Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 6PUO
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 ILE 237 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.4 24.0 - - + -
165B ASP* 4.7 9.6 - - - +
202B GLY 6.4 0.7 - - - -
203B ALA 4.1 8.1 + - - +
204B TRP* 3.4 38.5 - - + +
205B ILE* 3.5 19.2 + - - +
234B GLY* 3.7 15.9 - - - +
235B GLU 3.5 10.3 - - - +
236B LEU* 1.3 75.8 - - - +
238B THR* 1.3 62.8 + - - +
239B ILE* 4.2 4.1 + - + +
282B SER* 4.5 6.5 - - - +
283B HIS* 4.4 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 3.4 32.5 - - + -
218B VAL* 5.9 1.3 - - + -
222B VAL* 4.1 27.2 - - + +
236B LEU* 4.9 6.3 - - + +
237B ILE* 1.3 79.7 - - - +
239B ILE* 1.3 63.8 + - - +
280B ASN 4.3 2.1 + - - -
281B HIS* 3.3 25.2 + - + +
282B SER* 2.9 36.8 + - - -
283B HIS* 3.0 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B MET* 4.6 27.4 - - + -
164B LEU* 5.4 6.1 - - + -
170B LEU* 6.6 0.2 - - + -
204B TRP* 5.4 18.2 - - + -
205B ILE 3.1 8.6 + - - +
206B ILE* 3.9 39.0 - - + -
207B THR* 3.5 22.2 + - - +
237B ILE* 5.0 4.5 - - + +
238B THR* 1.3 78.2 - - - +
240B GLY* 1.3 61.4 + - - +
241B VAL* 4.7 5.8 - - + -
281B HIS* 4.3 4.8 + - - -
283B HIS* 3.4 26.0 - - + +
285B ILE* 4.6 16.6 - - + -
305B LEU* 4.9 6.5 - - + -
309B ILE* 6.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR 3.3 6.5 - - - -
208B GLY 4.5 0.2 - - - -
209B GLY* 4.0 18.6 - - - -
239B ILE* 1.3 78.8 - - - +
241B VAL* 1.3 62.5 + - - -
242B ALA* 3.9 0.9 + - - +
281B HIS* 5.0 4.2 - - - +
283B HIS 2.9 13.4 + - - -
284B PHE* 3.6 9.6 - - - -
285B ILE 2.9 28.8 + - - +
286B LEU* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 4.6 20.4 - - + -
207B THR 2.9 12.9 + - - +
208B GLY* 3.3 20.6 - - - -
209B GLY 3.9 0.6 - - - +
239B ILE* 4.7 9.9 - - + -
240B GLY* 1.3 72.8 - - - -
242B ALA* 1.3 62.7 + - - +
285B ILE* 3.3 23.3 - - + +
287B VAL* 4.6 13.7 - - + -
298B GLU* 3.9 32.6 - - + +
301B LEU* 5.3 6.1 - - + -
302B ARG* 4.8 16.8 - - + +
305B LEU* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY* 4.4 20.2 - - - +
210B SER* 5.2 3.6 - - - +
240B GLY 3.9 1.3 + - - +
241B VAL* 1.3 77.1 - - - +
243B THR* 1.3 64.9 + - - +
247B VAL* 5.4 0.9 - - + -
277B LEU* 4.9 8.1 - - + -
284B PHE* 6.1 0.9 - - + -
285B ILE 3.0 6.3 + - - -
286B LEU* 3.0 22.4 - - + -
287B VAL* 2.9 30.1 + - - +
298B GLU* 4.6 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 1.3 73.8 - - - +
244B TRP* 1.3 65.6 + - - +
245B GLY* 3.3 10.8 + - - +
246B THR* 3.5 20.6 + - - +
247B VAL* 3.4 17.4 - - - +
286B LEU* 4.8 0.4 - - - -
287B VAL* 3.5 9.4 - - - +
288B ASP* 5.6 1.8 - - - -
289B ASP* 5.8 2.0 - - + +
291B THR 5.8 0.9 - - - +
294B GLN 4.1 16.3 + - - +
295B TYR* 5.2 2.6 - - - -
296B GLY 4.6 5.2 + - - -
297B VAL* 3.9 27.0 + - + -
298B GLU* 4.0 18.2 + - - +
----------------------------------------------------------
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