Contacts of the helix formed by residues 321 - 345 (chain B) in PDB entry 3WOO
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 TYR 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 3.6 31.4 - - + -
317B ILE* 2.8 23.3 + - + +
318B GLN 4.1 1.8 - - - +
320B LYS* 1.3 79.5 - - + +
322B ALA* 1.3 58.9 + - - +
323B ALA 3.4 2.2 - - - -
324B THR* 3.4 23.2 + - + -
325B MET* 2.9 30.9 + - - +
403B ALA* 5.7 0.3 - - - +
447B ARG 3.8 14.5 + - - -
448B TYR* 3.4 10.2 - - - -
449B VAL* 3.1 44.3 + - + -
452B MET* 3.7 31.4 - - + +
453B ASP* 3.8 11.2 + - - +
456B LEU* 4.3 16.2 - - + -
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.6 25.9 + - - +
93B GLN* 4.1 0.9 - - + -
103B ILE* 3.9 17.0 - - + -
318B GLN 3.4 12.8 + - - +
319B VAL* 3.3 17.0 + - - +
320B LYS 3.4 0.4 - - - -
321B TYR* 1.3 77.7 - - - +
323B ALA* 1.3 59.3 + - - +
325B MET* 3.4 7.6 - - - +
326B ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.8 23.5 - - + -
90B GLY* 4.6 5.2 - - - -
93B GLN* 4.0 24.2 - - + +
320B LYS 5.1 0.4 + - - -
321B TYR 3.4 0.4 - - - -
322B ALA* 1.3 76.5 - - - +
324B THR* 1.3 66.6 + - - +
326B ALA* 3.2 3.7 + - - +
327B GLY* 3.1 19.1 + - - -
447B ARG* 4.5 17.3 - - + +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LYS 5.2 1.8 + - - -
321B TYR* 3.4 23.9 + - + -
323B ALA* 1.3 76.7 - - - +
325B MET* 1.3 58.3 + - - +
327B GLY* 3.4 2.2 + - - -
328B TRP* 3.0 68.4 + - + +
447B ARG* 5.2 12.3 + - - +
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Residues in contact with MET 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ILE* 3.3 36.3 - - + +
307B VAL* 3.5 28.7 - - + -
308B GLU* 3.5 31.0 - - + +
321B TYR 2.9 16.2 + - - +
322B ALA* 3.4 9.9 - - - +
323B ALA 3.2 0.2 - - - -
324B THR* 1.3 77.8 - - - +
326B ALA* 1.3 61.2 + - - +
328B TRP* 3.4 19.8 + - - +
329B ASN* 3.0 39.0 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 4.3 18.8 - - + +
208B LYS* 3.7 26.7 + - - +
212B ASP* 5.0 1.4 - - - +
322B ALA 3.0 15.3 + - - +
323B ALA* 3.2 8.5 + - - +
325B MET* 1.3 77.0 - - - +
327B GLY* 1.3 56.5 + - - +
329B ASN* 3.5 4.3 + - - +
330B ASN* 2.9 33.0 + - - +
3D ILE* 5.3 5.6 - - + -
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 5.3 1.1 - - - -
323B ALA 3.1 12.5 + - - -
324B THR* 3.8 2.9 - - - -
326B ALA* 1.3 73.6 - - - +
328B TRP* 1.3 65.7 + - - +
330B ASN* 3.8 3.8 - - - +
331B THR* 2.9 31.0 + - - -
3D ILE* 4.9 10.2 - - - +
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B TYR* 3.7 46.7 - + + +
303B GLN* 3.6 39.9 + - + -
304B ILE* 3.6 23.9 - - + +
307B VAL* 3.6 24.2 - - + -
321B TYR* 5.2 1.8 - + - -
324B THR* 3.0 44.9 + - + +
325B MET* 3.4 23.3 + - - +
327B GLY* 1.3 76.0 - - - +
329B ASN* 1.3 54.9 + - - +
332B SER* 2.7 36.3 + - - -
456B LEU* 4.1 22.4 - - + -
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Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASP* 3.3 42.9 + - + +
304B ILE* 3.8 32.3 - - - +
