Contacts of the helix formed by residues 237 - 247 (chain C) in PDB entry 2GRA
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 ALA 237 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C SER* 5.8 2.0 - - - -
236C GLY* 1.3 73.8 - - - +
238C THR* 1.3 65.6 + - - +
240C HIS* 3.7 11.3 + - - +
241C ALA* 3.2 20.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
228C LYS* 5.4 1.3 - - + +
231C VAL* 3.7 25.0 + - + +
232C SER* 3.6 19.7 - - - +
233C SER 5.0 0.7 - - - -
236C GLY 3.0 3.0 + - - -
237C ALA* 1.3 75.4 - - - +
239C ILE* 1.3 61.8 + - - +
240C HIS 2.9 1.1 - - - -
241C ALA* 2.6 30.8 + - - +
242C LEU* 2.9 31.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 6.1 0.2 - - - -
232C SER* 3.4 17.6 + - - +
233C SER 3.7 8.1 - - - +
234C PRO 4.0 2.7 - - - +
235C GLY 3.8 4.3 - - - +
236C GLY* 3.2 29.3 + - - -
238C THR* 1.3 82.1 - - - +
240C HIS* 1.3 73.8 + - + +
242C LEU* 3.7 11.9 + - + +
243C HIS* 3.3 19.6 + - - +
190D ASP* 3.6 27.4 - - + +
193D VAL* 3.6 20.2 - - + -
194D LYS* 3.4 28.6 - - + +
199D ARG* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C GLY 3.7 10.3 + - - -
236C GLY* 3.1 29.8 - - - -
237C ALA* 3.7 12.3 + - - +
238C THR 2.8 4.8 + - - -
239C ILE* 1.3 82.6 - - + +
241C ALA* 1.3 66.1 + - - +
243C HIS* 3.2 17.8 + - - +
244C VAL* 3.4 5.5 + - - +
194D LYS* 3.5 36.6 + - + +
195D MET* 5.8 0.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
237C ALA 3.2 11.0 + - - +
238C THR* 2.6 17.1 + - - +
240C HIS* 1.3 74.9 - - - +
242C LEU* 1.3 67.2 + - + +
244C VAL* 2.8 33.7 + - + +
245C LEU* 3.3 4.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 3.7 41.5 - - + -
232C SER* 4.8 3.4 - - - +
238C THR* 2.9 38.5 + - + +
239C ILE* 3.8 17.3 - - + +
241C ALA* 1.3 74.7 - - + +
243C HIS* 1.3 54.5 - - - +
245C LEU* 2.6 48.5 + - + +
246C GLU* 2.8 20.8 + - + +
190D ASP* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ILE 3.3 10.1 + - - +
240C HIS 3.2 12.5 + - - +
242C LEU* 1.3 77.2 - - - +
244C VAL* 1.3 57.4 + - - +
246C GLU* 3.5 11.3 + - + +
247C SER* 2.9 36.1 + - - -
194D LYS* 2.9 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C HIS 3.4 4.6 + - - +
241C ALA* 2.8 26.2 + - + +
243C HIS* 1.3 78.5 - - - +
245C LEU* 1.3 76.7 + - + +
247C SER* 3.5 12.9 + - - -
248C GLY* 3.6 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ALA* 4.0 7.4 - - + +
242C LEU* 2.6 37.1 + - + +
244C VAL* 1.3 80.5 - - + +
246C GLU* 1.3 57.2 + - + +
247C SER 3.0 1.3 - - - -
248C GLY* 2.4 34.4 + - - -
249C GLY 3.2 4.2 + - - -
250C PHE* 3.5 56.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LYS* 5.8 1.4 - - - +
242C LEU* 2.8 22.1 + - + +
243C HIS* 3.7 16.2 - - + +
245C LEU* 1.3 78.7 - - + +
247C SER* 1.3 56.9 + - - +
248C GLY 3.1 3.6 + - - -
249C GLY* 3.4 11.6 + - - +
250C PHE* 5.0 1.6 - - - +
251C ARG* 3.2 51.1 + - - +
190D ASP* 4.5 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C HIS* 2.9 33.3 + - - -
244C VAL* 3.7 10.3 - - - -
245C LEU 2.8 0.6 + - - -
246C GLU* 1.3 75.4 - - - +
248C GLY* 1.3 56.6 + - - +
249C GLY 3.6 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