Contacts of the strand formed by residues 290 - 295 (chain A) in PDB entry 2OME
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 290 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 4.4 12.8 - - + +
261A MET* 4.0 33.9 - - + -
265A ALA* 3.4 16.4 - - + +
267A LEU* 4.4 12.1 - - + +
281A LEU* 3.9 23.8 - - + -
284A ALA* 3.3 20.9 + - + -
285A LEU* 3.7 30.7 - - + +
288A GLY* 3.9 7.0 - - - +
289A ARG* 1.3 83.4 - - - +
291A ARG* 1.3 65.4 + - - +
292A GLY 3.4 22.6 + - - +
315A ASN* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 6.0 0.4 - - - -
148A ARG* 5.9 5.6 - - - +
151A TRP* 5.2 0.5 - - - -
174A GLY* 3.8 30.7 + - - -
176A ALA* 3.9 17.8 - - - +
264A GLY* 3.2 36.3 + - - +
265A ALA 2.8 6.0 + - - +
266A PHE* 3.3 38.5 - - + -
288A GLY* 4.7 3.6 - - - +
290A ILE* 1.3 72.4 - - - +
292A GLY* 1.3 58.2 + - - +
315A ASN* 3.3 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.1 8.0 - - - +
151A TRP* 4.8 1.3 - - - -
266A PHE* 3.4 20.0 - - - +
267A LEU 3.1 21.8 + - - +
285A LEU* 3.9 5.2 - - - -
290A ILE* 3.2 6.9 - - - +
291A ARG* 1.3 82.9 - - - +
293A ALA* 1.3 61.2 + - - -
315A ASN* 3.3 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 4.0 6.4 - - - +
267A LEU* 3.1 13.9 - - + +
281A LEU* 4.3 22.0 - - + -
285A LEU* 4.0 18.4 - - + +
290A ILE* 4.8 0.4 - - + -
292A GLY* 1.3 75.6 - - - +
294A ALA* 1.3 53.9 + - - +
295A LEU* 4.7 3.6 - - + -
315A ASN 3.1 6.5 + - - +
316A LEU* 3.5 17.8 - - + +
317A ILE* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 3.7 36.2 - - + +
145A LEU* 3.7 21.5 - - + +
267A LEU 2.9 8.5 + - - -
268A VAL* 3.4 6.2 - - + +
269A ASN 2.9 25.6 + - - +
293A ALA* 1.3 74.1 - - - +
295A LEU* 1.3 61.3 + - - +
296A ASP 4.3 0.2 + - - -
317A ILE* 3.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A HIS* 4.9 3.1 - - - -
267A LEU* 4.8 5.6 - - + +
268A VAL 4.8 0.9 - - - -
269A ASN* 3.6 28.5 - - + +
276A VAL* 5.2 3.8 - - + -
278A GLU* 4.6 7.4 - - + +
281A LEU* 4.0 29.2 - - + -
293A ALA* 4.7 2.9 - - + -
294A ALA* 1.3 87.0 - - - +
296A ASP* 1.3 59.5 + - - +
297A VAL 3.9 9.0 - - - +
298A HIS* 3.6 21.8 - - + +
310A LEU* 4.0 23.3 - - + -
316A LEU* 4.2 11.9 - - + -
317A ILE 2.8 12.4 + - - +
318A CYS* 3.1 6.8 - - - +
319A THR* 3.0 23.8 + - - +
----------------------------------------------------------
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