Contacts of the strand formed by residues 250 - 256 (chain V) in PDB entry 3FKS
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 ASP 250 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V ARG* 6.1 7.4 - - + -
178V HIS* 2.8 41.8 - - + +
179V GLY 4.9 6.9 - - - +
180V GLY* 3.7 7.4 - - - -
181V PHE 3.8 0.2 + - - -
249V GLN* 1.3 81.3 + - - +
251V VAL* 1.3 61.8 + - - +
302V GLY* 5.1 1.4 - - - -
303V SER* 2.7 30.7 + - - +
305V THR* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178V HIS* 4.5 1.7 + - - -
181V PHE* 3.8 11.2 - - + +
183V VAL* 5.0 3.6 - - + -
240V ALA* 3.2 51.4 - - + +
243V PHE* 3.5 30.3 - - + -
244V ARG* 3.6 10.1 - - + +
249V GLN 3.6 8.1 - - - +
250V ASP* 1.3 77.7 - - - +
252V LEU* 1.3 71.3 + - - +
253V LEU 4.0 0.9 - - - -
303V SER 3.1 4.7 + - - +
304V VAL* 3.7 17.4 - - + -
305V THR* 3.2 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174V ILE* 4.2 19.3 - - + -
175V ALA* 4.6 4.3 - - - -
178V HIS* 3.5 34.8 - - + +
181V PHE 2.9 18.8 + - - +
182V SER* 3.2 10.8 - - - +
183V VAL 2.9 24.1 + - - -
251V VAL* 1.3 76.3 - - - +
253V LEU* 1.3 62.8 + - - +
254V PHE* 3.5 38.8 - - + -
305V THR* 3.9 19.5 - - + +
307V VAL* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183V VAL* 3.3 27.4 - - + +
185V THR* 3.9 10.8 - - - +
236V GLY 3.4 20.4 - - - +
237V LEU* 3.7 35.2 - - + -
240V ALA* 3.8 20.0 - - + -
251V VAL 4.0 0.4 - - - -
252V LEU* 1.3 73.6 - - - +
254V PHE* 1.3 63.5 + - - +
255V ILE* 3.5 24.0 - - + +
296V ILE* 4.0 9.4 - - + -
304V VAL* 4.2 5.8 - - + +
305V THR 3.2 12.5 + - - +
306V SER* 3.6 5.7 - - - +
307V VAL 3.3 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 254 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ILE* 5.8 0.9 - - + -
170V LEU* 4.8 14.4 - - + -
171V ILE* 3.7 31.0 - - + -
174V ILE* 5.8 1.6 - - + -
175V ALA* 5.3 2.7 - - + -
182V SER* 4.5 9.4 - - - -
183V VAL 2.8 20.3 + - - +
184V PHE* 3.8 30.1 - + + -
185V THR* 2.8 32.2 + - - -
252V LEU* 3.5 46.9 - - + -
253V LEU* 1.3 73.8 - - - +
255V ILE* 1.3 62.8 + - - +
256V ASP* 6.1 0.2 - - + -
307V VAL* 3.6 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185V THR* 3.9 7.6 - - - -
187V VAL* 4.5 13.2 - - + -
233V ALA* 5.5 9.0 - - + +
253V LEU* 3.5 37.0 - - + +
254V PHE* 1.3 80.6 - - - +
256V ASP* 1.3 68.8 + - - +
257V ASN* 4.4 1.8 - - - -
258V ILE* 3.9 37.0 - - + +
292V LEU* 5.9 2.7 - - + -
296V ILE* 4.3 8.3 - - + -
306V SER* 3.8 15.5 - - - +
307V VAL 3.3 5.8 + - - +
308V GLN* 3.4 16.2 - - + +
309V ALA 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 256 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167V ILE* 3.8 24.9 - - + +
184V PHE* 4.0 22.2 - - + -
185V THR 3.1 6.6 + - - +
186V GLY* 3.1 6.8 - - - -
187V VAL 2.7 24.2 + - - +
189V GLU* 2.8 44.3 - - - +
254V PHE* 6.1 0.2 - - + -
255V ILE* 1.3 80.5 - - - +
257V ASN* 1.3 68.1 + - - +
309V ALA* 4.0 15.9 - - + +
----------------------------------------------------------
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