Contacts of the strand formed by residues 363 - 368 (chain A) in PDB entry 1RPK
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 ALA 363 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.6 1.4 - - - +
358A MET* 3.5 31.2 - - - +
360A GLU* 3.0 31.3 + - + -
361A GLY 3.5 0.4 - - - -
362A ASP* 1.3 83.0 + - - +
364A TYR* 1.3 59.0 + - - +
365A VAL* 4.1 0.7 - - + -
375A LYS* 5.2 0.7 - - - -
376A ILE 3.6 5.4 - - - -
379A ARG* 3.9 25.6 - - + +
382A VAL* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.6 19.0 - - + +
265A LEU* 3.7 39.4 + - + -
272A ALA* 5.8 0.2 - - - +
312A TYR* 3.7 17.8 + + - -
316A HIS* 2.7 39.3 + + - -
354A LEU* 4.1 2.3 - - - +
356A ILE* 3.7 27.1 - - + +
358A MET 3.3 12.3 - - - -
359A HIS* 4.6 2.7 - - + +
363A ALA* 1.3 72.3 - - - +
365A VAL* 1.3 61.7 + - - +
366A ALA* 3.5 23.3 - - + +
374A VAL* 4.8 4.9 - - + -
375A LYS* 3.2 4.4 - - - -
376A ILE* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 3.6 1.2 - - - +
357A LEU* 2.6 40.9 + - + -
358A MET* 2.9 34.6 + - + +
364A TYR* 1.3 81.0 - - - +
366A ALA* 1.3 57.3 + - - +
373A VAL* 3.6 21.8 - - + -
374A VAL 3.2 12.3 - - - +
375A LYS* 3.9 18.4 - - + -
382A VAL* 4.1 19.5 - - + -
385A VAL* 4.4 6.5 - - + -
386A ILE* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A HIS* 4.0 7.6 - - + +
354A LEU* 3.6 18.6 - - + -
355A LYS 3.5 7.2 - - - +
356A ILE* 4.1 3.4 - - - -
357A LEU* 4.0 2.2 - - - +
364A TYR* 3.5 32.0 - - + +
365A VAL* 1.3 75.2 - - - +
367A GLU* 1.3 60.8 + - - +
368A ILE* 3.8 1.6 - - + +
373A VAL* 3.2 7.6 - - - +
374A VAL* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA 3.8 1.0 - - - +
354A LEU* 3.7 2.1 - - - -
355A LYS* 2.6 64.5 + - + +
357A LEU* 4.2 12.5 - - + +
366A ALA* 1.3 75.2 - - - +
368A ILE* 1.3 63.7 - - - +
369A ASP 4.1 0.5 + - - -
370A GLY* 3.4 27.9 + - - +
372A VAL 3.3 9.0 - - - +
373A VAL* 4.1 10.3 - - + +
387A PRO* 3.8 15.2 - - - +
390A PHE* 3.0 33.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A THR* 3.2 32.8 - - - +
316A HIS* 4.2 11.7 - - + -
317A PRO* 4.8 3.8 - - + -
348A ILE* 3.7 21.0 - - + +
352A SER* 3.7 21.3 - - - -
353A ALA 3.3 9.9 - - - +
354A LEU* 4.1 13.2 - - + -
366A ALA 3.8 12.3 - - - +
367A GLU* 1.3 79.8 - - - +
369A ASP* 1.3 63.1 + - - +
370A GLY 3.0 3.6 - - - -
371A LYS* 2.9 20.1 + - - +
372A VAL* 2.7 27.3 + - + +
374A VAL* 3.9 18.2 - - + -
----------------------------------------------------------
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