Contacts of the helix formed by residues 397 - 419 (chain P) in PDB entry 1HI0
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 ALA 397 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P PHE* 6.4 0.4 - - + -
283P ILE* 4.2 2.4 - - + +
287P ALA* 4.1 15.5 - - + -
291P ARG* 4.3 0.4 - - - +
357P PHE* 4.4 19.7 - - + -
395P GLN* 2.9 17.7 + - - +
396P GLY* 1.3 74.9 - - - +
398P THR* 1.3 66.9 + - - +
399P ASP* 2.9 12.9 + - - -
400P LEU* 2.9 24.0 + - + -
401P MET* 3.0 14.5 + - + +
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Residues in contact with THR 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 5.3 1.7 + - - -
329P ASP* 6.1 0.4 - - - -
391P LEU* 3.1 44.5 - - + +
392P SER 2.9 35.2 - - - +
393P SER* 3.1 21.3 + - - +
395P GLN* 3.3 19.1 + - + +
396P GLY 3.9 0.2 - - - -
397P ALA* 1.3 74.9 - - - +
399P ASP* 1.3 58.4 + - - +
401P MET* 4.0 1.3 - - - -
402P GLY* 3.1 9.5 + - - -
667P GTP 3.8 24.1 + - - -
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Residues in contact with ASP 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291P ARG* 2.7 49.3 + - - +
295P TYR* 4.1 10.0 + - - -
397P ALA 3.5 5.4 - - - +
398P THR* 1.3 74.7 + - - +
400P LEU* 1.3 71.1 + - - +
402P GLY 3.4 0.5 + - - -
403P THR* 2.9 35.2 + - - +
451P LYS* 5.1 15.2 + - + -
452P SER* 3.6 11.0 + - - +
629P GLN 6.1 1.6 - - - +
667P GTP 4.2 8.0 + - - +
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Residues in contact with LEU 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P MET* 4.8 8.8 - - + +
135P PHE* 5.3 5.6 - - + -
287P ALA* 3.6 39.7 - - + +
290P VAL* 3.7 29.2 - - + -
291P ARG* 4.2 14.1 - - + -
294P ILE* 4.0 23.8 - - + -
295P TYR* 5.7 1.3 - - - +
397P ALA* 2.9 11.8 + - + +
399P ASP* 1.3 93.1 + - - +
401P MET* 1.3 69.5 + - + +
403P THR* 3.6 3.9 - - - -
404P LEU* 2.7 38.0 + - - +
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Residues in contact with MET 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P MET* 6.4 0.2 - - - -
135P PHE* 4.6 16.2 - - + -
332P TRP* 3.0 46.5 + - + -
340P ILE* 3.9 21.8 - - + -
357P PHE* 3.6 33.7 - - + -
361P LEU* 4.3 3.8 - - + -
391P LEU* 3.7 20.9 - - + -
395P GLN* 4.4 6.3 - - - +
397P ALA* 3.0 18.4 + - + +
398P THR 4.1 0.4 - - - +
400P LEU* 1.3 88.1 - - + +
402P GLY* 1.3 63.4 + - - +
404P LEU* 3.8 6.8 - - + +
405P LEU 3.0 15.6 + - - -
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Residues in contact with GLY 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328P HIS* 3.4 26.7 - - - -
332P TRP* 4.0 2.2 - - - -
391P LEU* 3.8 1.0 - - - +
398P THR 3.1 13.0 + - - -
399P ASP 3.8 2.7 - - - -
400P LEU 3.2 0.2 - - - -
401P MET* 1.3 80.5 - - - +
403P THR* 1.3 56.0 + - - +
405P LEU* 3.6 1.2 - - - +
406P MET* 2.9 34.7 + - - +
452P SER* 3.9 11.0 - - - -
667P GTP 5.0 0.2 - - - -
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Residues in contact with THR 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134P MET* 4.2 10.1 - - + -
294P ILE* 5.0 4.0 - - + -
302P PHE* 3.4 41.3 - - + -
399P ASP* 2.9 23.7 + - - +
400P LEU* 3.6 7.9 - - - +
402P GLY* 1.3 73.0 - - - +
404P LEU* 1.3 62.1 + - - +
406P MET 3.3 0.2 + - - -
407P SER* 2.7 37.1 + - - +
450P SER* 4.9 2.9 - - - +
451P LYS* 4.2 6.5 - - - +
452P SER* 3.2 25.2 + - - +
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Residues in contact with LEU 404 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P PHE* 4.4 11.9 - - + +
130P ALA* 3.5 36.3 - - + -
131P VAL* 3.9 8.3 - - + +
134P MET* 3.2 34.9 - - - +
135P PHE* 5.1 4.7 - - + -
336P LEU* 4.2 13.9 - - + -
340P ILE* 3.9 28.9 - - + -
400P LEU 2.7 21.4 + - - +
