Contacts of the helix formed by residues 235 - 246 (chain B) in PDB entry 2YZ2
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 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 6.1 1.1 - - - -
199B GLU* 3.5 27.2 + - + +
233B PHE 3.6 3.6 + - - +
234B PHE* 1.3 75.9 - - - +
236B SER* 1.3 66.7 + - - +
237B LYS 3.8 1.8 + - - -
238B MET* 2.7 48.6 + - + +
239B LEU* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLU* 5.1 0.6 + - - -
237A LYS* 3.6 35.5 - - - +
256A ASP* 3.5 25.1 + - - +
259A LEU* 6.1 0.3 - - - +
235B THR* 1.3 73.6 - - - +
237B LYS* 1.3 61.4 + - - +
239B LEU* 3.2 12.0 + - - +
240B VAL* 3.2 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 3.3 35.1 + - - +
237A LYS* 5.6 0.9 - - + +
199B GLU* 2.9 39.0 - - + +
203B ASN* 4.4 16.6 - - - +
235B THR* 3.3 2.6 + - - -
236B SER* 1.3 76.8 - - - +
238B MET* 1.3 71.4 + - - +
239B LEU 3.1 1.6 - - - -
240B VAL* 3.2 8.5 + - - +
241B MET* 2.9 38.9 + - + +
256B ASP* 4.2 6.4 + - - -
258B GLU* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ILE* 4.5 16.8 - - + -
199B GLU* 3.8 33.4 - - + +
202B ILE* 5.3 2.9 - - + -
225B PHE* 5.5 2.9 - - - -
226B LEU* 4.6 5.1 - - + +
233B PHE 4.0 5.4 - - - +
234B PHE* 3.4 36.1 - - + -
235B THR* 2.7 62.0 + - + +
237B LYS* 1.3 77.4 - - - +
239B LEU* 1.4 52.6 + - - +
241B MET* 2.9 22.1 + - + +
242B ARG* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP* 6.4 2.0 - - + -
231B PRO* 4.0 24.5 - - + +
234B PHE* 3.8 31.0 - - + +
235B THR 3.0 15.2 + - - +
236B SER* 3.4 11.7 - - - +
237B LYS 3.1 0.2 - - - -
238B MET* 1.4 72.3 - - - +
240B VAL* 1.3 66.4 + - + +
242B ARG* 3.5 13.2 - - - +
243B ARG* 3.5 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 3.7 36.1 - - + -
236B SER* 3.2 16.3 + - - +
237B LYS* 3.7 10.3 - - - +
238B MET 3.2 0.2 - - - -
239B LEU* 1.3 78.9 - - + +
241B MET* 1.3 64.7 + - - +
242B ARG 3.1 0.4 + - - -
243B ARG* 3.7 11.1 + - - +
244B LEU* 3.1 26.3 + - + +
258B GLU* 3.8 35.4 - - + +
259B LEU* 5.4 3.8 - - + +
260B LEU 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 4.7 3.1 - - + +
202B ILE* 4.2 19.7 - - + -
203B ASN* 5.0 5.8 - - - +
226B LEU* 3.8 12.3 - - + -
237B LYS* 2.9 40.1 + - + +
238B MET* 2.9 37.2 + - + +
240B VAL* 1.3 77.9 - - - +
242B ARG* 1.3 54.5 + - - +
244B LEU* 3.3 3.0 - - - +
245B VAL* 2.9 35.8 + - - +
251B PRO* 3.4 31.2 - - + +
252B PHE* 4.5 17.9 - - - -
258B GLU* 4.0 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.0 33.2 + - + +
227B GLU 3.8 13.7 + - - -
228B LYS* 5.3 1.8 + - - +
229B TYR 4.5 4.9 + - - -
231B PRO* 3.7 45.1 - - - +
234B PHE* 4.0 5.6 - - + -
238B MET 2.9 11.0 + - - +
239B LEU* 3.5 18.1 - - - +
240B VAL 3.1 0.2 - - - -
241B MET* 1.3 73.6 - - - +
243B ARG* 1.3 57.2 + - + +
245B VAL* 3.0 7.7 + - - +
246B LEU* 2.5 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASP* 3.2 29.9 + - - -
260A LEU* 5.0 17.6 - - - +
239B LEU* 3.5 16.1 + - - +
240B VAL* 3.8 11.4 - - - +
242B ARG* 1.3 75.6 - - + +
244B LEU* 1.3 71.4 + - - +
246B LEU* 3.1 25.6 + - - +
247B LYS 4.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 3.1 13.4 + - + +
241B MET* 3.3 11.7 - - - +
243B ARG* 1.3 83.8 - - - +
245B VAL* 1.3 60.8 + - - +
247B LYS 3.7 2.1 - - - +
248B GLY* 3.6 7.1 - - - -
249B GLU* 3.3 48.0 + - + -
251B PRO* 3.5 33.0 - - + -
254B MET* 3.6 24.2 - - + -
258B GLU* 3.9 23.3 - - + +
260B LEU* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B MET* 3.8 18.2 - - + +
226B LEU* 3.3 27.1 - - + -
227B GLU* 3.5 36.3 - - + +
241B MET 2.9 24.3 + - - +
242B ARG* 3.3 7.2 - - - +
244B LEU* 1.3 71.1 - - - +
246B LEU* 1.3 54.2 + - - +
247B LYS* 2.4 27.7 + - - -
248B GLY 3.3 2.8 + - - -
249B GLU 3.6 10.3 - - - +
251B PRO* 3.3 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 3.7 34.8 - - + +
242B ARG* 2.5 67.4 + - + +
243B ARG* 3.1 18.0 + - - +
245B VAL* 1.3 66.2 - - - +
247B LYS* 1.3 73.2 + - - +
----------------------------------------------------------
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