Contacts of the helix formed by residues 238 - 245 (chain C) in PDB entry 2CMH
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 ASN 238 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LEU 2.9 25.0 + - - -
250B LYS* 3.1 32.3 - - + +
253B GLN* 3.4 15.3 + - - +
228C ILE* 4.3 7.0 - - + -
237C TYR* 1.3 86.9 - - - +
239C GLU* 1.3 65.3 + - - +
240C ASP* 2.9 8.6 + - - +
241C ILE* 2.8 37.7 + - - +
242C HIS* 3.1 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C LEU* 3.8 15.7 - - + -
225C THR* 4.1 22.5 + - - -
228C ILE* 4.1 17.9 - - + +
229C GLU* 5.7 0.2 - - - +
238C ASN* 1.3 73.1 - - - +
240C ASP* 1.3 68.5 + - - +
242C HIS* 3.3 5.2 + - - +
243C ARG* 2.8 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 3.9 22.0 - - + +
248B LEU 5.1 0.7 + - - -
253B GLN* 2.8 24.8 - - - +
238C ASN* 2.9 8.4 + - - +
239C GLU* 1.3 79.2 - - - +
241C ILE* 1.3 60.3 + - + +
243C ARG* 4.0 4.3 - - - +
244C ALA* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ALA* 4.6 2.5 - - + -
248B LEU 2.7 42.4 - - - +
249B PRO* 3.5 10.3 - - + -
61C LEU* 4.2 11.4 - - + -
201C PRO* 3.7 16.2 - - + +
236C TYR* 3.5 50.0 - - + +
237C TYR* 4.9 3.1 - - + -
238C ASN* 2.8 40.2 + - - +
240C ASP* 1.3 69.9 - - + +
242C HIS* 1.3 66.0 + - - +
244C ALA* 4.3 4.7 - - - -
245C ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 5.1 2.9 - - - -
65C MET* 3.3 38.1 - - + +
69C THR* 3.9 5.4 - - + -
219C PRO 2.9 25.5 + - - -
220C LEU* 4.4 9.0 - - + -
223C LEU* 3.5 30.3 - - + +
237C TYR* 2.8 35.5 + - + +
238C ASN 3.1 14.4 + - - +
239C GLU* 3.3 12.1 + - - +
241C ILE* 1.3 81.7 - - - +
243C ARG* 1.3 63.8 + - - +
245C ALA* 3.3 16.2 - - - +
246C PHE* 3.5 11.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 3.4 52.9 + - + +
223C LEU* 4.3 18.3 + - + +
239C GLU* 2.8 47.3 + - + +
240C ASP* 4.2 3.1 - - - +
242C HIS* 1.3 77.2 - - - +
244C ALA* 1.3 66.9 + - - +
245C ALA 3.2 0.9 + - - -
246C PHE* 3.2 16.8 + - - +
247C ALA* 4.0 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ALA* 4.1 24.3 - - + +
247B ALA* 3.6 22.0 - - + -
199C VAL* 5.4 1.7 - - - +
201C PRO* 4.0 13.0 - - + +
240C ASP 2.9 19.9 + - - +
241C ILE 3.8 3.4 - - - +
243C ARG* 1.3 76.4 - - - +
245C ALA* 1.3 62.5 + - - +
247C ALA* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.7 4.0 - - + -
65C MET* 4.5 5.6 - - + -
198C PHE* 3.1 19.7 - - + +
199C VAL* 3.0 49.4 + - - +
201C PRO* 3.7 9.6 - - + +
241C ILE 2.9 13.4 + - - +
242C HIS* 3.3 16.4 - - - +
243C ARG 3.1 0.6 - - - -
244C ALA* 1.3 76.5 - - - +
246C PHE* 1.3 59.0 + - + +
247C ALA 3.8 2.1 + - - +
----------------------------------------------------------
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