Contacts of the helix formed by residues 99 - 120 (chain A) in PDB entry 3UGV
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 GLY 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 1.3 72.7 - - - +
100A LEU* 1.3 66.2 + - - -
101A SER 3.2 2.9 - - - -
102A MET* 3.2 4.7 + - - +
103A ILE* 3.1 29.2 + - - +
257A TYR* 3.3 26.7 - - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 4.4 15.7 - - + -
62A TYR* 4.2 26.0 - - + -
63A LEU* 3.7 39.1 - - + +
66A ALA* 5.9 0.5 - - - +
92A LEU* 5.4 0.2 - - - +
98A ALA 3.9 0.6 + - - -
99A GLY* 1.3 68.7 - - - -
101A SER* 1.3 66.4 + - - +
103A ILE* 3.2 13.7 + - + +
104A ALA* 3.1 21.7 + - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.2 4.0 - - - +
89A ARG* 6.0 2.0 - - - -
92A LEU* 3.9 27.3 - - - +
95A VAL* 3.6 25.6 + - - +
96A GLY 2.8 29.8 + - - -
97A TYR* 4.5 1.8 - - - -
98A ALA 4.2 2.7 + - - -
99A GLY 3.2 0.2 - - - -
100A LEU* 1.3 79.3 - - - +
102A MET* 1.3 64.0 + - - +
104A ALA* 3.4 2.8 + - - +
105A ALA* 3.2 21.4 + - - +
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Residues in contact with MET 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.0 15.5 - - + -
89A ARG* 3.9 26.9 - - - +
97A TYR 3.3 17.7 + - - +
99A GLY 3.2 9.6 + - - +
101A SER* 1.3 77.5 - - - +
103A ILE* 1.3 57.2 + - - +
105A ALA* 3.2 19.9 + - + -
106A SER* 2.9 41.8 + - - +
257A TYR* 4.0 11.2 - - + -
258A GLY* 5.2 3.1 - - - -
279A MET 3.7 2.0 - - - +
280A ARG 3.0 31.4 - - - +
281A ILE 4.3 1.1 - - - +
282A GLY* 3.5 21.5 - - - -
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 3.8 13.9 - - + +
54A PRO* 5.1 1.1 - - + +
63A LEU* 3.8 27.4 - - + -
99A GLY 3.1 21.2 + - - +
100A LEU* 3.2 19.7 + - + +
102A MET* 1.3 76.5 - - - +
104A ALA* 1.3 62.0 + - - +
106A SER* 3.4 3.1 + - - -
107A GLY 3.3 15.8 + - - -
257A TYR* 4.4 16.2 - - + +
279A MET* 3.4 57.7 - - + +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.9 1.8 - - - -
63A LEU* 4.2 13.9 - - + -
66A ALA* 4.2 16.4 - - + -
67A LEU* 3.4 27.7 - - + +
70A MET* 3.8 20.2 - - + -
92A LEU* 5.6 0.4 - - + -
100A LEU 3.1 14.5 + - - +
101A SER* 4.0 1.1 - - - +
103A ILE* 1.3 77.3 - - - +
105A ALA* 1.3 62.8 + - - +
107A GLY 3.3 1.9 + - - -
108A VAL* 3.1 19.4 + - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MET* 3.9 12.0 - - + +
85A TYR* 4.9 4.4 - - + -
88A THR* 3.5 29.1 + - - +
89A ARG* 4.5 9.4 - - + -
101A SER 3.2 12.9 + - - +
102A MET* 3.2 22.4 + - + -
104A ALA* 1.3 79.5 - - - +
106A SER* 1.3 57.3 + - - +
108A VAL* 3.5 4.9 + - - +
109A ASP* 3.0 25.5 + - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A MET* 2.9 13.0 + - - +
103A ILE 3.7 2.0 - - - -
104A ALA 3.2 0.4 - - - -
105A ALA* 1.3 74.1 - - - +
107A GLY* 1.3 61.3 + - - +
109A ASP* 3.1 8.0 + - - +
110A MET* 2.9 36.7 + - - +
278A PHE 3.4 15.9 - - - -
