Contacts of the strand formed by residues 226 - 233 (chain B) in PDB entry 2OB1
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 226 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.1 11.8 - - - -
196B THR 2.9 17.3 - - - -
225B HIS* 1.3 75.9 - - - +
227B LEU* 1.3 59.5 + - - -
327B GLN* 3.3 7.8 - - - +
328B TRP* 2.9 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 3.7 24.7 - - + +
92B PHE* 3.8 33.7 - - + -
196B THR 2.8 8.8 + - - +
197B ILE* 3.2 8.5 - - + +
198B VAL 2.8 25.2 + - - +
226B GLY* 1.3 74.0 - - - +
228B TRP* 1.3 68.2 + - - +
229B ILE* 3.7 22.2 - - + -
325B LYS* 3.8 23.6 - - + -
326B ALA 3.2 8.7 - - - +
327B GLN* 3.6 25.1 - - + +
328B TRP* 3.7 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.8 15.7 - - + -
198B VAL* 3.3 34.9 - - + +
200B SER* 2.8 25.7 + - - -
204B LEU* 4.7 6.7 - - + -
215B LEU* 3.8 8.1 - - + -
216B ILE* 3.5 48.7 - - + -
219B ILE* 3.7 20.2 - - + -
220B MET* 3.8 18.6 - - + -
227B LEU* 1.3 72.7 - - - +
229B ILE* 1.3 74.6 + - - +
230B SER* 4.0 4.3 - - - -
275B TRP* 3.3 31.7 - + + +
324B MET* 3.4 3.4 - - + +
325B LYS* 3.3 5.0 - - - -
326B ALA* 2.7 37.3 + - + +
328B TRP* 3.6 7.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.0 15.0 - - + +
88B ALA* 3.6 16.2 - - + -
89B ILE* 3.4 47.8 - - + +
197B ILE* 3.9 9.0 - - + -
198B VAL 2.8 11.1 + - - +
199B ILE* 3.4 8.8 - - + +
200B SER 2.9 24.3 + - - +
227B LEU* 3.7 25.1 - - + -
228B TRP* 1.3 76.5 - - - +
230B SER* 1.3 61.8 + - - +
323B LEU* 3.6 27.8 - - + -
324B MET 3.3 4.5 - - - +
325B LYS* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B SER* 2.7 28.3 + - - -
204B LEU* 3.7 5.5 - - - +
228B TRP* 4.0 1.3 - - - -
229B ILE* 1.3 73.7 - - - +
231B TYR* 1.3 58.5 + - - +
232B ASP* 3.8 0.9 + - - -
271B TYR* 2.6 30.3 + - - -
275B TRP* 3.8 20.0 - - - -
322B ILE* 3.7 1.3 - - - +
323B LEU* 3.5 6.9 - - - +
324B MET* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLY 4.3 5.4 + - - -
81B ARG* 3.4 55.2 + - + +
85B ILE* 3.9 24.9 - - + -
200B SER 3.0 6.7 + - - +
201B GLU* 4.2 8.1 - - + -
202B CYS* 2.8 47.2 + - - -
229B ILE 4.4 0.2 + - - -
230B SER* 1.3 75.5 + - - +
232B ASP* 1.3 67.2 + - - +
271B TYR* 4.3 0.2 - - - -
286B MET* 3.7 33.8 - - + +
318B GLN* 4.6 3.1 + - - -
321B TYR* 3.3 33.3 - + + +
322B ILE 3.3 15.0 - - - -
323B LEU* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B CYS* 3.4 7.6 - - - -
203B LEU 3.9 0.2 + - - -
204B LEU* 3.6 10.9 + - - +
205B CYS* 3.1 46.5 + - + +
230B SER* 3.8 1.2 + - - -
231B TYR* 1.3 85.4 - - - +
233B PRO* 1.3 69.4 - - + +
271B TYR* 2.3 46.4 + - + +
321B TYR* 3.3 8.8 - - - -
322B ILE* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B CYS* 4.6 5.8 - - - -
205B CYS* 3.8 13.3 - - + +
232B ASP* 1.3 102.9 - - + +
234B ILE* 1.3 65.9 + - - +
247B MET* 3.3 27.4 - - + -
259B MET* 3.9 19.5 - - + -
262B LEU* 3.6 17.8 - - + +
265B TYR 4.7 0.7 - - - +
271B TYR* 4.6 2.6 - - - -
320B HIS 3.0 11.9 - - - +
321B TYR* 3.7 22.6 - - + -
----------------------------------------------------------
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