Contacts of the helix formed by residues 336 - 340 (chain E) in PDB entry 2POZ
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 336 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ARG* 5.0 8.3 - - - +
130E GLY* 4.1 23.8 - - - +
131E TRP* 5.3 0.9 - - - -
147E ARG* 3.9 15.7 - - - +
334E TYR 3.3 1.0 - - - -
335E PRO* 1.3 76.2 - - - +
337E PHE* 1.3 65.4 + - + +
338E LYS 3.1 3.1 - - - -
339E ALA* 2.8 32.0 + - - +
340E ASP* 3.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E SER 6.0 0.2 - - - -
17E ARG* 3.2 45.5 - - + -
18E LEU* 3.5 46.9 - - + -
130E GLY* 4.9 5.2 - - - -
309E CYS* 3.7 13.2 - - - -
310E GLY 5.1 3.6 - - - -
334E TYR* 3.5 49.8 - + + +
335E PRO 3.5 1.0 - - - -
336E ALA* 1.3 78.2 - - + +
338E LYS* 1.3 70.1 + - + +
339E ALA 3.0 0.2 - - - -
340E ASP* 3.0 28.1 + - - +
343E TYR* 3.6 14.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 338 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E GLY 5.1 4.4 + - - -
311E SER* 5.1 2.8 - - - +
312E SER* 3.9 18.9 + - - +
315E GLU* 4.2 17.2 + - - -
333E HIS* 4.7 11.8 - - + +
334E TYR 4.6 11.0 + - - +
335E PRO 3.9 11.6 + - - +
336E ALA 3.0 1.0 + - - -
337E PHE* 1.3 79.5 - - + +
339E ALA* 1.3 57.0 + - + +
340E ASP 3.3 1.4 + - - +
343E TYR* 3.1 59.5 + - + +
345E GLU* 4.6 3.8 - - - +
350E PRO* 5.7 2.7 - - - -
351E PRO* 5.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 339 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E PRO 4.8 0.9 + - - +
336E ALA* 2.8 15.6 + - + +
338E LYS* 1.3 76.4 - - - +
340E ASP* 1.3 64.7 + - - +
341E ASP* 3.6 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 340 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E SER 5.2 0.4 - - - +
16E GLY* 3.4 15.3 - - - -
17E ARG* 2.9 65.7 + - - +
336E ALA 4.2 5.5 - - - +
337E PHE* 3.0 20.3 + - + +
338E LYS 3.3 0.4 - - - +
339E ALA* 1.3 79.4 - - - +
341E ASP* 1.3 59.4 + - - +
342E GLY 3.0 0.5 + - - -
343E TYR* 2.9 27.3 + - + +
----------------------------------------------------------
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