Contacts of the strand formed by residues 243 - 249 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL 3.2 9.4 - - - -
158C THR* 3.7 21.8 - - - +
159C GLY 4.5 1.3 - - - +
232C VAL* 3.9 12.0 - - - +
236C LEU* 4.7 3.3 - - - +
241C LYS* 3.6 11.0 - - - +
242C ARG* 1.3 87.8 - - + +
244C TYR* 1.3 63.4 + - - +
245C ARG* 3.4 24.1 + - - +
255C GLU* 4.4 2.3 - - - +
257C SER* 3.1 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR* 3.4 36.2 + - + +
157C VAL* 2.7 43.2 + - + +
232C VAL* 4.3 7.9 - - + -
233C PRO* 3.4 38.5 - - + +
236C LEU* 3.5 25.4 - - + -
243C THR* 1.3 77.1 - - - +
245C ARG* 1.3 58.0 + - - +
246C SER* 3.5 17.9 + - - -
253C GLU* 2.8 29.3 + - - -
255C GLU* 3.5 17.7 - - + -
308C PHE* 4.4 5.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C THR 3.5 3.8 - - - -
156C TYR* 3.5 28.3 + - + +
157C VAL 4.4 6.3 - - - +
158C THR* 3.6 9.0 + - - -
243C THR* 3.4 20.7 + - - +
244C TYR* 1.3 76.1 - - - +
246C SER* 1.3 58.9 + - - +
255C GLU* 2.9 12.6 + - - +
256C PHE* 2.9 52.5 + - + -
257C SER* 3.0 39.2 + - - +
260C PHE* 3.6 34.5 - - - +
261C THR* 5.6 2.4 - - - +
312C AKG 3.0 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C VAL 3.7 1.4 + - - +
154C LEU* 3.4 6.9 - - - +
155C THR* 2.8 41.6 + - - +
244C TYR* 3.5 32.9 + - - -
245C ARG* 1.3 74.4 - - - +
247C ILE* 1.3 60.7 + - - +
248C ALA* 4.4 2.3 + - - +
253C GLU* 2.7 33.8 + - - +
254C VAL 3.4 5.8 - - - -
255C GLU* 4.4 1.6 - - - +
256C PHE* 3.9 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C LEU* 4.2 6.1 - - + -
139C LEU* 3.7 24.0 - - + -
152C VAL* 3.8 25.8 - - + -
153C VAL 3.7 2.5 - - - -
154C LEU* 3.8 13.5 - - + -
189C LEU* 4.3 4.9 - - + -
190C LEU* 4.3 12.8 - - + -
193C LEU* 3.8 27.6 - - + -
194C PHE* 4.5 4.0 - - + -
246C SER* 1.3 73.5 - - - +
248C ALA* 1.3 60.7 + - - +
249C VAL* 4.1 13.3 + - + +
253C GLU* 3.5 0.7 - - - -
254C VAL* 2.9 44.8 + - + +
256C PHE* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP 3.7 1.0 - - - +
152C VAL* 3.2 6.9 - - - +
153C VAL* 2.9 49.5 + - + +
246C SER* 4.2 1.5 - - - +
247C ILE* 1.3 71.4 - - - +
249C VAL* 1.3 60.2 + - - +
252C GLU 3.3 11.7 - - - +
253C GLU* 4.1 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.2 18.4 - - + -
143C LEU* 4.1 19.3 - - + -
150C LYS* 3.4 31.2 - - + -
151C ASP 3.6 9.2 - - - +
152C VAL* 3.7 23.8 - - + -
194C PHE* 4.4 2.9 - - + -
247C ILE* 4.3 16.8 - - + +
248C ALA* 1.3 76.6 - - - +
250C ASP* 1.3 76.3 + - + +
251C GLY 3.1 3.4 - - - -
252C GLU* 3.0 21.8 + - + +
----------------------------------------------------------
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