Contacts of the helix formed by residues 466 - 489 (chain B) in PDB entry 3PLZ
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 ASN 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368B GLU* 5.1 4.9 + - - +
369B LEU* 3.9 11.0 - - + +
370B LYS 6.2 0.2 - - - +
373B ASP* 2.8 15.9 + - - +
464B LEU* 4.5 2.7 - - - -
465B GLU* 1.3 76.1 - - + +
467B PHE* 1.3 64.4 + - - +
468B GLN* 3.6 10.6 + - - +
469B LEU* 3.1 45.8 + - - +
470B VAL* 3.4 16.5 + - - +
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Residues in contact with PHE 467 (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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462A LYS* 4.5 15.9 - - - -
458B SER 5.1 1.3 - - - -
459B LEU* 4.0 37.7 - - + -
461B VAL 4.6 8.5 - - - -
464B LEU* 4.1 32.7 - - + +
465B GLU 3.6 4.6 + - - -
466B ASN* 1.3 76.3 - - - +
468B GLN* 1.3 57.7 + - - +
470B VAL* 3.2 5.6 + - + -
471B GLU* 2.8 68.1 + - + +
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Residues in contact with GLN 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ASN* 3.1 9.5 - - - +
467B PHE* 1.3 81.5 - - - +
469B LEU* 1.3 62.1 + - - +
471B GLU* 3.9 8.9 - - - +
472B GLY* 3.0 19.4 + - - -
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Residues in contact with LEU 469 (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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365B PHE* 3.6 36.8 - - + +
368B GLU* 4.0 15.7 - - + -
369B LEU* 3.9 19.1 - - + -
457B PHE* 5.2 2.0 - - + -
466B ASN* 3.1 32.4 + - - +
468B GLN* 1.3 74.2 - - - +
470B VAL* 1.3 61.8 + - - +
472B GLY* 3.0 3.1 + - - -
473B VAL* 2.9 51.4 + - + +
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B LEU* 4.4 12.1 - - + -
373B ASP* 5.8 0.2 - - - +
377B LEU* 4.1 13.7 - - + -
457B PHE* 3.9 38.7 - - + +
458B SER 3.6 24.9 - - - +
459B LEU* 5.0 2.5 - - + -
464B LEU* 3.9 24.9 - - + -
466B ASN 3.4 14.3 + - - +
467B PHE* 3.2 9.5 + - + +
469B LEU* 1.3 76.9 - - - +
471B GLU* 1.3 63.0 + - - +
473B VAL* 3.4 2.3 + - - +
474B GLN* 3.1 22.0 + - - +
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Residues in contact with GLU 471 (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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462A LYS* 3.4 33.1 - - - +
459B LEU* 3.9 24.0 - - + +
467B PHE* 2.8 45.2 + - + +
468B GLN* 3.9 6.6 - - - +
470B VAL* 1.3 73.4 - - - +
472B GLY* 1.3 58.8 + - - +
474B GLN* 3.4 3.1 + - - +
475B GLU* 3.0 54.3 + - + +
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Residues in contact with GLY 472 (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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468B GLN 3.0 15.8 + - - -
469B LEU* 3.0 5.1 + - - -
471B GLU* 1.3 73.4 - - - +
473B VAL* 1.3 58.8 + - - +
475B GLU* 3.3 10.1 + - - +
476B GLN* 2.9 40.1 + - - +
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Residues in contact with VAL 473 (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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365B PHE* 3.6 46.4 - - + -
453B PHE* 4.5 4.9 - - + +
457B PHE* 3.7 38.1 - - + -
469B LEU* 2.9 32.1 + - + +
470B VAL 3.4 3.6 + - - +
472B GLY* 1.3 71.0 - - - +
474B GLN* 1.3 63.8 - - - +
476B GLN* 4.6 4.0 - - - -
477B VAL* 2.9 41.3 + - + +
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Residues in contact with GLN 474 (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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453B PHE 6.5 0.2 - - - -
