Contacts of the helix formed by residues 279 - 282 (chain X) in PDB entry 2W6C
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 TRP 279 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70X TYR* 3.6 40.1 - + - +
121X TYR* 4.0 33.4 - + - -
275X ILE 5.0 2.9 - - - -
276X ASP 6.4 0.2 - - - -
277X VAL 3.1 1.4 + - - -
278X GLU* 1.3 91.0 + - + +
280X ASN* 1.3 60.9 + - - +
281X VAL 3.1 6.8 + - - -
282X LEU* 3.7 36.1 + - + +
289X ARG 3.3 22.4 - - - -
290X PHE* 3.9 25.4 - + - -
291X SER* 3.8 8.3 - - - -
601X BM4 4.0 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 280 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247X GLU* 4.5 9.2 - - - +
251X ASN* 2.9 29.4 + - - +
276X ASP 4.9 1.6 + - - +
277X VAL* 2.9 34.7 + - - +
279X TRP* 1.3 79.5 - - - +
281X VAL* 1.3 58.4 + - - +
282X LEU 3.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243X ARG* 3.1 22.5 + - - -
244X ARG* 3.8 28.2 - - + +
247X GLU* 3.8 15.9 - - + +
248X LEU* 3.7 37.5 - - + +
251X ASN* 4.4 3.4 - - - +
277X VAL 4.5 5.2 - - - +
278X GLU 3.2 20.0 - - - +
279X TRP 3.1 1.6 + - - -
280X ASN* 1.3 80.6 - - - +
282X LEU* 1.3 70.3 + - - +
283X PRO 3.3 0.7 - - - -
291X SER* 3.4 21.5 - - - +
292X PHE* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 282 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243X ARG* 4.4 1.6 + - - -
244X ARG* 3.9 13.9 - - - +
279X TRP* 3.9 31.0 - - + +
280X ASN 3.6 3.5 - - - +
281X VAL* 1.3 82.0 - - - +
283X PRO* 1.3 70.3 - - + +
284X PHE 3.4 14.7 + - - +
286X SER* 4.1 18.4 - - - +
289X ARG* 3.8 24.2 - - + +
290X PHE 3.8 33.7 - - - +
291X SER* 4.0 7.0 - - - +
----------------------------------------------------------
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