Contacts of the strand formed by residues 262 - 269 (chain A) in PDB entry 5ES4
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 262 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 3.8 31.2 - - + -
221A PHE* 3.4 48.5 - - + -
233A LYS* 3.4 20.0 - - + +
235A LEU* 4.0 11.2 - - + +
257A ALA* 3.0 24.9 + - + +
258A ASP* 4.3 3.7 - - - +
260A ALA* 4.1 10.5 - - + -
261A GLY* 1.3 79.1 - - - +
263A ILE* 1.3 76.1 + - - +
264A ARG* 3.6 15.0 + - + +
287A SER* 4.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 5.7 0.4 - - + -
233A LYS 2.8 17.4 + - - +
234A ILE* 3.9 16.6 - - + -
235A LEU* 2.8 32.7 + - - +
261A GLY 5.7 1.3 - - - +
262A ILE* 1.3 74.2 - - - +
264A ARG* 1.3 59.6 + - - +
265A TYR* 3.6 21.3 - - + +
287A SER* 4.3 3.1 - - - +
293A HIS* 3.5 31.4 - - + +
317A ILE* 3.7 30.3 - - + -
318A GLU 5.7 2.5 - - - +
320A THR* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 5.4 11.4 - - - -
235A LEU* 3.8 11.0 - - + -
237A VAL* 6.5 1.1 - - + -
254A ILE* 3.2 26.6 + - - +
257A ALA* 3.1 35.6 - - + +
258A ASP* 2.6 45.0 + - - +
262A ILE* 3.9 7.9 + - + +
263A ILE* 1.3 76.4 - - - +
265A TYR* 1.3 62.0 + - - +
284A ASP 4.4 3.5 + - - -
285A ILE 3.2 26.5 + - - +
286A ALA* 3.3 11.6 + - - -
287A SER* 2.9 45.7 + - - +
293A HIS* 3.2 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 3.7 25.8 - - + -
235A LEU 3.0 12.1 + - - +
236A ILE* 4.3 15.9 - - + -
237A VAL* 3.1 30.6 + - - +
263A ILE* 3.6 21.6 - - + +
264A ARG* 1.3 73.0 - - - +
266A ALA* 1.3 61.2 + - - +
267A ILE* 5.5 2.7 - - + -
285A ILE* 4.4 1.7 - - - +
286A ALA* 4.4 1.3 - - - -
292A GLU 3.5 20.4 - - - -
293A HIS* 3.3 25.7 - + - -
295A PHE* 4.3 11.2 - + + -
310A LEU* 4.5 9.6 - - + -
313A LYS* 2.9 40.2 + - + +
314A ILE* 3.7 28.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A VAL 3.8 2.5 - - - -
265A TYR* 1.3 73.5 - - - +
267A ILE* 1.3 64.5 + - - +
268A GLY 4.0 0.4 - - - -
282A LEU* 3.9 24.7 - - + +
285A ILE* 3.8 19.7 - - + -
286A ALA* 3.8 19.5 - - + -
293A HIS 2.7 10.9 + - - +
294A ILE* 3.3 6.7 - - + +
295A PHE* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 4.4 12.6 - - + -
236A ILE* 3.9 17.7 - - + -
237A VAL 2.9 16.1 + - - +
238A ILE* 3.6 32.7 - - + -
239A THR* 3.0 32.2 + - - +
265A TYR* 5.5 2.7 - - + -
266A ALA* 1.3 75.5 - - - +
268A GLY* 1.3 59.0 + - - +
269A VAL* 4.5 4.9 - - + -
282A LEU* 4.7 1.1 - - - -
295A PHE* 3.6 13.9 - - + +
297A VAL* 3.8 25.1 - - + -
303A LEU* 4.1 13.5 - - + -
306A ILE* 5.0 4.0 - - + -
310A LEU* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A THR* 3.5 4.5 - - - -
266A ALA 4.0 1.2 - - - -
267A ILE* 1.3 73.3 - - - +
269A VAL* 1.3 56.6 + - - -
273A PHE* 3.6 23.2 - - - -
282A LEU* 4.1 15.3 - - - +
295A PHE 3.2 8.7 + - - -
296A LYS* 3.6 4.4 - - - +
297A VAL* 2.7 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ILE* 4.9 6.7 - - + -
239A THR 3.0 18.3 + - - +
240A ASP* 3.4 18.1 - - + +
267A ILE* 4.5 10.8 - - + -
268A GLY* 1.3 74.1 - - - -
270A GLY* 1.3 66.3 + - - +
272A ALA* 4.9 1.2 - - - +
273A PHE* 3.2 17.2 - - - -
297A VAL* 3.2 14.4 - - + -
299A ASP* 3.1 29.6 - - - +
300A PHE* 3.6 42.4 - - + -
303A LEU* 5.3 3.6 - - + -
----------------------------------------------------------
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