Contacts of the strand formed by residues 424 - 430 (chain A) in PDB entry 3RT0
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 ASP 424 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 4.9 0.5 - - - +
351A LEU* 3.8 14.6 - - + +
352A PHE 3.6 3.1 - - - -
353A ARG* 2.5 47.6 + - - +
420A ARG* 3.6 11.3 - - + +
421A SER 2.8 35.5 + - - +
422A ARG 4.0 0.9 - - - +
423A GLU* 1.3 77.2 - - - +
425A GLU* 1.3 61.3 + - - +
501A LEU* 3.9 28.6 - - + +
502A LYS* 3.3 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 2.8 28.9 + - + +
354A GLY* 4.1 17.2 - - - +
423A GLU 3.8 9.0 - - - +
424A ASP* 1.3 76.3 - - - +
426A CYS* 1.3 62.4 + - - +
448A ARG* 3.3 38.4 + - + -
500A ASP* 3.2 0.3 - - - +
501A LEU* 3.0 18.0 + - - -
502A LYS* 3.6 19.8 + - - -
505A ARG* 2.9 53.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL 4.1 0.3 - - - +
351A LEU* 3.7 3.8 - - - +
352A PHE* 2.9 45.0 + - - -
425A GLU* 1.3 87.4 - - - +
427A LEU* 1.3 62.0 + - - +
428A ILE* 4.2 9.1 - - - +
444A CYS 4.3 0.7 - - - -
447A ALA* 4.2 23.3 - - - -
448A ARG* 4.3 11.9 - - - -
451A ILE* 4.4 14.6 - - + -
498A VAL* 5.0 2.9 - - + -
499A ILE 3.1 17.0 - - - +
501A LEU* 3.8 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ALA* 4.1 11.2 - - + -
334A VAL* 4.0 20.6 - - + -
339A ILE* 4.0 17.7 - - + -
341A VAL* 5.2 0.2 - - + -
349A ALA* 4.5 2.7 - - + -
350A VAL 3.5 27.8 - - - +
351A LEU* 4.1 3.6 - - + +
360A LEU* 4.0 21.1 - - + -
426A CYS* 1.3 75.3 - - - +
428A ILE* 1.3 64.2 + - - +
429A LEU* 4.0 13.2 - - + -
497A ILE 3.7 1.6 - - - +
499A ILE* 2.9 59.1 + - + +
501A LEU* 4.1 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG 3.8 0.9 - - - +
349A ALA* 3.3 3.6 - - - -
350A VAL 2.8 40.0 + - - +
426A CYS* 4.2 8.3 - - - -
427A LEU* 1.3 78.7 - - - +
429A LEU* 1.3 70.2 + - - +
430A ALA* 4.6 1.3 - - + -
434A LEU* 4.7 0.9 - - + -
435A TRP* 4.2 19.6 - - + -
443A VAL* 3.7 26.9 - - + -
444A CYS* 4.0 23.8 - - - -
447A ALA* 3.8 21.3 - - + -
481A LEU* 5.0 0.4 - - + -
496A ILE* 4.0 20.6 - - + -
497A ILE 3.4 7.6 - - - +
498A VAL* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 3.6 34.5 - - + +
240A GLY* 4.4 2.7 - - - +
241A VAL* 3.8 14.7 - - + +
330A VAL* 3.7 23.6 - - + +
331A VAL 4.3 0.7 - - - -
332A ALA* 4.0 19.3 - - + +
348A ARG 3.5 3.4 - - - +
349A ALA* 3.8 21.8 - - + -
427A LEU* 4.0 19.5 - - + -
428A ILE* 1.3 80.8 - - - +
430A ALA* 1.3 65.7 + - - +
496A ILE* 3.3 1.4 - - - +
497A ILE* 2.8 38.6 + - + -
499A ILE* 4.7 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 4.1 10.1 - - - +
330A VAL* 4.8 0.2 - - - +
347A SER* 3.6 2.4 - - - -
348A ARG 3.2 22.8 + - - -
428A ILE* 4.6 0.7 - - + -
429A LEU* 1.3 77.6 - - - +
431A SER* 1.3 63.6 - - - +
434A LEU* 3.8 22.0 - - + -
435A TRP* 2.9 34.9 + - + +
495A SER 3.1 13.7 - - - +
496A ILE* 4.2 4.9 - - + -
----------------------------------------------------------
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