Contacts of the strand formed by residues 280 - 283 (chain F) in PDB entry 4O9U
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 VAL 280 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F ALA* 4.0 16.6 - - + +
150F LEU* 4.0 20.9 - - + +
151F SER* 3.6 35.9 - - - +
152F PRO* 4.4 0.7 - - + -
250F ASP 3.2 7.6 + - - +
251F VAL* 3.4 7.9 - - + +
252F LEU* 2.8 32.6 + - - +
278F GLY 3.8 7.2 - - - +
279F THR* 1.3 82.6 - - - +
281F VAL* 1.3 62.6 + - - +
282F VAL* 4.0 22.2 - - + -
307F ARG* 3.9 11.7 - - + +
309F TYR* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F LEU* 3.2 30.5 - - + +
254F THR* 4.9 4.0 - - - +
267F LEU* 3.7 24.2 - - + -
272F VAL* 5.5 0.9 - - + -
275F LEU* 4.2 17.3 - - + -
280F VAL* 1.3 78.5 - - - +
282F VAL* 1.3 69.8 + - - +
283F ASP* 4.9 2.7 - - + +
292F CYS* 4.5 19.1 - - + -
306F VAL* 4.3 8.1 - - + -
307F ARG 3.2 11.2 + - - +
308F VAL* 3.8 13.1 - - + +
309F TYR* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ALA* 3.8 27.8 - - + +
146F HIS* 4.4 11.2 - - + +
147F ALA* 3.8 26.2 - - + +
150F LEU* 5.1 4.7 - - + -
251F VAL* 5.4 0.4 - - + -
252F LEU 2.8 9.0 + - - +
253F ILE* 3.4 10.2 - - + +
254F THR* 2.8 28.8 + - - +
280F VAL* 4.0 9.9 - - + -
281F VAL* 1.3 74.1 - - - +
283F ASP* 1.3 62.6 + - - +
284F LEU* 3.8 23.3 + - + -
309F TYR* 3.9 7.9 - - + +
311F PRO* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F THR* 3.0 19.1 + - - +
281F VAL* 3.9 7.4 + - + -
282F VAL* 1.3 72.9 - - - +
284F LEU* 1.3 61.0 + - - +
285F ALA* 3.4 7.5 + - - +
286F ALA* 3.5 13.2 + - - +
290F GLY* 3.6 6.6 - - - -
291F ASN* 3.2 36.9 + - - +
292F CYS* 4.3 2.9 - - + +
295F THR* 3.2 37.0 + - + +
309F TYR 3.0 14.1 + - - +
310F GLY* 3.7 0.3 - - - -
311F PRO* 3.1 18.4 - - - +
----------------------------------------------------------
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