Contacts of the helix formed by residues 282 - 291 (chain A) in PDB entry 1WLZ
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 THR 282 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 3.5 0.4 - - - -
280A ILE 5.1 2.9 - - - +
281A LEU* 1.3 76.5 - - - +
283A ASP* 1.3 65.7 + - - +
284A GLU* 3.6 7.6 + - - +
285A GLN* 3.0 40.1 + - - +
286A PHE* 2.8 21.5 + - - +
268C GLU* 3.4 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG* 2.7 40.5 + - - +
282A THR* 1.3 70.8 - - - +
284A GLU* 1.3 57.7 + - - +
286A PHE* 3.8 0.9 - - - +
287A ASP* 2.9 43.0 + - - +
261B LYS* 5.2 6.6 - - - -
267C ARG* 3.9 20.6 + - - -
268C GLU* 3.0 24.2 + - - +
271C ARG* 5.0 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A THR* 4.5 2.9 + - - -
282A THR* 3.1 7.3 + - - +
283A ASP* 1.3 76.4 - - - +
285A GLN* 1.3 66.9 + - + +
287A ASP* 3.3 6.9 + - - +
288A ARG* 2.8 72.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ASP* 4.6 5.6 + - + -
235A ILE* 3.9 24.3 - - + +
279A GLN* 4.2 9.7 + - - +
280A ILE 4.4 1.0 - - - +
281A LEU* 3.5 21.6 - - + +
282A THR* 3.0 46.3 + - - +
284A GLU* 1.3 80.1 - - + +
286A PHE* 1.3 58.1 + - - +
288A ARG* 3.4 6.8 + - - +
289A LEU* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.5 67.3 - - + -
268A GLU* 5.8 0.2 - - - -
270A PHE* 3.8 19.3 - + - -
271A ARG* 3.5 57.9 - - + +
274A CYS* 4.7 1.6 - - - -
281A LEU* 4.0 23.9 - - + +
282A THR 2.8 16.5 + - - +
283A ASP 3.8 2.9 - - - +
285A GLN* 1.3 75.4 - - - +
287A ASP* 1.3 60.5 + - - +
289A LEU* 3.2 4.2 + - + +
290A TRP* 2.8 40.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 2.8 30.1 + - - +
271A ARG* 5.7 0.9 + - - -
283A ASP* 2.9 31.4 + - - +
284A GLU* 3.3 9.7 + - - +
286A PHE* 1.3 78.6 - - - +
288A ARG* 1.3 84.1 + - - +
290A TRP* 3.4 3.5 + - - +
291A ASN* 3.2 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A MET* 3.9 24.5 - - + +
230A THR* 3.3 34.1 - - - +
231A ALA* 5.2 5.1 - - - -
232A ASP 6.0 0.4 - - - +
284A GLU* 2.8 59.0 + - + +
285A GLN* 3.8 5.6 - - - +
287A ASP* 1.3 94.4 + - - +
289A LEU* 1.3 65.7 + - - +
291A ASN* 2.9 49.8 + - - +
292A GLU* 3.6 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 4.6 16.2 - - + -
236A LEU* 3.7 31.6 - - + -
239A LEU* 4.1 13.2 - - + -
270A PHE* 4.3 10.1 - - + -
274A CYS* 4.0 21.1 - - - -
278A VAL* 6.5 0.2 - - + -
281A LEU* 3.6 25.4 - - + -
285A GLN 3.0 18.1 + - - +
286A PHE* 3.2 7.8 + - + +
288A ARG* 1.3 76.5 - - - +
290A TRP* 1.3 58.7 + - - +
292A GLU* 2.9 27.0 + - - +
293A MET* 3.4 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.2 65.5 - - + +
270A PHE* 3.6 35.4 - + + -
286A PHE* 2.8 22.4 + + + +
287A ASP 3.6 5.8 - - - +
289A LEU* 1.3 76.7 - - - +
291A ASN* 1.3 65.5 - - - +
292A GLU 3.0 0.2 - - - -
293A MET* 3.1 27.2 + - + +
295A VAL* 3.5 31.7 - - + +
299A GLY* 3.4 23.1 + - - -
301A LEU* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS* 4.1 13.5 - - - +
228A MET* 3.5 29.2 - - + +
287A ASP 3.2 11.3 + - - -
288A ARG* 2.9 47.0 + - - +
289A LEU 3.1 0.6 - - - -
290A TRP* 1.3 81.3 - - - +
292A GLU* 1.3 59.4 + - - +
293A MET 3.4 3.0 + - - +
----------------------------------------------------------
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