401P MET* 3.8 9.0 - - + +
403P THR* 1.3 73.9 - - - +
405P LEU* 1.3 66.2 + - - +
407P SER* 4.5 1.7 - - - -
408P ILE* 3.6 18.8 + - - +
440P TRP* 5.9 1.1 - - - -
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Residues in contact with LEU 405 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P PHE* 4.0 11.5 - - + -
328P HIS* 3.8 7.0 - - + -
332P TRP* 3.5 31.0 - - + +
333P PRO* 4.0 16.8 - - + -
335P TRP* 5.2 1.3 - - + -
336P LEU* 3.4 29.4 - - + +
401P MET 3.0 7.7 + - - +
402P GLY 3.6 1.3 - - - +
404P LEU* 1.3 81.6 - - - +
406P MET* 1.3 81.4 + - - +
408P ILE* 3.9 2.1 - - - +
409P THR* 3.0 38.1 + - - +
485P TYR* 5.1 5.4 - - + -
486P MET* 3.8 22.4 - - + -
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Residues in contact with MET 406 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325P VAL* 3.2 32.3 - - + -
328P HIS* 3.7 19.7 - - + +
402P GLY 2.9 17.5 + - - +
405P LEU* 1.3 96.3 - - - +
407P SER* 1.3 61.2 + - - +
409P THR* 3.5 7.1 - - + -
410P TYR* 2.8 54.5 + - + +
452P SER 3.1 30.1 - - - +
453P ASP* 4.1 1.1 - - - -
486P MET* 3.6 12.8 - - + -
488P ILE* 3.9 15.5 - - + -
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Residues in contact with SER 407 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302P PHE* 3.7 14.6 - - - -
403P THR* 2.7 23.5 + - - -
404P LEU* 4.5 1.1 - - - -
406P MET* 1.3 72.0 - - - +
408P ILE* 1.3 63.6 + - - +
410P TYR* 4.3 2.0 - - - -
411P LEU* 3.0 21.1 + - - +
439P TYR* 4.9 0.3 - - - -
440P TRP* 2.9 31.4 + - - -
448P GLN* 2.6 41.9 + - - +
450P SER* 4.4 3.5 + - - -
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Residues in contact with ILE 408 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 3.8 36.1 - - + +
127P PHE* 3.5 41.3 - - + -
130P ALA* 3.7 23.1 - - + -
404P LEU 3.6 14.1 + - - +
405P LEU 3.5 1.0 + - - -
406P MET 3.3 0.2 - - - -
407P SER* 1.3 74.5 - - - +
409P THR* 1.3 66.1 + - - +
411P LEU* 3.1 7.9 + - + +
412P VAL* 2.8 30.8 + - + +
436P LEU* 3.9 25.1 - - + -
440P TRP* 4.4 6.1 - - + -
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Residues in contact with THR 409 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P PHE* 4.5 1.9 - - - -
405P LEU* 3.0 39.0 + - - +
406P MET* 3.2 25.4 + - + -
408P ILE* 1.3 76.8 - - - +
410P TYR* 1.3 59.5 + - + +
412P VAL* 3.3 7.3 + - - +
413P MET* 2.8 26.1 + - + +
483P SER* 3.5 27.7 + - - +
485P TYR* 3.8 21.4 - - + +
486P MET* 4.8 1.8 - - + +
488P ILE* 4.6 9.0 - - + -
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Residues in contact with TYR 410 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323P THR* 3.4 25.5 + - - -
325P VAL* 3.2 14.4 - - - +
406P MET* 2.8 55.3 + - + +
407P SER* 4.3 1.3 - - - -
409P THR* 1.3 69.8 - - + +
411P LEU* 1.3 66.7 + - - +
413P MET* 3.1 28.2 + - + +
414P GLN* 2.9 27.8 + - - +
448P GLN* 3.6 13.9 - - - +
450P SER* 4.8 1.6 - - - -
452P SER 4.1 4.5 - - - -
453P ASP 2.8 24.8 + - - -
455P ALA* 3.5 24.7 - - + -
457P LEU* 3.5 24.9 - - + +
488P ILE* 4.3 6.5 - - + -
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Residues in contact with LEU 411 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 3.9 31.6 - - + -
407P SER 3.0 15.1 + - - +
408P ILE* 3.5 11.0 - - + +
410P TYR* 1.3 74.6 - - - +
412P VAL* 1.3 59.6 + - - +
414P GLN* 2.9 7.4 + - - +
415P LEU* 2.8 35.3 + - + +
435P PHE* 4.0 20.2 - - + -
436P LEU* 4.0 21.3 - - + -
439P TYR* 3.7 40.4 - - + -
446P ILE* 3.9 15.3 - - + -
448P GLN* 4.1 0.4 + - - -
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Residues in contact with VAL 412 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 3.7 3.4 - - - +
