Contacts of the helix formed by residues 220 - 229 (chain E) in PDB entry 2WP9
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 GLY 220 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E THR 5.9 0.4 + - - -
203E GLY 5.0 4.0 - - - -
204E GLY 3.2 13.5 + - - -
205E ALA* 3.4 20.2 - - - +
219E THR* 1.3 77.3 - - - +
221E ASP* 1.3 65.4 + - - +
222E GLY 3.0 4.0 - - - -
223E VAL* 2.9 26.0 + - - +
224E GLY* 3.1 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E LYS* 2.8 27.5 + - - +
165E TYR* 3.1 34.3 + - + +
166E ALA 5.3 1.8 - - - +
202E THR* 4.7 14.3 + - + -
219E THR* 2.6 25.7 + - - +
220E GLY* 1.3 75.5 - - - +
222E GLY* 1.3 57.6 + - - +
224E GLY* 4.0 1.3 - - - +
225E MET* 3.0 41.8 + - + +
228E ARG* 4.8 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 222 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E LEU* 4.3 19.9 - - - +
202E THR* 3.1 31.2 + - - -
220E GLY 3.0 1.2 - - - -
221E ASP* 1.3 76.0 - - - +
223E VAL* 1.3 63.7 + - - +
225E MET* 4.0 1.3 - - - +
226E ALA* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 223 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205E ALA* 5.6 4.7 - - + -
220E GLY* 2.9 18.2 + - - +
222E GLY* 1.3 75.8 - - - +
224E GLY* 1.3 57.7 + - - +
226E ALA* 3.3 5.2 + - - +
227E ILE* 2.9 48.5 + - + +
233E VAL* 4.1 16.1 - - + +
236E MET* 4.3 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E GLY 3.1 11.7 + - - -
221E ASP* 4.0 2.9 - - - -
223E VAL* 1.3 75.9 - - - +
225E MET* 1.3 64.7 + - - +
227E ILE* 3.3 6.9 + - - +
228E ARG* 2.9 47.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 225 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 4.2 9.2 - - + -
166E ALA* 3.9 36.1 - - + +
167E LEU 3.5 15.5 - - - +
168E ASP* 3.5 37.9 - - - +
169E LEU* 3.6 29.4 + - + +
180E CYS* 4.2 1.8 - - + -
200E LEU* 4.5 12.3 - - + -
202E THR* 5.6 1.1 - - - -
221E ASP* 3.0 27.7 + - + +
222E GLY* 4.0 4.0 - - - +
224E GLY* 1.3 77.9 - - - +
226E ALA* 1.3 63.0 + - - +
228E ARG* 3.6 10.0 - - - +
229E ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E LEU* 4.5 8.9 - - + +
200E LEU* 4.9 8.5 - - + +
222E GLY 3.0 18.3 + - - +
223E VAL* 3.7 4.5 - - - +
225E MET* 1.3 76.1 - - - +
227E ILE* 1.3 64.1 + - - +
229E ALA* 2.9 8.1 + - - -
231E VAL* 2.9 49.0 + - + +
232E PRO 5.2 0.2 - - - +
233E VAL* 4.5 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223E VAL* 2.9 39.3 + - + +
224E GLY* 3.9 5.8 - - - +
226E ALA* 1.3 75.7 - - - +
228E ARG* 1.3 64.0 + - + +
230E GLY* 2.9 19.8 + - - -
231E VAL 3.7 7.9 - - - +
232E PRO* 5.9 0.4 - - + -
233E VAL* 4.2 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 228 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E LEU 3.7 12.1 + - - -
168E ASP* 2.9 37.2 + - - +
221E ASP* 4.8 2.0 + - - +
224E GLY* 2.9 39.0 + - - +
225E MET* 3.6 6.5 - - - +
227E ILE* 1.3 81.3 - - + +
229E ALA* 1.3 58.9 + - - +
230E GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E LEU* 3.9 29.8 - - + +
171E LYS* 3.0 44.1 + - + +
177E VAL* 5.6 0.4 - - + -
225E MET 3.1 14.9 + - - +
226E ALA 2.9 6.4 + - - +
228E ARG* 1.3 78.3 - - - +
230E GLY* 1.3 58.1 + - - +
231E VAL* 3.3 4.9 + - + -
----------------------------------------------------------
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