Contacts of the helix formed by residues 282 - 292 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 3.9 17.3 - - - +
271C ARG* 3.5 0.4 - - - -
280C ILE 5.2 2.0 - - - +
281C LEU* 1.3 76.3 - - - +
283C ASP* 1.3 65.6 + - - +
284C GLU* 3.6 7.7 + - - +
285C GLN* 2.9 39.9 + - - +
286C PHE* 2.9 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.9 20.6 + - - -
268A GLU* 3.9 16.8 + - - +
271A ARG* 4.9 3.5 + - - -
271C ARG* 2.7 41.8 + - - +
282C THR* 1.3 73.7 - - - +
284C GLU* 1.3 57.5 + - - +
286C PHE* 3.3 1.2 + - - +
287C ASP* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C THR* 4.4 3.8 + - - +
282C THR* 3.2 7.7 + - - +
283C ASP* 1.3 79.1 - - - +
285C GLN* 1.3 65.6 + - + +
287C ASP* 3.2 8.2 + - - +
288C ARG* 2.8 69.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ASP* 4.7 6.0 + - + -
235C ILE* 3.8 26.2 - - + +
279C GLN* 4.3 8.3 + - - +
280C ILE 4.4 1.4 - - - +
281C LEU* 3.5 21.4 - - + +
282C THR* 2.9 46.4 + - - +
284C GLU* 1.3 79.1 - - + +
286C PHE* 1.3 58.5 + - - +
288C ARG* 3.4 6.3 + - - +
289C LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ARG* 3.5 66.4 - - + -
268C GLU* 5.9 0.2 - - - -
270C PHE* 3.8 18.2 - + - -
271C ARG* 3.6 58.1 - - + +
274C CYS* 4.8 1.6 - - - -
281C LEU* 4.0 23.5 - - + +
282C THR 2.9 17.8 + - - +
283C ASP 3.8 2.7 - - - +
285C GLN* 1.3 75.8 - - - +
287C ASP* 1.3 62.5 + - - +
289C LEU* 3.2 3.7 + - + +
290C TRP* 2.8 42.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B GLU* 4.3 8.9 - - - +
261B LYS* 4.9 8.9 + - - -
267C ARG* 2.8 30.5 + - - +
271C ARG* 5.7 0.7 + - - -
283C ASP* 2.8 27.8 + - - +
284C GLU* 3.2 9.8 + - - +
286C PHE* 1.3 78.1 - - - +
288C ARG* 1.3 83.6 + - - +
290C TRP* 3.4 3.5 + - - +
291C ASN* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 288 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 4.1 17.0 - - - +
255B GLU* 2.6 35.2 + - - +
229C ALA 6.2 0.7 - - - +
230C THR* 3.3 34.5 - - - +
231C ALA* 5.2 6.7 - - - +
232C ASP 5.9 0.7 - - - +
284C GLU* 2.8 61.5 + - + +
285C GLN* 3.8 6.3 - - - +
287C ASP* 1.3 86.7 + - - +
289C LEU* 1.3 64.9 + - - +
291C ASN* 2.8 52.1 + - - +
292C GLU* 3.5 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ILE* 4.7 15.0 - - + -
236C LEU* 3.6 31.4 - - + -
239C LEU* 4.0 14.1 - - + -
270C PHE* 4.3 9.6 - - + -
274C CYS* 4.0 20.9 - - - -
278C VAL* 6.5 0.4 - - + -
281C LEU* 3.6 26.2 - - + -
285C GLN 2.9 18.4 + - - +
286C PHE* 3.7 7.6 - - + +
288C ARG* 1.3 76.7 - - - +
290C TRP* 1.3 59.0 + - - +
292C GLU* 2.9 27.5 + - - +
293C MET* 3.4 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LYS* 2.9 27.8 + - + -
263B ASN* 3.0 25.8 + - - -
267C ARG* 3.1 63.7 - - + +
270C PHE* 3.6 35.2 - + + -
286C PHE* 2.8 22.0 + + + +
287C ASP 3.6 6.3 - - - +
288C ARG 3.3 0.2 - - - -
289C LEU* 1.3 76.8 - - - +
291C ASN* 1.3 63.8 + - - +
293C MET* 3.0 19.0 + - + +
295C VAL* 3.5 20.9 - - + +
299C GLY 3.4 21.3 - - - -
301C LEU* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 5.2 3.2 - - - +
255B GLU* 5.8 0.3 - - - +
263B ASN* 3.0 24.7 + - - +
303B TYR* 3.8 20.7 + - - -
304B PRO* 3.4 36.0 - - + +
307B LEU* 6.3 1.2 - - - +
287C ASP 3.2 8.7 + - - +
288C ARG* 2.8 53.2 + - - +
289C LEU 3.1 0.4 - - - -
290C TRP* 1.3 78.1 - - - +
292C GLU* 1.3 63.0 + - + +
293C MET 3.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B PRO* 5.7 3.4 - - - +
229C ALA 5.9 0.5 + - - -
231C ALA* 3.8 23.1 - - + +
236C LEU* 4.4 25.4 - - + -
288C ARG 3.5 16.5 - - - +
289C LEU* 2.9 11.2 + - - +
291C ASN* 1.3 84.8 - - - +
293C MET* 1.3 73.9 + - + +
294C PRO* 4.4 2.1 - - - +
310C PHE* 4.9 5.2 - - + -
----------------------------------------------------------
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