Contacts of the strand formed by residues 243 - 249 (chain B) in PDB entry 3O9Z
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 THR 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL 3.2 9.6 - - - -
158B THR* 3.8 20.0 - - - +
232B VAL* 3.9 12.0 - - - +
236B LEU* 4.7 4.0 - - - +
241B LYS* 3.6 14.4 - - - +
242B ARG* 1.3 89.7 - - + +
244B TYR* 1.3 63.5 + - - +
245B ARG* 3.4 22.6 + - - +
255B GLU* 4.4 2.3 - - - +
257B SER* 3.3 18.4 + - - -
313B EDO 3.9 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 3.5 32.6 - - + +
157B VAL* 2.8 44.8 + - + +
232B VAL* 4.3 2.9 - - + -
233B PRO* 3.4 40.4 - - + +
236B LEU* 3.6 23.1 - - + -
243B THR* 1.3 76.8 - - - +
245B ARG* 1.3 60.6 + - - +
246B SER* 3.5 15.2 + - - -
253B GLU* 2.6 23.8 + - - -
255B GLU* 3.5 25.4 - - + -
308B PHE* 4.5 5.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR 3.5 4.7 - - - -
156B TYR* 3.5 27.8 + - + +
157B VAL 4.3 4.3 - - - +
158B THR* 3.5 9.4 + - - -
243B THR* 3.4 21.8 + - - +
244B TYR* 1.3 77.9 - - - +
246B SER* 1.3 58.5 + - - +
255B GLU* 2.8 14.0 + - - -
256B PHE* 2.8 55.1 + - + -
257B SER* 2.9 37.7 + - - +
260B PHE* 3.6 33.5 - - - +
261B THR* 5.6 1.8 - - - +
312B AKG 3.0 40.6 + - - -
313B EDO 4.4 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL 3.8 1.0 + - - +
154B LEU* 3.5 6.8 - - - +
155B THR* 2.9 36.6 + - - +
244B TYR* 3.5 27.6 + - - -
245B ARG* 1.3 75.7 - - - +
247B ILE* 1.3 59.2 + - - +
248B ALA* 4.4 1.4 + - - +
253B GLU* 2.4 42.9 + - - +
254B VAL 3.3 5.2 - - - -
255B GLU* 4.5 0.7 - - - -
256B PHE* 3.8 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.2 5.8 - - + -
139B LEU* 3.7 23.1 - - + -
152B VAL* 3.7 25.8 - - + -
153B VAL 3.6 2.2 - - - -
154B LEU* 3.8 13.2 - - + -
189B LEU* 4.5 4.5 - - + -
190B LEU* 4.3 11.7 - - + -
193B LEU* 3.8 28.9 - - + -
194B PHE* 4.4 4.3 - - + -
246B SER* 1.3 73.9 - - - +
248B ALA* 1.3 60.9 + - - +
249B VAL* 4.2 11.4 + - + +
252B GLU* 4.1 0.5 - - - +
253B GLU* 3.4 2.8 - - - -
254B VAL* 2.8 48.6 + - + +
256B PHE* 3.9 11.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASP 3.7 0.5 - - - +
152B VAL* 3.2 4.2 - - - +
153B VAL* 2.9 49.3 + - + +
246B SER* 4.2 1.5 - - - +
247B ILE* 1.3 71.8 - - - +
249B VAL* 1.3 63.1 + - - +
252B GLU 3.3 9.4 - - - +
253B GLU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.1 27.6 - - + -
143B LEU* 4.1 10.1 - - + -
150B LYS* 3.5 32.5 - - + -
151B ASP 3.5 7.2 - - - +
152B VAL* 3.7 17.5 - - + -
194B PHE* 4.4 3.1 - - + -
247B ILE* 4.2 17.9 - - + +
248B ALA* 1.3 79.0 - - - +
250B ASP* 1.3 81.2 + - + +
251B GLY 3.0 3.3 - - - +
252B GLU* 2.9 30.0 + - + +
254B VAL* 6.4 0.2 - - + -
----------------------------------------------------------
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