Contacts of the helix formed by residues 468 - 470 (chain J) in PDB entry 2ONM
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 TYR 468 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I GLU* 3.1 23.8 + - - +
487I LYS* 3.8 38.7 - - + +
488I VAL 3.9 4.3 - - - -
489I LYS* 2.9 31.9 + - - +
426J GLY* 3.1 16.6 + - - +
447J GLN* 3.7 32.3 - - + +
448J ALA 3.7 15.5 - - - -
449J GLY* 3.8 13.2 - - - -
467J GLY* 1.3 74.1 - - - -
469J LYS* 1.3 83.9 + - + +
471J SER* 3.1 18.7 + - - -
475J ARG* 3.4 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 469 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I ASP* 6.0 2.9 - - - +
261I ASN 4.9 5.7 - - - +
262I LEU* 5.0 6.1 - - - +
487I LYS* 4.4 11.7 - - - +
421J ASN* 3.1 25.5 + - - +
423J SER 3.6 18.9 + - - +
424J THR* 3.5 8.3 - - - +
425J TYR 4.2 11.0 + - - +
447J GLN* 2.9 41.1 + - - +
468J TYR* 1.3 81.5 - - + +
470J MET* 1.3 64.0 + - + +
471J SER 3.1 5.4 + - - -
472J GLY* 3.5 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 470 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I GLU* 4.9 6.1 - - - +
260I SER 4.6 0.2 - - - +
261I ASN* 3.9 33.9 - - + +
262I LEU* 4.5 12.8 - - - -
247J THR* 3.6 17.6 - - + +
251J ARG* 3.8 32.3 - - - +
269J LEU* 3.2 21.0 - - - +
424J THR* 3.1 42.7 + - + +
425J TYR* 3.8 6.0 - - + -
469J LYS* 1.3 79.8 - - + +
471J SER* 1.3 55.9 + - - +
472J GLY 3.2 5.6 - - - +
----------------------------------------------------------
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