Contacts of the strand formed by residues 319 - 322 (chain D) 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 319 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D PHE* 4.2 16.8 - - + -
316D PRO* 3.6 34.5 - - + +
317D ASP 3.3 1.9 - - - +
318D LEU* 1.3 77.5 - - - +
320D GLU* 1.3 71.9 - - - +
321D GLU* 4.9 2.2 - - + +
335D HIS* 3.2 26.7 - - - -
336D PRO* 3.7 24.2 - - + -
360D PRO* 5.3 0.4 - - + -
361D ARG 3.7 4.7 - - - -
362D TYR* 4.2 10.5 - - + -
465D MET* 5.0 7.6 - - + -
467D SER* 5.3 1.6 - - - +
469D TRP* 4.2 11.2 - - + -
483D VAL* 4.9 10.8 - - + -
488D TRP* 4.1 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ASP 5.9 0.9 - - - +
318D LEU 3.9 3.8 + - - +
319D ILE* 1.3 78.9 - - - +
321D GLU* 1.3 58.9 + - - +
322D HIS* 4.2 6.0 + - - +
333D ALA* 2.5 52.3 - - + +
334D HIS* 2.6 12.1 + - - -
335D HIS* 3.5 15.1 + - + +
360D PRO* 3.5 1.2 - - - +
361D ARG* 2.8 39.3 + - + +
364D GLY 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ILE* 5.0 3.8 - - + -
320D GLU* 1.3 73.6 - - - +
322D HIS* 1.3 64.8 + - - +
323D VAL* 4.7 2.6 - - - +
332D GLY 3.8 2.1 - - - +
333D ALA* 3.0 18.5 - - - -
334D HIS* 3.2 18.0 + - + +
336D PRO* 4.9 4.9 - - + +
339D GLY* 5.8 0.7 - - - -
358D LYS* 4.0 31.2 + - + +
359D ALA 3.7 3.6 - - - -
360D PRO* 3.8 20.2 - - + +
481D GLN* 3.9 19.2 + - - -
482D LEU 4.0 5.0 - - - +
483D VAL* 3.3 42.3 - - + +
487D THR* 4.1 5.9 - - - +
540D MG 4.0 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D GLU* 4.2 6.2 - - - +
321D GLU* 1.3 72.6 - - - +
323D VAL* 1.3 71.0 + - - +
324D LYS 4.4 2.2 - - - +
326D SER* 3.9 0.7 + - - -
331D ALA 5.1 1.6 + - - -
333D ALA* 3.4 27.5 + - + +
358D LYS* 3.6 5.0 - - - +
359D ALA* 2.8 53.1 + - + +
361D ARG* 3.6 29.2 - - + +
364D GLY* 5.7 2.6 - - - -
494D CYS* 3.6 15.0 - - + -
495D ALA* 3.3 34.6 + - + +
496D GLU* 5.0 8.3 - - - -
----------------------------------------------------------
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