279A MET* 3.0 32.9 + - - -
282A GLY* 3.1 23.8 - - - -
283A GLY 3.2 3.7 + - - +
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.6 27.0 - - - +
50A ALA* 4.9 1.3 - - - +
51A TYR 5.9 0.2 - - - -
52A LEU* 3.7 23.0 - - - +
103A ILE 3.3 4.9 + - - -
104A ALA 3.3 6.5 + - - -
106A SER* 1.3 77.7 - - - +
108A VAL* 1.3 65.3 + - - +
110A MET* 3.6 7.0 + - - +
111A ALA* 3.3 18.2 + - - +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 5.1 1.1 - - + -
10A LEU* 3.8 29.4 - - + -
38A ILE* 4.5 0.4 - - - +
40A ILE* 4.9 0.4 - - + -
67A LEU* 3.9 8.1 - - + -
70A MET* 3.9 27.4 - - + -
74A LEU* 4.2 11.0 - - + -
84A ILE* 3.8 28.7 - - + -
88A THR* 4.6 2.5 - - + -
104A ALA 3.1 14.5 + - - +
105A ALA* 3.7 8.3 - - - +
106A SER 3.2 0.2 - - - -
107A GLY* 1.3 75.4 - - - +
109A ASP* 1.3 57.6 + - - +
111A ALA* 3.3 3.0 + - - +
112A VAL* 2.9 42.4 + - + +
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Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.8 13.7 - - - +
84A ILE* 5.9 2.2 - - - -
85A TYR* 3.9 10.9 - - + +
105A ALA 3.0 18.4 + - - +
106A SER* 3.1 9.6 + - - +
108A VAL* 1.3 78.9 - - - +
110A MET* 1.3 62.7 + - - +
112A VAL* 3.2 5.8 + - - +
113A TRP* 2.9 35.6 + - - -
282A GLY 3.9 7.4 - - - +
283A GLY* 4.5 0.2 - - - -
284A VAL 2.9 28.9 + - - -
285A SER* 2.8 31.6 + - - -
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Residues in contact with MET 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.8 16.3 - - + +
51A TYR 3.9 13.2 - - - +
52A LEU* 3.8 26.7 - - + -
106A SER 2.9 24.9 + - - +
107A GLY* 4.0 3.4 - - - +
108A VAL 3.4 0.2 - - - -
109A ASP* 1.3 76.8 - - - +
111A ALA* 1.3 57.6 + - - +
113A TRP* 3.5 2.4 + - - +
114A ASP* 3.0 27.2 + - - +
124A LEU* 5.9 0.5 - - - +
278A PHE* 4.0 30.7 - - + +
283A GLY* 4.0 13.9 - - - -
284A VAL* 4.2 17.2 - - + +
306A TYR* 4.1 14.1 - - + -
309A VAL* 4.0 23.6 - - + -
352A LEU* 4.4 4.1 - - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.7 20.2 - - + -
40A ILE* 3.6 21.7 - - + +
48A GLY* 3.6 14.4 - - - +
49A ARG 4.6 0.4 - - - +
50A ALA* 3.8 19.2 - - + +
107A GLY 3.3 14.6 + - - +
108A VAL 3.3 1.3 + - - +
109A ASP 3.2 0.6 - - - -
110A MET* 1.3 79.6 - - - +
112A VAL* 1.3 62.2 + - - +
114A ASP* 3.5 5.5 + - - +
115A ALA* 3.1 18.5 + - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 4.8 1.3 - - + -
40A ILE* 3.4 19.7 - - + -
79A LEU* 3.8 26.5 - - + +
81A PRO* 3.4 38.8 - - + -
84A ILE* 4.1 12.8 - - + -
108A VAL* 2.9 35.2 + - + +
109A ASP* 3.7 5.4 - - - +
111A ALA* 1.3 75.3 - - - +
113A TRP* 1.3 64.0 + - - +
115A ALA* 3.3 6.0 + - - +
116A LEU* 3.0 21.1 + - - +
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Residues in contact with TRP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 3.2 29.8 - - + +
82A ALA* 5.1 5.2 - - + -
109A ASP* 2.9 40.4 + - - +
110A MET 3.9 4.0 - - - +