308B GLU* 5.7 1.0 + - - -
325B MET* 3.0 34.9 + - - +
326B ALA* 3.8 3.6 - - - +
328B TRP* 1.3 77.9 - - - +
330B ASN* 1.3 62.9 + - - +
332B SER* 3.2 6.7 + - - -
333B LYS* 3.0 27.2 + - - +
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Residues in contact with ASN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASP* 4.7 0.6 + - - +
215B ASN* 2.9 22.5 + - - +
216B TRP* 3.1 17.8 + - - -
326B ALA 2.9 21.0 + - - +
327B GLY* 3.8 4.7 - - - +
329B ASN* 1.3 77.9 - - - +
331B THR* 1.3 62.6 + - - +
334B ASN* 2.9 25.6 + - - +
1D VAL* 2.8 56.9 + - + +
3D ILE* 3.5 22.8 + - + +
5D PRO 4.7 4.9 - - - -
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Residues in contact with THR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ILE* 4.7 0.2 - - + -
300B TYR* 3.9 22.7 - - + -
327B GLY* 2.9 17.5 + - - -
330B ASN* 1.3 77.9 + - - +
332B SER* 1.3 67.4 + - - +
334B ASN* 3.2 6.6 + - + +
335B TYR* 3.0 59.0 + - + +
5D PRO* 3.4 33.5 + - + +
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Residues in contact with SER 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 4.1 24.6 - - - +
300B TYR* 4.0 18.3 - - - -
301B LYS* 4.2 12.2 - - - +
304B ILE* 3.9 8.1 - - - +
328B TRP 2.7 23.3 + - - -
329B ASN* 3.2 12.1 + - - -
331B THR* 1.3 81.5 - - - +
333B LYS* 1.3 55.1 + - - +
335B TYR* 3.3 2.5 + - - +
336B ASP* 2.9 33.7 + - - +
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ASP* 3.0 28.6 + - + +
213B ILE* 3.0 17.6 + - - +
215B ASN* 2.8 33.0 + - + +
216B TRP* 3.8 14.8 - - + -
217B MET* 3.8 8.0 - - - +
329B ASN 3.0 19.5 + - - +
332B SER* 1.3 76.7 + - - +
334B ASN* 1.3 63.3 + - - +
336B ASP* 3.3 9.9 + - + +
337B GLY 2.9 18.9 + - - -
677B TRP* 3.7 28.4 - - + -
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Residues in contact with ASN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 3.3 40.2 - - + +
330B ASN* 2.9 19.3 + - - +
331B THR* 3.2 7.6 + - - +
333B LYS* 1.3 77.2 - - - +
335B TYR* 1.3 69.2 + - - +
337B GLY* 3.1 4.1 + - - -
338B GLN* 2.8 50.9 + - - +
677B TRP* 5.7 0.2 - - - -
680B VAL* 3.6 16.7 - - - +
2D TYR* 5.0 2.3 - - - -
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Residues in contact with TYR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B THR* 5.9 0.3 - - - +
293B TYR* 3.4 69.0 - + + +
296B ILE* 3.6 32.4 - - + +
297B ALA* 4.3 7.2 - - + -
331B THR* 3.0 43.5 + - + +
332B SER 3.7 4.0 - - - +
334B ASN* 1.3 88.3 - - - +
336B ASP* 1.3 64.4 + - - +
337B GLY 3.1 0.9 - - - -
338B GLN* 3.1 6.5 + - - +
339B LEU* 3.0 30.3 + - - +
5D PRO* 5.3 6.1 + - - +
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Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 4.1 8.1 - - - +
301B LYS* 2.7 38.5 + - - -
332B SER 2.9 16.9 + - - +
333B LYS* 3.6 14.5 - - + +
335B TYR* 1.3 73.3 - - - +
337B GLY* 1.3 57.7 + - - +
339B LEU* 3.5 11.6 + - - +
340B GLU* 3.2 26.7 + - - +
677B TRP* 4.0 11.0 - - + -
