Contacts of the helix formed by residues 902 - 908 (chain A) in PDB entry 4OGH
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 GLN 902 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735A ALA* 5.6 0.5 - - - -
738A GLN* 3.6 45.8 + - + +
739A TYR* 3.2 32.0 + - + -
897A GLU* 5.5 3.2 + - - -
898A ILE* 3.0 25.6 + - + +
901A VAL* 1.3 97.0 - - + +
903A VAL* 1.3 68.4 + - + +
904A PRO 3.3 1.6 - - - -
905A LYS* 3.1 38.5 + - - +
906A ILE* 3.4 10.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A GLN 5.9 0.7 - - - +
741A TRP* 5.0 3.8 - - + -
874A HIS* 3.5 44.9 - - + +
877A ALA* 6.0 0.9 - - + -
878A PHE* 4.2 4.7 - - + -
898A ILE* 2.9 24.8 + - + +
899A ILE* 3.3 30.1 - - + +
902A GLN* 1.3 75.7 - - + +
904A PRO* 1.4 58.0 - - - +
906A ILE* 2.8 27.3 + - + +
907A LEU* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A PHE* 4.1 18.2 - - + -
899A ILE 3.0 21.8 - - - +
900A SER 3.3 26.5 - - - +
901A VAL 3.7 5.2 - - - +
902A GLN 3.5 3.8 - - - -
903A VAL* 1.4 88.0 - - + +
905A LYS* 1.3 50.8 + - + +
907A LEU* 3.8 10.2 - - + +
908A SER* 2.6 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A TYR* 3.7 18.0 + - - +
901A VAL* 3.2 31.1 - - - +
902A GLN* 3.1 31.8 + - - +
904A PRO* 1.3 77.2 - - + +
906A ILE* 1.3 59.8 + - - +
908A SER* 3.4 8.7 + - - -
910A LYS* 2.9 50.4 + - + +
911A VAL* 3.0 21.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A GLN 5.0 1.8 - - - +
739A TYR* 3.9 31.4 - - + +
815A ILE* 4.0 13.7 - - + -
871A ARG* 3.8 20.3 + - + +
874A HIS* 3.8 42.8 - - + +
902A GLN 3.4 9.6 + - - +
903A VAL* 2.8 12.3 + - + +
905A LYS* 1.3 76.5 - - - +
907A LEU* 1.3 68.1 + - + +
909A GLY* 3.1 14.7 + - - -
911A VAL* 3.5 33.9 - - + +
913A PRO* 5.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ARG* 3.6 33.8 + - - +
874A HIS* 3.8 18.8 - - + -
875A GLN* 3.5 35.2 - - + +
878A PHE* 3.8 32.8 - - + -
903A VAL* 2.9 35.7 + - + +
904A PRO* 3.8 6.5 - - + +
906A ILE* 1.3 77.5 - - + +
908A SER* 1.3 58.1 + - - +
909A GLY 3.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A PRO* 2.6 21.9 + - - -
905A LYS* 3.4 10.6 + - - -
906A ILE 3.2 0.2 - - - -
907A LEU* 1.3 72.0 - - - +
909A GLY* 1.3 58.5 + - - +
910A LYS* 3.5 21.1 + - - +
----------------------------------------------------------
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