Contacts of the strand formed by residues 477 - 483 (chain L) 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 ILE 477 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L LEU* 3.8 38.1 - - + +
50L LYS* 4.3 3.8 - - - +
51L GLY* 2.7 30.5 + - - -
52L ARG* 2.8 26.7 + - + +
53L ASP 4.5 1.1 - - - +
54L PRO* 3.8 27.1 - - + -
57L ALA* 4.4 6.3 - - + -
470L ILE* 3.9 8.3 - - + -
471L VAL 3.9 4.3 - - - -
472L GLN* 4.6 1.1 - - - +
476L LYS* 1.3 70.4 - - - +
478L GLU* 1.3 65.4 + - - +
479L ASN* 3.7 26.2 - - - +
480L PHE* 3.9 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 478 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L LYS* 2.8 41.6 + - - +
471L VAL* 2.9 27.7 + - + +
472L GLN 4.4 1.6 - - - -
473L ARG* 4.0 32.6 - - + +
476L LYS* 3.5 9.4 + - - +
477L ILE* 1.3 79.7 - - - +
479L ASN* 1.3 61.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 479 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L LYS* 5.7 2.7 - - - +
336L PRO 5.0 0.2 - - - -
337L TYR 3.3 22.8 + - - +
338L LYS* 4.2 1.2 - - - +
339L GLY 3.2 27.7 + - - +
469L TRP 4.3 1.6 - - - -
470L ILE* 3.4 7.1 - - - +
471L VAL* 2.9 44.4 + - + +
477L ILE* 3.6 4.3 - - - +
478L GLU* 1.3 80.0 - - + +
480L PHE* 1.3 66.9 + - - +
481L GLN* 3.4 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L GLU* 3.2 28.9 + - - +
49L LEU* 3.5 27.6 - - + -
50L LYS* 6.2 0.2 - - - +
57L ALA* 3.6 19.3 - - + -
61L THR* 4.0 3.4 - - + -
76L SER* 3.1 30.1 - - - -
79L ALA* 5.0 1.6 - - + -
80L VAL* 4.7 5.2 - - + -
468L HIS* 3.7 27.4 - - + -
469L TRP 3.2 5.4 - - - -
470L ILE* 3.8 33.0 - - + -
477L ILE* 3.9 25.2 - - + +
479L ASN* 1.3 74.1 + - - +
481L GLN* 1.3 64.7 + - - +
482L LEU* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 481 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L GLU* 3.7 12.7 + - - +
321L GLU* 3.9 10.1 + - - +
336L PRO* 3.0 39.9 - - + +
339L GLY* 3.8 22.4 - - - +
340L VAL* 4.5 0.7 - - - -
341L THR* 3.5 14.4 + - - -
358L LYS* 3.4 25.5 - - - +
468L HIS* 3.5 2.1 - - - -
469L TRP* 2.7 41.3 + - + +
479L ASN* 3.4 20.9 - - - +
480L PHE* 1.3 79.9 - - - +
482L LEU* 1.3 61.4 + - - +
483L VAL 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L LEU* 5.2 3.4 - - + -
46L GLU* 3.4 14.4 + - + +
49L LEU* 4.6 3.4 - - + -
61L THR* 4.0 14.4 - - + -
64L ALA* 4.4 7.9 - - + -
72L HIS* 3.9 16.6 - - + +
321L GLU* 4.0 0.5 - - - +
467L SER 3.7 4.5 - - - -
468L HIS* 3.7 26.7 - - + +
480L PHE* 3.6 32.1 - - + -
481L GLN* 1.3 71.2 - - - +
483L VAL* 1.3 67.9 + - - +
484L VAL* 4.0 5.6 - - + -
536L HIS* 3.1 38.8 + - + +
540L MG 2.2 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 483 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319L ILE* 4.9 5.2 - - + -
321L GLU* 3.3 39.7 - - + +
336L PRO* 3.9 28.3 - - + -
360L PRO* 3.8 23.6 - - + -
465L MET 3.8 2.6 - - - +
466L LEU* 3.7 3.6 - - - +
467L SER* 2.9 40.6 + - - +
469L TRP* 4.1 4.9 - - + +
481L GLN* 5.1 0.4 - - + -
482L LEU* 1.3 76.0 - - - +
484L VAL* 1.3 61.5 + - - +
487L THR* 4.9 0.4 - - - -
488L TRP* 3.8 19.0 + - + +
----------------------------------------------------------
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