ASN* 2.9 42.1 + - + +
869F PHE* 3.7 23.3 + - + +
870F ALA 3.6 0.2 - - - -
871F GLY* 1.3 76.5 - - - +
873F LEU* 1.3 63.7 + - + +
876F GLY* 2.9 36.3 + - - +
877F LEU* 3.6 34.3 - - + -
878F ARG* 3.8 11.9 - - - +
920F LEU* 3.8 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 873 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672F LEU* 6.3 1.8 - - + -
676F ILE* 5.2 5.2 - - + -
797F LEU* 3.5 23.1 - - + +
799F THR* 3.2 48.3 - - + +
801F ILE* 4.4 14.6 - - + -
839F ILE* 4.6 20.6 - - + -
841F ARG* 2.8 25.9 + - + +
869F PHE* 3.4 39.6 + - + +
870F ALA 4.5 0.2 - - - +
871F GLY 3.3 0.6 - - - -
872F ILE* 1.3 82.7 - - + +
874F SER* 1.3 56.2 + - - +
920F LEU* 5.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 874 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773F VAL* 4.7 0.2 - - - +
777F LEU* 4.2 29.7 - - - +
796F LYS 4.5 1.8 - - - -
797F LEU* 3.4 16.5 - - - +
798F LYS* 4.8 14.9 + - - +
841F ARG* 3.1 10.6 + - - -
870F ALA 3.5 13.4 + - - -
871F GLY* 3.0 17.4 + - - -
873F LEU* 1.3 81.0 - - - +
875F GLN* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 875 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773F VAL* 3.7 32.7 - - - +
777F LEU* 5.6 1.2 - - - +
841F ARG* 3.6 11.8 + - - +
847F ARG* 4.6 8.5 + - - -
871F GLY 3.0 12.4 + - - +
874F SER* 1.3 87.8 + - - +
876F GLY* 1.3 62.4 + - - +
877F LEU 4.9 1.0 - - - +
878F ARG* 3.4 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 876 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841F ARG* 3.2 27.8 - - - +
844F GLU* 4.7 2.7 - - - -
847F ARG* 5.0 3.8 - - - -
872F ILE* 2.9 24.3 + - - +
875F GLN* 1.3 78.5 - - - +
877F LEU* 1.3 63.4 + - - -
878F ARG* 2.9 24.8 + - - -
----------------------------------------------------------
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