Contacts of the helix formed by residues 6331 - 6338 (chain F) in PDB entry 2H7C
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 THR6331 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6258F LYS* 5.4 11.4 - - + -
6323F ILE* 3.9 17.2 - - + +
6330F LYS* 1.3 77.9 - - - +
6332F PRO* 1.3 75.0 - - + +
6333F GLU* 3.8 11.9 + - - +
6334F GLU* 3.1 47.8 + - - +
6335F LEU* 3.1 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO6332 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6232F LEU* 3.8 25.0 - - + +
6250F ALA* 3.8 30.5 - - + +
6251F LEU* 4.0 10.8 - - + -
6256F VAL* 4.6 15.3 - - + -
6323F ILE* 4.2 12.3 - - + -
6328F LEU* 4.9 10.3 - - + -
6330F LYS 4.3 0.2 - - - +
6331F THR* 1.3 83.1 - - + +
6333F GLU* 1.3 69.7 + - - +
6335F LEU* 3.3 5.7 + - + +
6336F GLN* 2.9 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU6333 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6251F LEU* 3.7 24.6 - - + +
6331F THR* 3.1 10.6 - - - +
6332F PRO* 1.3 94.4 - - - +
6334F GLU* 1.3 61.8 + - + +
6336F GLN* 3.4 11.6 + - - +
6337F ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU6334 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6330F LYS* 3.6 38.4 + - + +
6331F THR* 3.1 32.3 + - - +
6333F GLU* 1.3 75.9 - - + +
6335F LEU* 1.3 65.5 + - - +
6337F ALA* 3.3 7.2 + - - +
6338F GLU* 3.2 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU6335 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6232F LEU* 3.8 33.4 - - + +
6328F LEU* 4.0 15.7 - - + -
6329F LEU* 4.9 7.6 - - + +
6330F LYS* 3.6 47.8 - - + +
6331F THR 3.1 11.1 + - - +
6332F PRO* 3.7 6.5 - - + +
6334F GLU* 1.3 76.5 - - - +
6336F GLN* 1.3 62.1 + - - +
6338F GLU* 3.2 6.7 + - - +
6339F ARG 3.1 2.8 + - - -
6340F ASN* 3.0 58.8 + - + +
6341F PHE* 4.0 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN6336 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6232F LEU* 4.6 16.5 - - + +
6251F LEU* 3.7 19.4 - - - +
6332F PRO* 2.9 27.6 + - + +
6333F GLU* 3.7 12.8 - - - +
6334F GLU 3.2 0.2 - - - -
6335F LEU* 1.3 77.2 - - - +
6337F ALA* 1.3 57.0 + - - +
6339F ARG* 2.8 37.5 + - - -
6341F PHE* 4.0 10.8 - - + -
6432F ILE* 4.2 1.1 + - - +
6433F VAL* 3.5 45.1 + - - +
6436F ASN* 3.7 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA6337 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6333F GLU 3.1 14.9 + - - +
6334F GLU* 3.6 8.3 - - - +
6335F LEU 3.3 0.2 - - - -
6336F GLN* 1.3 78.6 - - - +
6338F GLU* 1.3 58.8 + - + +
6339F ARG* 3.3 18.7 + - - +
6436F ASN* 4.7 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU6338 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6330F LYS* 2.7 41.3 + - - -
6334F GLU* 3.2 19.1 + - - +
6335F LEU* 3.7 7.0 - - - +
6336F GLN 3.1 1.0 - - - -
6337F ALA* 1.3 78.5 - - + +
6339F ARG* 1.3 73.2 + - - +
6340F ASN* 2.9 21.5 + - + +
----------------------------------------------------------
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