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LYS 2.9 11.4 + - - -
334B ASN* 3.1 4.9 + - - -
336B ASP* 1.3 75.0 - - - +
338B GLN* 1.3 58.3 + - - +
340B GLU* 3.8 1.9 - - - +
341B GLY* 2.8 26.0 + - - -
677B TRP* 3.4 33.3 + - - +
680B VAL* 3.3 16.2 - - - +
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Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 3.4 27.8 + - + -
334B ASN* 2.8 40.8 + - - +
335B TYR* 3.1 7.2 + - - +
337B GLY* 1.3 70.3 - - - +
339B LEU* 1.3 60.1 + - - +
341B GLY 3.3 0.3 + - - -
342B PHE* 2.8 46.9 + - + -
680B VAL* 3.5 27.8 + - + +
681B SER* 4.0 5.8 - - - +
683B ASN* 3.5 16.2 + - - +
684B TRP* 3.1 33.9 - - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ALA* 3.6 23.8 - - + +
293B TYR* 3.8 30.1 - - + +
294B PRO* 4.0 26.9 - - + -
297B ALA* 6.0 0.7 - - + -
335B TYR 3.0 20.9 + - - +
336B ASP* 3.7 11.9 - - - +
338B GLN* 1.3 76.4 - - - +
340B GLU* 1.3 64.4 + - - +
342B PHE* 3.1 28.0 + - + +
343B LYS* 3.3 24.1 + - - +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ASP 3.2 13.9 + - - +
337B GLY 3.8 3.8 - - - +
339B LEU* 1.3 78.2 - - - +
341B GLY* 1.3 57.0 + - - +
343B LYS* 3.3 15.0 + - + +
344B ARG* 3.0 26.4 + - + +
677B TRP* 3.0 39.5 + - + +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLY 2.8 20.0 + - - -
338B GLN 3.3 0.4 + - - -
340B GLU* 1.3 71.5 - - - +
342B PHE* 1.3 65.3 + - - +
344B ARG* 3.2 14.9 + - - +
345B ILE* 3.1 28.6 + - - +
678B GLU* 5.4 5.2 - - - -
681B SER* 3.6 21.7 + - - -
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B PHE* 3.5 37.5 - + + -
288B THR* 5.5 0.2 - - + -
289B ALA* 3.8 19.5 - - + -
293B TYR* 4.1 7.6 - + - -
338B GLN* 2.8 41.0 + - + -
339B LEU* 3.1 24.6 + - + +
341B GLY* 1.3 73.7 - - - +
343B LYS* 1.3 52.7 + - + +
345B ILE* 4.5 0.4 - - + -
346B ASP* 2.8 16.3 + - - -
347B ALA* 2.8 41.7 + - + +
348B ALA* 5.4 0.7 - - + +
681B SER* 3.7 19.3 - - - -
684B TRP* 3.4 39.0 - + + -
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 3.3 19.4 + - - +
340B GLU* 3.5 13.5 - - + +
341B GLY 3.3 0.6 - - - -
342B PHE* 1.3 74.3 - - + +
344B ARG* 1.3 66.7 + - - +
345B ILE 3.4 0.5 + - - -
346B ASP* 3.5 9.8 + - - +
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU* 3.0 16.3 + - + +
341B GLY* 3.2 11.7 + - - +
343B LYS* 1.3 77.8 - - - +
345B ILE* 1.3 79.1 + - - +
346B ASP 3.7 0.3 + - - -
591B PRO 6.2 0.2 - - - -
678B GLU* 3.2 43.2 + - - +
681B SER* 4.1 7.3 + - - -
682B SER* 5.9 0.2 + - - -
687B ASP* 2.7 36.0 + - - +
690B MET* 3.1 24.6 - - - +
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY 3.1 13.7 + - - +
342B PHE 3.8 0.2 - - - +
344B ARG* 1.3 116.8 - - - +
346B ASP* 1.3 64.1 + - - +
347B ALA* 3.7 15.3 - - + +
350B GLN* 2.4 32.3 - - - +
353B ARG* 5.6 0.2 + - - -
681B SER* 4.7 9.0 - - - +
685B VAL* 3.7 44.6 - - + +
687B ASP* 3.9 12.8 - - + +
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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