Contacts of the helix formed by residues 90 - 112 (chain F) in PDB entry 1BJJ
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 90 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C CYS 4.5 4.4 + - - -
67C ASN* 3.2 51.9 + - - +
68C THR* 5.1 2.0 + - - +
69C LYS* 3.6 23.1 - - + +
70C SER* 4.6 3.6 - - - +
55F LEU* 5.6 2.3 - - - +
61F CYS* 5.1 5.9 - - - -
89F THR* 1.3 71.1 - - - +
91F CYS* 1.3 59.5 + - - +
93F GLU* 3.8 5.2 + - - +
94F GLN* 2.9 58.1 + - - +
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Residues in contact with CYS 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ASN* 4.2 7.9 - - - -
61F CYS* 2.0 57.9 - - + -
71F ASP* 3.7 16.8 - - - +
89F THR* 3.1 6.5 + - - +
90F ASN* 1.3 78.6 - - - +
92F GLU* 1.3 65.7 + - - +
94F GLN* 4.6 1.3 - - - -
95F ILE* 2.9 33.0 + - - +
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Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASP* 3.4 4.5 - - - +
72B ILE* 2.9 33.3 + - + +
71F ASP* 3.5 14.7 + - - +
72F ILE 3.3 18.1 - - - +
73F TYR* 3.6 19.3 - - + +
74F SER 5.2 0.7 - - - +
88F GLY* 3.4 11.3 - - - -
89F THR* 2.9 43.1 + - - +
91F CYS* 1.3 77.7 - - - +
93F GLU* 1.3 63.4 + - - +
95F ILE* 4.0 3.1 - - - -
96F CYS* 3.0 26.0 + - - +
134F CA 2.5 21.7 - - - -
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Residues in contact with GLU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LYS* 2.8 36.4 + - - -
84F CYS* 4.6 5.0 - - + +
85F GLY 3.8 14.6 - - - +
86F LYS* 3.9 10.3 - - - +
88F GLY 2.9 28.5 + - - +
89F THR 2.9 10.4 + - - +
90F ASN* 3.8 6.2 + - - +
92F GLU* 1.3 78.8 - - - +
94F GLN* 1.3 66.7 + - + +
96F CYS* 3.4 7.5 + - - +
97F GLU* 3.1 21.5 + - - +
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Residues in contact with GLN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C VAL 5.2 5.4 - - - +
51F CYS* 6.0 1.2 - - - -
55F LEU* 3.9 32.1 - - + +
90F ASN* 2.9 51.7 + - - +
91F CYS 4.0 1.1 - - - +
93F GLU* 1.3 75.7 - - - +
95F ILE* 1.3 66.3 + - - +
97F GLU* 3.0 24.8 + - - +
98F CYS* 3.0 18.2 + - - -
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Residues in contact with ILE 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ASN 4.6 2.2 - - - +
52F TYR* 3.6 23.1 - - + +
55F LEU* 3.9 20.0 - - + -
61F CYS* 4.0 10.3 - - + -
67F ASN 3.9 8.5 - - - +
68F THR* 3.5 37.9 - - + +
71F ASP* 4.0 16.2 - - + +
73F TYR* 3.9 17.3 - - + -
91F CYS 2.9 33.8 + - - +
92F GLU* 4.0 2.9 - - - +
94F GLN* 1.3 71.2 - - - +
96F CYS* 1.3 62.8 + - - +
98F CYS* 3.3 5.0 + - - +
99F ASP* 3.0 22.2 + - - +
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Residues in contact with CYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F MET* 5.2 3.1 - - - -
73F TYR* 3.7 39.7 - - + -
74F SER 4.5 1.6 - - - +
75F TYR* 3.8 9.0 - - - -
84F CYS* 2.0 51.8 - - + -
85F GLY 5.9 0.2 - - - +
92F GLU 3.0 19.6 + - - +
93F GLU* 3.5 4.3 - - - +
94F GLN 3.1 0.2 - - - -
95F ILE* 1.3 77.5 - - - +
97F GLU* 1.3 52.2 + - - +
99F ASP* 3.1 1.9 + - - +
100F ARG* 2.7 34.7 + - - +
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F CYS* 4.9 0.4 - - - -
84F CYS* 3.7 12.1 - - - +
93F GLU 3.1 10.2 + - - +
94F GLN* 3.0 22.6 + - - +
96F CYS* 1.3 77.2 - - - +
98F CYS* 1.3 65.0 + - - +
100F ARG* 2.5 42.3 + - - +
101F VAL* 3.0 38.1 + - + +
