Contacts of the helix formed by residues 236 - 247 (chain C) in PDB entry 2O2C
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 ASP 236 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP* 3.5 11.3 - - - +
396B GLN* 2.8 30.7 + - + +
465B SER* 4.4 8.1 + - - -
472B HIS* 4.6 0.3 + - - -
473B HIS* 4.7 4.0 - - - -
476B PHE* 3.7 30.0 - - + -
234C ASN* 3.1 30.8 + - + +
235C VAL* 1.3 78.2 - - - +
237C GLY* 1.3 62.4 + - - +
238C THR* 2.9 32.3 + - - -
239C HIS* 3.0 13.3 + - - +
240C ILE* 4.3 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B SER* 5.5 0.8 + - - -
467B ASN* 4.4 7.9 - - - -
469B ILE* 3.6 13.4 - - - +
472B HIS* 3.7 30.9 - - - +
473B HIS* 5.1 2.0 - - - +
235C VAL 3.1 5.1 + - - -
236C ASP* 1.3 73.4 + - - +
238C THR* 1.3 56.5 + - - +
239C HIS 3.3 0.4 - - - -
240C ILE* 3.3 7.1 - - - +
241C ALA* 3.0 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ASP* 5.3 0.3 + - - -
396B GLN* 3.9 19.7 - - + -
397B TYR* 3.4 43.5 - - + -
465B SER* 4.4 4.3 + - - -
466B GLN 5.5 0.3 + - - -
467B ASN* 3.0 26.9 + - - +
7006B GOL 4.3 2.0 - - - -
236C ASP* 3.3 21.8 + - - -
237C GLY* 1.3 77.1 - - - +
239C HIS* 1.3 57.6 + - - +
241C ALA* 4.1 0.2 - - - -
242C GLU* 2.9 34.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLN* 3.6 32.6 + - + +
439B ASN* 5.0 0.2 - - - -
7006B GOL 3.4 24.5 + - - -
231C PHE 3.4 22.2 + - - -
232C VAL* 4.4 7.6 - - + -
233C SER* 3.1 26.5 + - - -
234C ASN* 3.0 34.6 + - + +
236C ASP 3.0 13.4 + - - +
238C THR* 1.3 81.1 - - - +
240C ILE* 1.3 61.7 + - - +
242C GLU* 4.3 0.7 - - - +
243C VAL* 3.4 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ILE* 3.9 22.7 - - + -
472B HIS* 4.0 18.2 - - + +
203C ILE* 5.4 1.3 - - + -
232C VAL* 4.3 21.2 - - + +
236C ASP 4.3 0.6 + - - -
237C GLY* 3.3 12.1 - - - +
239C HIS* 1.3 78.8 - - - +
241C ALA* 1.3 62.0 + - - +
243C VAL* 3.4 2.8 + - + +
244C LEU* 2.9 52.6 + - + +
254C PHE* 5.6 2.5 - - + -
269C ASN* 3.5 34.1 + - - +
272C SER* 4.2 6.3 - - - -
273C ALA* 3.8 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASN* 3.7 26.9 - - - +
469B ILE* 3.9 20.0 - - + -
237C GLY 3.0 19.4 + - - +
238C THR 3.6 4.7 - - - +
239C HIS 3.3 0.2 - - - -
240C ILE* 1.3 79.7 - - - +
242C GLU* 1.3 61.2 + - + +
244C LEU* 3.3 9.1 + - - +
245C LYS* 3.2 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LYS* 3.5 15.3 + - - +
225B ARG* 2.9 42.7 + - - -
397B TYR* 2.5 31.9 + - + +
467B ASN* 4.7 1.3 + - - +
7006B GOL 3.7 28.0 - - - +
238C THR* 2.9 21.0 + - + +
239C HIS 4.3 1.1 - - - +
241C ALA* 1.3 74.7 - - + +
243C VAL* 1.3 64.1 + - + +
245C LYS* 3.4 15.1 + - - +
246C SER* 2.9 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7006B GOL 5.7 0.9 - - - +
201C VAL* 3.8 37.0 - - + -
230C HIS* 4.0 19.3 - - + +
231C PHE 5.0 6.5 - - - +
232C VAL* 3.7 17.7 - - + -
239C HIS* 3.4 21.2 + - + +
240C ILE* 3.4 5.3 + - + +
241C ALA 3.3 0.4 - - - -
242C GLU* 1.3 78.8 - - + +
244C LEU* 1.3 65.4 + - + +
246C SER* 3.1 15.5 + - - -
247C ILE* 3.1 24.6 + - + +
254C PHE* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ILE* 5.5 9.2 - - + -
240C ILE* 2.9 43.9 + - + +
241C ALA* 3.3 9.8 + - - +
243C VAL* 1.3 77.0 - - + +
245C LYS* 1.3 61.0 + - + +
247C ILE* 3.8 34.5 - - + +
249C ILE* 4.4 7.2 - - + -
254C PHE* 4.8 7.2 - - + -
272C SER 5.2 1.3 - - - +
273C ALA* 5.5 0.2 - - - -
276C ALA* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ARG* 3.7 28.2 - - - +
467B ASN* 4.6 15.6 + - - -
241C ALA* 3.2 17.9 + - - +
242C GLU* 3.6 26.2 - - - +
243C VAL 3.2 0.4 - - - -
244C LEU* 1.3 78.1 - - + +
246C SER* 1.3 58.2 + - - +
247C ILE 4.7 2.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
199C HIS* 3.6 15.6 - - - -
230C HIS* 4.0 20.3 - - - -
242C GLU* 2.9 17.8 + - - -
243C VAL* 3.1 7.2 + - - -
245C LYS* 1.3 80.2 - - - +
247C ILE* 1.3 59.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
199C HIS* 4.0 12.3 - - + +
201C VAL* 4.1 2.5 - - + -
230C HIS* 3.7 31.9 - - + +
243C VAL* 3.3 27.1 - - + +
244C LEU* 3.8 30.0 - - + +
245C LYS 4.7 2.6 - - - +
246C SER* 1.3 79.1 - - - +
248C ASP* 1.3 60.2 - - - +
249C ILE* 3.9 12.9 + - + +
252C THR* 3.6 28.3 - - + +
254C PHE* 4.0 19.3 - - + -
----------------------------------------------------------
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