Contacts of the helix formed by residues 501 - 506 (chain F) 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 ALA 501 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F THR* 4.0 8.0 - - + +
366F ALA* 5.0 3.3 - - - +
367F PHE 3.8 21.5 + - - +
368F GLU* 4.1 15.3 - - + +
488F TRP 4.4 3.0 + - - -
489F ASN* 3.6 8.1 + - - +
500F SER* 1.3 73.1 - - - +
502F VAL* 1.3 57.3 + - - +
504F GLN* 3.8 4.4 - - - -
505F ALA* 2.9 23.0 + - - +
527F TYR* 3.1 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 502 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ILE* 5.1 2.9 - - + -
37F SER* 3.7 31.6 - - - +
489F ASN 2.9 24.0 + - - +
490F LEU* 3.9 19.5 - - + -
500F SER* 3.8 3.8 - - - +
501F ALA* 1.3 70.7 - - - +
503F GLU* 1.3 73.1 + - + +
505F ALA* 3.2 2.3 + - - +
506F LEU* 3.0 30.1 + - + +
523F THR* 4.9 1.6 - - + -
524F VAL* 4.2 28.0 - - + -
527F TYR* 4.1 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 503 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ALA* 3.6 20.4 - - + +
36F TRP* 3.5 1.0 - - - -
37F SER* 2.9 35.4 + - - +
354F TYR* 2.7 32.2 + - - -
491F GLY 4.0 3.1 - - - -
492F PRO* 3.8 1.4 - - - +
493F ARG* 3.9 13.0 + - - +
499F LEU* 3.7 21.5 - - + -
500F SER* 3.2 32.0 + - - +
502F VAL* 1.3 80.9 - - + +
504F GLN* 1.3 61.9 + - - +
506F LEU* 3.0 16.2 + - + +
507F ILE* 3.2 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 504 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F LYS 4.3 12.8 - - - +
277F THR* 5.4 5.6 - - + -
499F LEU* 4.0 29.1 - - + +
500F SER 3.1 17.1 + - - +
501F ALA* 4.0 4.9 - - - +
503F GLU* 1.3 74.9 - - - +
505F ALA* 1.3 65.6 + - - +
506F LEU 3.2 0.7 + - - -
507F ILE* 3.4 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 505 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F GLY* 3.2 40.2 + - - +
276F LYS 4.4 3.8 - - - -
277F THR* 4.4 1.2 - - + +
501F ALA 2.9 19.7 + - - +
502F VAL 3.2 5.8 + - - +
504F GLN* 1.3 77.6 - - - +
506F LEU* 1.3 61.0 + - - +
507F ILE 3.9 3.8 - - - +
509F THR* 3.7 6.1 + - - -
523F THR* 3.6 20.8 - - + +
527F TYR* 3.5 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ILE* 3.9 34.3 - - + -
25F VAL* 4.0 5.2 - - + -
32F ILE* 3.1 30.5 - - + +
35F ALA* 3.8 25.1 - - + -
36F TRP 5.9 0.7 - - - +
502F VAL* 3.0 18.4 + - + +
503F GLU* 3.0 12.0 + - + +
505F ALA* 1.3 77.8 - - - +
507F ILE* 1.3 65.2 + - - +
509F THR* 2.7 24.2 + - - +
520F ILE* 4.3 16.6 - - + +
523F THR* 3.9 27.4 - - + -
524F VAL* 4.6 4.0 - - + -
----------------------------------------------------------
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