Contacts of the helix formed by residues 236 - 241 (chain B) in PDB entry 2GH0
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 236 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TYR* 5.2 0.7 - - + -
186B CYS* 3.3 40.2 - - + +
233B ASN* 2.8 15.5 + - - -
234B THR 3.2 1.2 - - - -
235B ILE* 1.3 80.1 - - - +
237B PRO* 1.3 64.8 - - - +
238B ASN 3.2 3.1 - - - -
239B CYS* 3.0 4.2 + - + +
240B ALA 2.9 23.4 + - - -
205D TRP* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG* 3.5 33.0 - - - +
233B ASN* 3.5 21.8 - - - +
235B ILE* 3.4 9.6 - - + +
236B ALA* 1.3 90.0 - - - +
238B ASN* 1.3 66.9 + - - +
240B ALA* 4.2 4.3 - - + +
241B LEU* 3.0 53.9 + - + +
303B ASN* 3.7 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG* 5.6 2.6 + - - -
233B ASN* 4.8 11.5 + - - +
236B ALA 3.2 1.4 + - - -
237B PRO* 1.3 83.7 - - - +
239B CYS* 1.3 58.4 + - - +
241B LEU 4.1 6.8 - - - +
243B PRO* 5.9 2.4 - - - +
204D THR* 5.9 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B CYS* 3.5 16.4 - - - +
188B GLY 5.5 0.9 - - - +
191B CYS* 2.1 52.5 - - + -
193B ARG* 3.0 32.7 - - - +
196B CYS* 3.4 26.2 - - - -
236B ALA* 3.0 7.7 + - + +
238B ASN* 1.3 81.5 - - - +
240B ALA* 1.3 59.0 + - - +
241B LEU 3.4 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 3.7 12.6 + - - +
196B CYS* 4.1 7.4 - - - -
197B LEU* 3.4 35.1 - - + +
200B LEU* 3.9 11.9 - - + -
235B ILE* 3.9 15.9 - - + +
236B ALA 2.9 17.3 + - - +
237B PRO* 4.3 2.9 - - + -
239B CYS* 1.3 77.5 - - - +
241B LEU* 1.3 69.1 + - + +
242B PRO* 4.4 1.6 - - - +
301B THR* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 4.1 3.4 - - - -
235B ILE* 5.1 0.7 - - + -
237B PRO* 3.0 40.8 + - + +
238B ASN 4.1 7.1 - - - +
239B CYS 4.0 6.6 - - - +
240B ALA* 1.3 83.8 - - + +
242B PRO* 1.3 77.7 - - + +
243B PRO* 3.5 3.6 - - - +
301B THR* 3.8 43.7 - - + +
303B ASN* 4.8 12.3 - - + +
315B SER* 3.9 27.6 - - - +
----------------------------------------------------------
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