454B LEU* 3.1 44.1 + - - +
457B PHE* 2.8 32.1 + - - +
458B SER* 4.6 2.6 - - - +
459B LEU* 3.8 32.7 - - + +
470B VAL 3.1 17.2 + - - +
471B GLU 3.7 4.3 - - - +
473B VAL* 1.3 76.0 - - - +
475B GLU* 1.3 63.8 + - + +
478B ASN* 2.8 47.0 + - - +
503B LEU* 6.0 0.5 - - - +
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Residues in contact with GLU 475 (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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459B LEU* 6.4 1.3 - - + -
471B GLU* 3.0 46.6 + - + +
472B GLY* 3.6 9.5 - - - +
473B VAL 3.3 0.2 - - - -
474B GLN* 1.3 78.6 - - + +
476B GLN* 1.3 68.9 + - + +
478B ASN* 3.5 6.7 + - - +
479B ALA* 3.1 22.7 + - - +
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Residues in contact with GLN 476 (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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304B LEU* 3.5 20.3 - - + +
365B PHE* 6.2 2.2 - - + -
472B GLY* 2.9 25.0 + - - +
473B VAL* 3.9 4.3 - - - +
475B GLU* 1.3 79.3 + - - +
477B VAL* 1.3 62.1 + - - +
479B ALA* 3.3 9.1 + - - +
480B ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 477 (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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304B LEU* 4.0 18.4 - - + -
308B LEU* 4.2 18.4 - - + -
365B PHE* 5.5 0.7 - - + -
450B CYS* 3.6 43.5 - - + +
453B PHE* 4.3 8.5 - - + -
454B LEU* 3.8 15.9 - - + -
473B VAL* 2.9 36.2 + - + +
476B GLN* 1.3 72.7 - - - +
478B ASN* 1.3 60.7 + - - +
480B ALA* 3.8 2.3 - - - +
481B LEU* 2.9 29.1 + - - +
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Residues in contact with ASN 478 (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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454B LEU* 3.9 17.1 - - - +
474B GLN* 2.8 47.0 + - - +
475B GLU* 3.5 7.2 - - - +
477B VAL* 1.3 78.7 - - - +
479B ALA* 1.3 62.2 + - - +
481B LEU* 3.4 2.9 + - - -
482B LEU* 3.0 21.0 + - - +
496B PHE* 3.5 31.1 - - + -
500B LEU* 3.8 14.8 - - - +
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Residues in contact with ALA 479 (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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475B GLU 3.1 14.7 + - - +
476B GLN* 3.6 10.8 - - - +
477B VAL 3.3 0.2 - - - -
478B ASN* 1.3 80.1 - - - +
480B ALA* 1.3 57.5 + - - +
482B LEU* 3.5 9.3 + - - +
483B ASP* 3.1 28.2 + - - +
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Residues in contact with ALA 480 (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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302B PRO* 3.6 17.5 - - + +
304B LEU* 4.2 17.7 - - + -
305B ILE* 3.6 21.9 - - + +
308B LEU* 6.4 0.2 - - + -
450B CYS* 5.2 0.4 - - - -
476B GLN 2.9 17.0 + - - +
477B VAL* 3.8 4.3 - - - +
479B ALA* 1.3 74.2 - - - +
481B LEU* 1.3 60.9 + - - +
483B ASP* 3.4 4.2 + - - -
484B TYR* 2.9 30.0 + - - +
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Residues in contact with LEU 481 (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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305B ILE* 4.4 0.4 - - - +
447B GLU* 3.7 33.4 - - + -
450B CYS* 3.7 28.9 - - + -
451B LEU* 4.0 26.2 - - + -
454B LEU* 4.4 4.0 - - + -
477B VAL* 2.9 18.7 + - + +
478B ASN* 3.8 4.3 - - - +
480B ALA* 1.3 73.7 - - - +
482B LEU* 1.3 65.9 + - - +
484B TYR* 3.2 7.5 + - + +
485B THR* 2.9 35.1 + - + +
496B PHE* 3.9 20.2 - - + -
