Contacts of the strand formed by residues 263 - 268 (chain F) in PDB entry 2ORE
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 GLU 263 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 3.6 30.1 - - + +
181F ASP* 5.5 0.3 - - - +
184F TYR* 3.0 33.9 + - - -
226F SER* 4.7 6.8 - - - -
227F ASN* 3.2 20.7 + - - +
228F HIS* 3.6 16.6 + - - -
229F ASP* 4.4 0.7 - - - -
244F VAL* 3.5 3.1 - - - +
245F VAL* 2.7 55.5 + - + +
247F VAL* 5.0 8.6 - - + +
261F VAL 3.9 3.8 + - - +
262F ASP* 1.3 74.5 - - - +
264F LEU* 1.3 62.3 + - - +
265F LEU* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ARG* 6.1 0.2 - - - -
225F ILE 3.8 0.3 - - - +
226F SER* 3.4 6.1 - - - -
227F ASN* 2.7 37.9 + - - +
228F HIS 3.8 8.3 - - - +
229F ASP* 3.9 21.8 - - + +
233F THR* 3.6 32.5 - - - +
234F ARG* 4.3 6.1 - - + +
237F TYR* 4.0 11.9 - - + -
242F LEU* 3.6 45.1 - - + -
243F HIS 3.7 12.6 - - - +
244F VAL* 4.3 6.3 - - + -
262F ASP 4.0 0.4 + - - -
263F GLU* 1.3 75.5 - - - +
265F LEU* 1.3 72.3 + - - +
266F ALA 4.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F LEU* 4.8 8.7 - - + -
20F ASP* 3.5 32.1 - - + +
21F ILE* 4.3 17.3 - - + -
24F HIS* 3.7 22.2 - - + +
224F LEU* 4.4 12.1 - - + -
225F ILE 3.4 3.8 - - - +
226F SER* 3.8 21.3 - - - -
241F LYS 3.5 2.3 - - - +
242F LEU* 3.3 4.5 - - - -
243F HIS* 2.9 47.2 + - + +
245F VAL* 4.3 17.0 - - + -
263F GLU* 5.3 0.9 - - + -
264F LEU* 1.3 84.9 - - - +
266F ALA* 1.3 60.2 + - - +
267F LEU* 4.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F VAL 3.6 2.1 - - - +
224F LEU* 3.2 3.7 - - - +
225F ILE* 2.9 37.0 + - + +
237F TYR* 3.6 42.2 - - + -
240F ALA* 3.8 8.3 - - + -
241F LYS 3.9 3.4 - - - -
242F LEU* 3.6 11.0 - - + -
264F LEU 4.2 0.6 - - - -
265F LEU* 1.3 73.0 - - - +
267F LEU* 1.3 60.4 + - - +
268F TYR* 3.9 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F HIS* 3.8 33.4 - - + +
26F PRO* 3.8 29.4 - - + -
223F VAL 3.7 9.4 - - - +
224F LEU* 3.9 11.9 - - + -
240F ALA* 3.3 2.7 - - - +
241F LYS* 2.9 45.2 + - + +
243F HIS* 5.1 7.6 - - + +
265F LEU 4.0 0.2 - - - -
266F ALA* 1.3 73.0 - - - +
268F TYR* 1.3 69.7 - - - +
269F LYS* 3.6 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 268 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F ALA* 4.1 8.7 + - - -
213F ALA* 3.7 30.1 - - + +
214F GLU* 4.0 18.5 + - + +
217F VAL* 3.4 34.7 - - + +
222F PRO* 3.3 8.3 - - - +
223F VAL* 2.7 45.6 + - + +
225F ILE* 3.9 14.8 - - + -
236F TRP 4.2 3.5 + - - -
237F TYR* 3.5 30.0 - - - +
239F ARG* 4.4 9.0 - - + -
240F ALA* 3.5 33.2 - - + +
266F ALA* 3.9 9.0 - - + -
267F LEU* 1.3 76.6 - - - +
269F LYS* 1.3 61.0 + - - +
----------------------------------------------------------
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