Contacts of the strand formed by residues 452 - 461 (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 GLU 452 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D PRO* 3.9 6.1 - - - +
451D THR* 1.3 77.0 - - + +
453D SER* 1.3 62.0 + - - +
472D GLN* 3.2 10.8 - - - +
473D ARG* 3.6 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D CYS* 2.6 35.1 + - - -
450D PRO* 3.1 12.4 - - - +
452D GLU* 1.3 72.9 - - - +
454D GLN* 1.3 60.0 + - - +
471D VAL* 3.5 3.5 - - - +
472D GLN* 2.7 57.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ASN* 4.4 2.8 + - - +
83D CYS* 3.2 15.8 - - - +
337D TYR* 3.6 43.6 + - + +
453D SER* 1.3 74.9 - - - +
455D GLY* 1.3 57.2 + - - +
470D ILE 3.0 15.3 - - - +
471D VAL* 4.0 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ALA* 3.7 9.9 - - - -
82D ASN* 3.3 13.0 - - - -
83D CYS* 3.3 15.8 - - - +
337D TYR* 3.1 14.3 + - - -
454D GLN* 1.3 75.1 - - - +
456D VAL* 1.3 59.7 - - - +
468D HIS 4.0 0.2 - - - +
469D TRP* 3.6 0.2 - - - -
470D ILE* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 4.0 1.4 - - - +
79D ALA* 3.7 4.5 - - - -
82D ASN* 3.0 29.4 + - - +
316D PRO* 5.9 1.1 - - + -
337D TYR* 3.8 11.9 - - + +
455D GLY* 1.3 75.5 - - - +
457D GLY* 1.3 64.4 + - - +
458D PHE* 3.5 48.9 + - + -
467D SER* 4.2 0.9 - - - -
468D HIS 3.3 11.7 - - - +
469D TRP* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ALA* 3.6 25.4 - - - +
78D ARG* 3.8 9.6 - - - -
79D ALA* 3.6 7.9 - - - +
456D VAL* 1.3 72.7 - - - +
458D PHE* 1.3 60.5 + - - -
459D VAL 4.0 0.4 - - - -
466D LEU 3.7 0.5 - - - +
467D SER* 3.0 8.8 - - - -
468D HIS 3.0 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 458 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 3.0 15.3 + - - +
283D CYS* 3.7 18.6 - - + -
293D LEU* 4.3 20.2 - - + -
296D ARG* 2.9 27.0 + - - +
314D PHE* 4.0 10.5 - + - -
316D PRO* 3.6 33.0 - - + -
319D ILE* 5.2 0.2 - - + -
456D VAL* 3.5 37.0 - - + -
457D GLY* 1.3 71.4 - - - -
459D VAL* 1.3 62.3 - - - +
465D MET* 3.0 34.1 - - + -
466D LEU 3.4 0.4 - - - -
467D SER* 3.6 15.7 - - - -
469D TRP* 4.3 4.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 459 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 4.0 12.1 - - + +
74D LEU* 3.8 5.8 - - + -
75D ALA* 3.5 36.3 - - + +
78D ARG* 3.6 15.7 - - - +
100D MET* 3.3 34.1 - - + -
283D CYS* 3.5 7.1 - - - -
285D GLU* 3.4 6.3 - - - +
458D PHE* 1.3 78.5 - - - +
460D ASN* 1.3 59.7 + - - +
461D ALA* 3.5 7.6 - - - +
466D LEU* 2.6 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 460 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D MET* 4.5 0.3 - - - +
104D TYR* 2.6 37.2 + - - -
281D LEU 5.0 1.0 + - - -
282D THR* 3.1 25.3 + - - +
283D CYS* 4.0 2.5 - - - +
284D GLY 3.5 24.0 - - - +
285D GLU* 2.7 21.1 + - + +
298D THR* 5.7 0.7 + - - -
370D GLY 5.4 0.4 - - - +
374D SER* 3.1 21.6 + - - -
417D GLN* 4.2 3.6 - - - +
459D VAL* 1.3 74.2 - - - +
461D ALA* 1.3 63.8 + - - +
464D GLY* 3.4 5.9 - - - -
465D MET* 3.3 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 461 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D VAL* 3.9 17.7 - - + -
100D MET* 4.8 0.2 - - - -
104D TYR* 4.1 2.6 + - - -
417D GLN* 4.5 1.9 + - - -
459D VAL* 3.5 4.0 - - + -
460D ASN* 1.3 83.5 - - - +
462D PRO* 1.3 78.6 - - + +
463D ARG 4.2 0.2 - - - +
464D GLY* 2.8 25.7 + - - +
466D LEU* 4.4 5.6 - - + -
485D PRO* 4.6 0.2 - - + -
537D 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