499B LEU* 4.3 8.7 - - + -
500B LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 482 (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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478B ASN 3.0 16.7 + - - +
479B ALA* 3.7 9.0 - - - +
481B LEU* 1.3 76.0 - - - +
483B ASP* 1.3 62.9 + - - +
485B THR* 3.0 13.6 + - - -
486B MET* 3.2 46.9 + - + +
496B PHE* 3.5 45.0 - - + -
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Residues in contact with ASP 483 (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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302B PRO* 3.7 19.6 - - + +
479B ALA 3.1 17.3 + - - +
480B ALA* 3.6 6.7 - - - +
481B LEU 3.3 0.2 - - - -
482B LEU* 1.3 79.2 - - - +
484B TYR* 1.3 62.4 + - - +
486B MET* 3.5 17.4 + - - +
487B CYS* 3.1 27.3 + - - +
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Residues in contact with TYR 484 (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 SER 3.9 9.6 - - - -
301B ILE* 4.3 8.3 - - + -
302B PRO* 3.9 15.7 - - + +
305B ILE* 3.6 18.2 - - + -
444B ASP* 2.6 32.9 + - - -
446B ARG* 2.8 47.0 + - + -
447B GLU* 3.7 24.0 - - + -
480B ALA 2.9 18.1 + - - +
481B LEU* 3.2 5.1 + - + +
483B ASP* 1.3 76.7 - - - +
485B THR* 1.3 59.1 + - + +
487B CYS* 3.3 1.1 + - - -
488B ASN* 3.0 67.3 + - + +
489B TYR* 4.1 6.7 - + - -
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Residues in contact with THR 485 (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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447B GLU* 3.7 20.0 - - + +
481B LEU* 2.9 26.5 + - + +
482B LEU 3.0 13.5 + - - -
484B TYR* 1.3 75.0 - - - +
486B MET* 1.3 61.5 + - - +
489B TYR* 3.0 40.0 + - - +
492B GLN 5.1 1.1 - - - +
495B LYS* 4.4 10.8 - - + -
496B PHE* 3.6 27.5 + - - +
499B LEU* 3.9 21.3 - - + -
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Residues in contact with MET 486 (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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482B LEU* 3.2 46.8 + - + +
483B ASP* 3.7 22.7 - - + +
485B THR* 1.3 79.1 + - - +
487B CYS* 1.3 60.1 + - - +
489B TYR 5.0 0.2 - - - -
490B PRO* 3.5 25.9 - - - +
492B GLN 6.0 0.7 - - - -
493B THR 5.9 2.9 - - - +
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Residues in contact with CYS 487 (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 SER* 4.2 26.9 - - - +
483B ASP* 3.1 21.5 + - - +
484B TYR* 3.6 4.3 - - - +
486B MET* 1.3 81.2 - - - +
488B ASN* 1.3 72.5 + - - +
490B PRO* 3.7 10.6 - - - +
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Residues in contact with ASN 488 (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 SER 2.9 42.5 + - - +
301B ILE* 5.7 0.5 - - - +
484B TYR* 3.0 48.1 + - + +
487B CYS* 1.3 82.1 - - - +
489B TYR* 1.3 86.0 + - + +
490B PRO* 3.4 6.5 - - - +
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Residues in contact with TYR 489 (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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442B GLN* 3.7 25.7 + - + +
444B ASP* 2.5 39.3 + - - +
446B ARG* 4.7 1.7 + - - -
447B GLU* 3.4 8.3 - - - -
484B TYR* 4.1 2.5 - + - -
485B THR* 3.0 21.4 + - - +
486B MET* 5.0 0.3 - - - -
488B ASN* 1.3 98.9 - - + +
490B PRO* 1.3 66.2 - - - +
491B GLN* 3.1 3.6 - - - -
492B GLN* 3.1 41.3 + - - +
495B LYS* 3.3 39.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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