Contacts of the strand formed by residues 301 - 304 (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 GLY 301 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J LEU* 3.7 1.2 - - - -
282J THR 3.1 31.9 + - - +
300J GLN* 1.3 81.3 + - - +
302J VAL* 1.3 66.5 + - - +
311J VAL* 3.6 10.1 - - - -
312J ASP 3.0 15.7 - - - -
314J PHE* 4.1 1.3 - - - +
377J VAL* 3.8 12.4 - - - +
381J LYS* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 302 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280J PHE 3.5 4.7 - - - -
281J LEU* 4.1 13.2 - - + -
301J GLY* 1.3 77.4 - - - +
303J ILE* 1.3 61.1 - - - +
304J TRP* 3.3 36.1 + - + +
310J LYS 4.1 1.2 - - - +
311J VAL* 3.6 3.6 - - - +
312J ASP* 2.9 38.0 + - + +
313J ASP 4.2 0.7 - - - +
314J PHE* 3.8 24.7 - - + -
362J TYR* 3.9 21.5 - - + +
367J PHE* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J ASN* 3.2 4.3 - - - -
280J PHE* 3.0 55.1 + - + +
302J VAL* 1.3 73.9 - - - +
304J TRP* 1.3 68.4 + - - +
305J GLY 4.0 3.6 - - - +
306J ASN 4.5 1.3 - - - -
307J ASP 3.6 20.9 - - - +
308J LEU* 3.3 34.1 - - + -
310J LYS 4.4 3.6 - - - -
311J VAL* 4.1 22.4 - - + -
367J PHE* 3.5 6.4 - - - -
376J LEU* 3.7 28.5 - - + +
377J VAL* 4.1 11.7 - - + +
380J ALA* 4.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 304 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279J ASN* 3.8 13.0 - - - -
302J VAL* 3.3 23.5 + - + +
303J ILE* 1.3 72.4 - - - +
305J GLY* 1.3 68.7 + - - +
306J ASN 3.0 3.1 + - - -
307J ASP* 3.2 23.5 + - + +
310J LYS 4.7 4.1 + - - -
312J ASP* 3.6 26.8 + - - -
318J LEU* 5.9 0.2 - - + -
362J TYR* 3.9 29.6 - + - -
363J LYS* 3.9 32.2 - - + +
365J GLU* 3.5 26.9 - - + -
367J PHE* 3.7 22.7 - + - -
----------------------------------------------------------
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