Contacts of the strand formed by residues 265 - 269 (chain G) 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 ALA 265 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G SER 4.3 9.4 - - - +
237G ASP* 3.4 15.3 - - - +
239G VAL* 5.7 1.6 - - + -
261G MET* 4.5 16.4 - - + -
262G ARG* 3.0 28.0 + - + +
263G GLN 3.3 0.6 - - - -
264G GLY* 1.3 76.9 - - - +
266G PHE* 1.3 65.0 + - - +
289G ARG 3.9 3.7 + - - +
290G ILE* 3.1 9.8 - - + +
291G ARG* 2.8 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G LEU* 3.7 46.0 - - + -
146G TYR* 3.5 52.5 - + - -
151G TRP* 5.6 3.4 - + - -
174G GLY 5.3 1.1 - - - -
237G ASP 3.0 9.1 + - - +
238G CYS* 3.6 11.2 - - - -
239G VAL* 3.0 26.4 + - - +
261G MET* 5.1 1.5 - - - +
264G GLY 5.4 1.1 - - - -
265G ALA* 1.3 78.8 - - - +
267G LEU* 1.3 61.4 + - - +
290G ILE* 4.4 1.1 - - - -
291G ARG* 3.9 34.3 - - + -
292G GLY* 3.3 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G LEU* 4.3 0.5 - - - +
239G VAL* 3.5 30.3 - - + +
241G LEU* 4.6 6.3 - - + -
253G ILE* 4.4 27.1 - - + -
261G MET* 4.7 7.9 - - + -
266G PHE* 1.3 74.1 - - - +
268G VAL* 1.3 72.2 + - - +
276G VAL* 4.1 23.8 - - + -
281G LEU* 4.2 26.5 - - + -
290G ILE* 4.1 17.4 - - + +
292G GLY 3.1 7.5 + - - +
293G ALA* 3.1 7.6 - - + +
294G ALA 3.0 23.7 + - - +
295G LEU* 4.6 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G THR* 4.5 12.8 - - + -
141G HIS* 3.7 26.9 - - + +
142G ILE* 3.9 17.5 - - + -
145G LEU* 3.5 25.4 - - + -
238G CYS* 4.1 10.5 - - - -
239G VAL 2.8 7.9 + - - +
240G SER* 3.3 17.0 - - - +
241G LEU* 3.0 27.9 + - - +
267G LEU* 1.3 83.4 - - - +
269G ASN* 1.3 67.8 + - - +
270G ALA* 4.2 1.1 - - + +
294G ALA* 3.4 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G HIS* 6.2 0.2 - - - -
241G LEU* 3.6 20.7 - - + +
267G LEU* 5.2 0.7 - - + -
268G VAL* 1.3 74.1 - - - +
270G ALA* 1.3 58.9 + - - +
271G ALA* 2.8 32.7 + - - +
272G ARG 2.7 29.7 + - - +
273G GLY* 4.3 2.8 - - - -
275G LEU* 4.4 0.4 - - - +
276G VAL* 3.7 21.4 - - + +
294G ALA 3.0 10.4 + - - -
295G LEU* 3.7 18.9 - - + +
296G ASP 3.1 23.9 + - - -
297G VAL* 3.5 17.2 + - - +
----------------------------------------------------------
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