123P ASP* 3.5 25.6 - - + +
126P LEU* 4.1 19.3 - - + -
408P ILE* 2.8 26.8 + - + +
409P THR* 3.5 10.3 - - - +
411P LEU* 1.3 73.3 - - - +
413P MET* 1.3 65.5 + - - +
414P GLN 3.1 0.2 + - - -
415P LEU* 3.1 7.2 + - - -
416P ASP* 2.8 28.1 + - - +
483P SER* 5.7 0.2 - - - +
484P PRO* 5.3 4.0 - - + -
485P TYR* 4.3 11.9 - - + -
20R ASN* 3.2 31.6 - - - +
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Residues in contact with MET 413 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323P THR* 5.2 1.3 - - - -
409P THR* 2.8 12.6 + - + +
410P TYR* 3.1 40.4 + - + +
412P VAL* 1.3 77.1 - - - +
414P GLN* 1.3 61.3 + - + +
416P ASP* 4.6 2.0 - - - -
417P HIS* 3.2 32.5 + - + +
457P LEU* 4.0 12.8 - - + -
471P LEU* 4.1 19.0 - - + +
475P LEU* 5.1 3.8 - - - -
482P PRO* 3.5 53.2 - - + +
483P SER* 4.6 4.3 - - - +
488P ILE* 3.8 24.5 - - + -
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Residues in contact with GLN 414 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410P TYR 2.9 14.0 + - - +
411P LEU* 2.9 8.5 + - - +
413P MET* 1.3 75.2 - - - +
415P LEU* 1.3 67.2 + - - +
418P THR* 2.8 39.0 + - - +
419P ALA* 3.2 1.8 + - - -
439P TYR* 2.7 37.0 + - - -
446P ILE* 3.8 17.9 - - + +
447P ARG 3.4 11.5 + - - -
457P LEU* 3.9 14.7 - - + +
458P GLY 3.3 24.9 + - - -
459P TRP* 3.5 30.4 - - + -
471P LEU* 4.9 1.6 - - + -
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Residues in contact with LEU 415 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 3.5 42.0 - - - +
126P LEU* 3.9 19.5 - - + -
411P LEU* 2.8 36.9 + - + +
412P VAL* 3.6 6.7 - - - +
414P GLN* 1.3 75.7 - - - +
416P ASP* 1.3 64.7 + - - +
418P THR 3.5 0.2 + - - -
419P ALA* 3.2 21.2 + - + +
420P PRO* 3.6 12.9 - - - +
422P LEU* 4.0 27.8 - - + -
423P ASN* 4.1 5.1 + - - +
426P ILE* 3.9 10.8 - - + -
435P PHE* 4.5 6.1 - - + -
446P ILE* 4.3 10.8 - - + -
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Residues in contact with ASP 416 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 2.6 29.2 + - - +
412P VAL* 2.8 22.9 + - - +
413P MET* 4.0 1.5 - - - +
415P LEU* 1.3 75.4 - - - +
417P HIS* 1.3 78.7 + - + +
420P PRO* 5.2 3.3 - - - +
482P PRO 5.2 1.9 - - - +
484P PRO* 4.8 7.8 - - - +
20R ASN* 2.5 42.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 417 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413P MET* 3.2 27.3 + - + +
416P ASP* 1.3 89.5 + - + +
418P THR* 1.3 70.9 + - + +
420P PRO* 5.2 1.6 - - - -
467P GLY* 3.7 12.5 - - - +
470P ARG* 4.2 12.6 + - - +
471P LEU* 4.0 22.2 - - + +
474P MET* 3.1 36.2 - - + +
480P VAL* 5.8 0.9 - - + -
482P PRO* 3.0 30.0 + - + +
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Residues in contact with THR 418 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414P GLN* 2.8 25.2 + - - +
415P LEU 3.5 0.6 + - - -
417P HIS* 1.3 88.1 - - + +
419P ALA* 1.3 61.6 + - - +
420P PRO* 3.5 7.8 - - - +
421P HIS* 4.0 1.9 - - - -
446P ILE* 4.0 2.1 - - - +
459P TRP* 3.1 26.0 + - + +
463P ARG 4.6 0.7 - - - +
464P ALA* 3.1 37.0 - - - +
467P GLY* 3.2 10.0 - - - +
468P GLY* 3.2 27.1 - - - +
470P ARG* 5.6 1.1 - - - +
471P LEU* 4.3 5.4 - - + -
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Residues in contact with ALA 419 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414P GLN 3.2 3.3 + - - +
415P LEU* 3.2 19.1 + - + +
418P THR* 1.3 88.3 + - - +
420P PRO* 1.3 53.0 - - - +
421P HIS* 3.0 17.5 - - + -
422P LEU* 2.7 56.5 + - + +
423P ASN 3.9 1.0 + - - -
446P ILE* 4.6 5.6 - - + -
464P ALA* 4.0 6.7 - - + -
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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