Contacts of the strand formed by residues 452 - 461 (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 GLU 452 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450F PRO* 3.9 6.6 - - - +
451F THR* 1.3 77.3 - - + +
453F SER* 1.3 60.4 + - - +
472F GLN* 3.2 11.0 - - - +
473F ARG* 3.6 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 453 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F CYS* 2.6 35.7 + - - -
450F PRO* 3.1 12.0 - - - +
452F GLU* 1.3 73.0 - - - +
454F GLN* 1.3 59.3 + - - +
471F VAL* 3.5 3.7 - - - +
472F GLN* 2.7 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ASN* 4.4 2.8 + - - +
83F CYS* 3.2 14.9 - - - +
337F TYR* 3.6 41.1 + - + +
453F SER* 1.3 76.8 - - - +
455F GLY* 1.3 57.7 + - - +
470F ILE 3.0 15.5 - - - +
471F VAL* 4.0 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ALA* 3.7 9.2 - - - -
82F ASN* 3.3 13.9 - - - -
83F CYS* 3.3 15.7 - - - +
337F TYR* 3.1 15.2 + - - -
454F GLN* 1.3 75.8 - - - +
456F VAL* 1.3 59.0 - - - -
468F HIS 4.0 0.2 - - - +
469F TRP* 3.6 0.2 - - - -
470F ILE* 2.8 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ARG 4.0 1.0 - - - +
79F ALA* 3.7 4.9 - - - -
82F ASN* 3.0 29.9 + - - +
316F PRO* 5.9 1.1 - - + -
337F TYR* 3.8 12.1 - - + +
455F GLY* 1.3 74.7 - - - +
457F GLY* 1.3 64.0 + - - +
458F PHE* 3.5 49.0 + - + -
467F SER* 4.2 1.1 - - - -
468F HIS 3.3 11.7 - - - +
469F TRP* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ALA* 3.6 26.3 - - - +
78F ARG* 3.8 9.6 - - - -
79F ALA* 3.6 8.3 - - - +
456F VAL* 1.3 70.6 - - - +
458F PHE* 1.3 61.4 + - - -
459F VAL 4.0 0.2 - - - -
466F LEU 3.7 0.5 - - - +
467F SER* 3.0 8.8 - - - -
468F HIS 3.0 31.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 458 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ARG* 3.0 14.6 + - - +
283F CYS* 3.7 18.4 - - + -
293F LEU* 4.3 20.6 - - + -
296F ARG* 2.9 27.2 + - - +
314F PHE* 4.0 11.9 - + - -
316F PRO* 3.6 34.3 - - + -
456F VAL* 3.5 35.7 - - + -
457F GLY* 1.3 71.6 - - - -
459F VAL* 1.3 62.3 - - - +
465F MET* 3.0 34.8 - - + -
466F LEU 3.4 0.9 - - - -
467F SER* 3.6 15.5 - - - -
469F TRP* 4.3 4.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 459 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F VAL* 4.0 12.1 - - + +
74F LEU* 3.8 6.7 - - + -
75F ALA* 3.5 37.0 - - + +
78F ARG* 3.6 16.2 - - - +
100F MET* 3.3 33.7 - - + -
283F CYS* 3.5 8.0 - - - -
285F GLU* 3.4 5.2 - - - +
458F PHE* 1.3 77.8 - - - +
460F ASN* 1.3 58.9 + - - +
461F ALA* 3.5 7.9 - - - +
466F LEU* 2.6 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 460 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F MET* 4.5 0.3 - - - +
104F TYR* 2.6 36.2 + - - -
281F LEU 5.0 0.6 + - - -
282F THR* 3.1 24.9 + - - +
283F CYS* 4.0 2.8 - - - +
284F GLY* 3.5 24.0 - - - +
285F GLU* 2.7 20.3 + - + +
298F THR* 5.7 1.0 + - - -
374F SER* 3.1 21.5 + - - -
417F GLN* 4.2 4.2 - - - +
459F VAL* 1.3 73.9 - - - +
461F ALA* 1.3 63.8 + - - +
464F GLY* 3.4 6.0 - - - -
465F MET* 3.3 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F VAL* 3.9 16.8 - - + -
100F MET* 4.8 0.2 - - - -
104F TYR* 4.1 3.0 + - - -
417F GLN* 4.5 1.7 + - - +
459F VAL* 3.5 3.8 - - - -
460F ASN* 1.3 83.1 - - - +
462F PRO* 1.3 79.6 - - + +
463F ARG 3.0 0.7 - - - +
464F GLY* 2.8 25.0 + - - +
466F LEU* 4.4 6.1 - - + -
485F PRO* 4.6 0.7 - - + -
537F FCO 3.5 33.7 - - - +
----------------------------------------------------------
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