Contacts of the helix formed by residues 269 - 273 (chain J) in PDB entry 2FRV
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 LYS 269 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E PRO 4.7 6.5 + - - -
124E ASN* 5.7 3.8 + - - +
265J ALA 3.9 6.1 - - - +
266J GLY* 3.8 24.7 - - - +
267J PHE 3.7 1.2 - - - -
268J TYR* 1.3 76.0 - - - +
270J ASN* 1.3 60.1 + - - +
271J TRP 3.0 1.1 - - - -
272J ALA* 3.2 21.0 + - + +
273J GLY 4.4 0.5 + - - -
397J LEU* 2.8 38.5 + - + +
398J GLY* 4.1 8.7 + - - -
399J VAL* 4.2 13.9 - - + +
408J LEU* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 270 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ASP* 5.7 7.2 - - - +
267J PHE 5.4 0.4 + - - -
268J TYR* 3.0 12.3 + - - +
269J LYS* 1.3 77.7 - - - +
271J TRP* 1.3 74.0 + - - +
272J ALA 3.1 1.3 - - - -
273J GLY* 3.2 14.3 + - - -
274J ILE* 3.4 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 271 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J TRP* 4.0 13.2 - + + -
268J TYR* 2.8 31.8 + + - +
270J ASN* 1.3 95.5 + - - +
272J ALA* 1.3 56.2 + - - +
273J GLY 2.8 9.2 + - - -
274J ILE* 3.2 55.0 - - + +
406J SER* 3.6 0.2 + - - -
407J THR* 4.1 15.7 - - + -
408J LEU* 3.1 34.1 + - + +
509J THR* 4.0 6.3 - - + -
510J PRO* 5.1 3.6 - - + -
519J GLU* 3.6 41.5 - - + -
522J ARG* 3.7 39.6 - - + +
523J THR* 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J LYS* 3.2 16.5 + - - +
270J ASN 3.1 0.4 - - - -
271J TRP* 1.3 77.3 - - - +
273J GLY* 1.3 57.9 + - - +
399J VAL* 5.3 7.2 - - + -
402J GLU 4.7 2.9 - - - +
403J ALA* 4.1 30.9 - - + +
405J PHE 5.0 0.3 - - - +
406J SER* 3.2 24.9 - - - +
408J LEU* 3.6 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F LYS* 6.0 1.5 + - - -
269J LYS 4.4 0.4 + - - -
270J ASN 3.2 8.1 + - - -
271J TRP 2.8 0.8 - - - -
272J ALA* 1.3 85.3 - - - +
274J ILE* 1.3 64.0 + - - +
276J LYS* 5.5 7.1 - - - +
406J SER* 4.5 1.8 - - - -
----------------------------------------------------------
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