Contacts of the strand formed by residues 286 - 293 (chain B) in PDB entry 3BFO
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 GLY 286 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LYS* 4.7 0.4 - - - -
263B ASN* 3.6 12.6 - - - -
284B HIS 3.5 2.0 + - - -
285B GLN* 1.3 79.6 - - - +
287B THR* 1.3 64.2 + - - -
288B TYR* 3.6 11.9 - - - -
305B GLU* 3.5 3.7 - - - +
306B ILE 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE 4.0 0.2 - - - +
262B LYS* 3.4 2.6 - - - -
263B ASN* 2.9 36.1 + - - -
286B GLY* 1.3 73.4 - - - -
288B TYR* 1.3 63.5 + - - +
289B TRP* 4.6 3.6 - - + -
303B LYS* 3.4 43.1 - - + +
304B VAL 3.4 12.8 - - - +
305B GLU* 3.8 20.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.8 11.7 - - + +
246B LEU* 3.6 24.7 - - + -
260B TRP* 4.7 4.9 - + + -
261B PHE 3.2 14.1 - - - +
262B LYS* 3.7 30.2 - - + +
267B LEU* 3.9 10.1 - - + -
275B TYR* 3.6 25.6 + + - -
284B HIS* 2.6 38.8 + - - +
286B GLY 3.6 20.9 - - - -
287B THR* 1.3 73.9 - - - +
289B TRP* 1.3 68.2 + - - +
303B LYS* 3.4 2.1 - - - -
304B VAL* 2.9 40.8 + - + +
306B ILE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PRO* 5.4 0.4 - - - -
260B TRP* 3.5 11.1 - - - -
261B PHE* 2.8 81.4 + + + +
264B GLU* 4.7 30.5 + - - +
287B THR* 4.6 4.9 - - + -
288B TYR* 1.3 84.4 - - - +
290B CYS* 1.3 66.0 + - - +
291B HIS* 3.9 7.4 - - + -
300B ASP* 3.0 39.5 - - + -
301B SER* 3.4 16.2 - - - +
302B LYS 3.8 7.9 - - - +
303B LYS* 3.9 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B CYS* 3.9 17.7 - - + -
258B TYR* 3.8 31.4 - - - -
259B GLN 3.4 18.6 - - - -
260B TRP* 3.8 33.2 - - + -
289B TRP* 1.3 80.0 - - - +
291B HIS* 1.3 64.5 + - - +
292B VAL* 3.8 4.3 + - - +
300B ASP* 3.5 1.4 - - - -
301B SER* 2.8 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B HIS 3.7 0.5 - - - +
258B TYR* 3.3 5.5 - - - -
259B GLN* 2.9 33.4 + - + +
261B PHE* 3.8 23.3 - + + -
289B TRP* 3.9 5.0 - + + -
290B CYS* 1.3 70.7 - - - +
292B VAL* 1.3 61.0 + - - +
293B TYR* 3.6 34.7 - + + +
298B SER* 3.4 36.9 - - - -
299B GLN 3.9 2.9 + - - -
300B ASP* 2.6 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 4.1 10.2 - - + +
229B ILE* 3.7 15.3 - - + -
248B CYS* 3.7 30.1 - - - -
250B ALA* 3.5 28.7 - - + -
256B PRO* 3.8 11.2 - - + -
257B HIS 3.3 9.2 - - - +
258B TYR* 3.8 13.2 - - + -
290B CYS* 4.0 5.6 - - - +
291B HIS* 1.3 78.3 - - - +
293B TYR* 1.4 64.6 + - - +
298B SER* 3.2 3.8 - - - -
299B GLN 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.5 6.5 - - - -
257B HIS* 2.8 80.2 + + + +
258B TYR 4.1 12.1 + - - -
259B GLN* 4.7 6.8 - - + +
291B HIS* 3.6 27.1 - + - +
292B VAL* 1.4 78.7 - - - +
294B ASN* 1.3 73.4 + - - +
297B ASP 3.4 5.6 - - - +
298B SER* 3.7 16.6 - - - -
----------------------------------------------------------
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