Contacts of the strand formed by residues 292 - 296 (chain D) in PDB entry 2PS2
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 SER 292 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D PHE* 5.5 0.5 - - - -
243D ILE* 3.7 14.0 - - - +
264D GLU 3.1 9.8 + - - -
265D GLY* 3.1 13.2 - - - -
266D ILE 3.0 25.6 + - - -
290D GLY 3.9 1.6 + - - -
291D TYR* 1.3 75.7 - - - +
293D VAL* 1.3 61.7 + - - +
319D SER* 3.4 8.1 - - - +
321D ARG* 3.6 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ILE* 3.5 5.8 - - + +
268D LEU* 4.0 24.5 - - + -
283D ARG* 5.2 6.3 - - - +
286D CYS* 3.6 33.9 - - + -
287D LEU* 5.3 4.9 - - + -
291D TYR 3.9 3.6 - - - +
292D SER* 1.3 82.7 - - - +
294D SER* 1.3 72.0 + - - +
295D VAL* 4.3 0.7 - - + -
315D ILE* 3.9 30.7 - - + -
319D SER 2.8 12.6 + - - +
320D LEU* 3.3 11.4 - - - +
321D ARG* 2.8 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ILE* 5.3 0.5 - - - +
222D GLU* 5.7 2.2 - - - -
243D ILE* 6.3 0.7 - - - -
266D ILE 3.1 12.6 + - - -
267D ASP* 4.2 6.7 - - - -
268D LEU* 2.7 30.5 + - - +
293D VAL* 1.3 74.1 - - - +
295D VAL* 1.3 59.7 + - - +
296D GLN* 2.9 31.0 + - - +
321D ARG* 2.9 27.2 + - - +
322D CYS* 3.1 11.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 3.3 9.0 - - + +
270D ILE* 4.0 22.0 - - + -
293D VAL* 4.3 3.4 - - + -
294D SER* 1.3 76.3 + - - +
296D GLN* 1.3 64.9 + - - +
308D ILE* 3.5 26.8 - - + +
311D LEU* 4.3 11.0 - - + -
312D ALA* 3.9 23.3 - - + +
315D ILE* 3.6 30.7 - - + -
320D LEU* 4.1 3.8 - - + -
322D CYS 3.2 7.9 + - - -
323D ILE* 3.0 27.1 - - + +
324D LEU 3.1 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ILE* 4.3 22.4 - - - +
166D SER* 6.2 0.2 - - - -
222D GLU* 5.2 1.8 + - - -
267D ASP* 3.0 35.3 + - - +
268D LEU 2.9 7.5 + - - +
269D LYS* 3.1 29.0 + - + +
270D ILE* 3.1 9.2 + - - +
294D SER* 2.9 23.1 + - - +
295D VAL* 1.3 79.7 - - - +
297D GLU* 1.3 65.1 + - - +
308D ILE* 3.7 13.7 - - - +
323D ILE 4.4 0.4 - - - -
324D LEU* 3.3 41.0 - - + +
----------------------------------------------------------
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