112A VAL* 1.3 75.7 - - - +
114A ASP* 1.3 63.9 + - - +
116A LEU* 3.3 13.1 + - + +
117A ALA* 3.0 24.4 + - - +
124A LEU* 4.0 16.3 - - + +
127A LEU* 3.5 33.7 - - + -
128A LEU* 3.7 22.9 - - + -
284A VAL* 3.5 24.2 - - + -
285A SER* 2.9 29.4 + - - +
288A MET* 6.1 1.8 - - + -
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Residues in contact with ASP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 3.4 1.6 - - - -
49A ARG* 2.7 40.2 + - - +
110A MET 3.0 18.0 + - - +
111A ALA 3.6 5.6 - - - +
113A TRP* 1.3 76.9 - - - +
115A ALA* 1.3 55.0 + - - +
117A ALA* 3.4 3.4 + - - +
118A ARG* 3.0 55.2 + - - +
124A LEU* 4.9 2.2 - - - +
351A GLY* 3.3 8.3 - - - -
352A LEU* 2.5 43.9 + - + +
353A GLY 4.1 1.2 + - - -
354A LEU 6.0 0.2 - - - -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.2 0.3 - - - +
40A ILE* 5.0 4.5 - - + -
46A VAL* 3.4 12.2 - - + +
47A PRO 3.4 25.1 - - - +
48A GLY* 3.7 5.2 - - - -
79A LEU* 3.6 21.3 - - + -
111A ALA 3.1 14.5 + - - +
112A VAL* 3.6 8.7 - - - +
114A ASP* 1.3 76.0 + - - +
116A LEU* 1.3 60.5 + - - +
118A ARG* 3.4 0.6 + - - +
119A ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.0 23.8 - - + -
79A LEU* 4.2 10.0 - - + +
80A ALA* 6.0 0.2 - - - -
81A PRO* 4.0 23.6 - - + -
112A VAL 3.0 14.9 + - - +
113A TRP* 3.3 16.8 + - + +
115A ALA* 1.3 76.2 - - - +
117A ALA* 1.3 63.6 + - - +
119A ALA* 3.2 4.9 + - + +
120A ALA* 3.0 21.7 + - + +
127A LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TRP 3.0 16.6 + - - +
116A LEU* 1.3 78.6 - - - +
118A ARG* 1.3 56.5 + - - +
120A ALA* 3.2 2.3 + - - -
121A ASN 3.0 6.4 + - - -
122A MET* 2.8 43.6 + - - +
124A LEU* 3.9 20.4 - - + -
127A LEU* 4.3 16.9 - - + +
351A GLY* 3.6 17.3 - - - -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.9 10.2 - - + +
47A PRO* 3.4 33.2 + - + +
49A ARG* 3.5 22.4 - - - +
114A ASP* 3.0 37.5 + - - +
115A ALA 3.8 4.7 - - - +
117A ALA* 1.3 72.1 - - - +
119A ALA* 1.3 62.1 + - - +
121A ASN* 2.8 19.4 + - - +
350A PRO* 3.8 40.7 + - + +
351A GLY* 4.2 0.2 - - - -
353A GLY* 3.9 9.5 - - - +
354A LEU 3.3 37.6 + - - +
355A ASP* 4.8 2.0 + - - -
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.5 28.5 - - + -
46A VAL* 3.8 17.4 - - + +
115A ALA 2.9 18.3 + - - +
116A LEU* 3.2 7.6 + - + +
118A ARG* 1.3 79.5 - - - +
120A ALA* 1.3 57.6 + - - +
121A ASN* 3.4 1.2 + - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.0 13.4 + - + +
117A ALA 3.2 7.4 + - - +
118A ARG 3.1 0.4 - - - -
119A ALA* 1.3 75.2 - - - +
121A ASN* 1.3 70.1 + - - +
122A MET* 3.2 24.2 + - + +
127A LEU* 3.8 22.4 - - + -
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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) + - + + + + + -
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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