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Residues in contact with CYS 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F HIS* 3.2 14.4 - - + -
51F CYS* 2.0 63.3 - - + -
52F TYR* 3.5 28.5 - - + -
55F LEU* 4.0 9.2 - - - -
94F GLN* 3.0 19.4 + - - -
95F ILE 3.6 1.8 - - - +
97F GLU* 1.3 75.9 - - - +
99F ASP* 1.3 63.8 + - - +
101F VAL* 4.0 3.9 - - - +
102F ALA* 3.0 18.5 + - - +
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Residues in contact with ASP 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F ASN 4.1 3.6 + - - +
5F PHE* 3.4 26.5 - - + +
8F MET* 3.0 25.5 - - + +
48F HIS* 3.0 15.6 + - - -
52F TYR* 2.5 27.4 + - - -
73F TYR* 2.5 31.5 + - - +
95F ILE* 3.0 11.4 + - - +
96F CYS 3.4 6.3 - - - +
98F CYS* 1.3 75.9 - - - +
100F ARG* 1.3 69.6 + - - +
103F ALA 3.0 16.6 + - - -
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F MET* 3.2 10.9 - - + +
82F ILE* 3.2 41.1 + - + +
83F THR* 4.7 2.5 - - - +
84F CYS* 4.2 15.0 - - - +
96F CYS 2.7 20.7 + - - +
97F GLU* 2.5 40.2 + - - +
99F ASP* 1.3 76.3 - - - +
101F VAL* 1.3 79.2 + - - +
103F ALA* 3.0 11.5 + - - +
104F GLU* 3.1 41.8 + - + +
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Residues in contact with VAL 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F VAL* 5.4 12.3 - - + -
97F GLU* 3.0 26.4 + - + +
98F CYS* 4.0 4.3 - - - +
100F ARG* 1.3 104.2 - - - +
102F ALA* 1.3 63.6 + - - +
104F GLU* 3.4 6.0 + - - +
105F CYS* 3.0 23.4 + - + +
108F ARG* 4.5 8.7 + - - +
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 3.6 14.1 - - + -
44F CYS 4.8 7.2 - - - +
48F HIS* 3.3 29.6 - - + -
98F CYS 3.0 19.7 + - - +
99F ASP 3.7 0.2 - - - +
101F VAL* 1.3 77.5 - - - +
103F ALA* 1.3 63.8 + - - +
105F CYS* 3.1 10.0 + - - +
106F PHE* 3.0 33.4 + - + -
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 4.0 5.3 - - + -
8F MET* 3.9 39.0 - - + +
9F ILE* 4.2 3.4 - - - +
13F GLU* 3.3 21.5 - - + +
14F THR* 4.3 0.5 - - - +
82F ILE* 4.6 1.3 - - + -
99F ASP 3.0 12.0 + - - +
100F ARG 3.0 9.5 + - - +
102F ALA* 1.3 75.9 - - - +
104F GLU* 1.3 62.3 + - - +
106F PHE* 3.5 20.0 + - - +
107F ARG 3.5 5.9 + - - -
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Residues in contact with GLU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 3.6 26.7 - - + +
81F TYR* 4.7 18.6 - - - -
82F ILE* 4.7 8.2 + - + +
100F ARG* 3.1 45.5 + - + +
101F VAL* 3.9 7.4 - - - +
103F ALA* 1.3 73.6 - - - +
105F CYS* 1.3 68.0 + - - +
106F PHE 3.1 0.2 - - - -
107F ARG* 2.9 25.0 + - - +
108F ARG* 3.0 28.3 + - - +
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Residues in contact with CYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F ARG* 6.2 0.4 - - - -
44F CYS* 2.0 51.6 - - + -
47F VAL* 6.3 0.9 - - - -
101F VAL* 3.0 16.8 + - + +
102F ALA* 3.2 12.1 - - - +
104F GLU* 1.3 76.9 - - - +
106F PHE* 1.3 60.2 + - - +
108F ARG* 3.3 27.2 + - - +
109F ASN* 2.7 36.9 + - - -
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Residues in contact with PHE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 4.2 13.2 - + - -
9F ILE* 3.6 41.1 - - + -
14F THR* 3.5 17.9 - - + -
22F TYR* 3.9 37.6 + + + +
29F CYS* 4.5 0.2 - - - -
41F THR* 3.9 9.4 + - + -
44F CYS* 3.4 30.3 - - + -
45F CYS* 3.5 31.0 - - - -
48F HIS* 6.3 0.2 - - + -
102F ALA* 3.0 22.5 + - + -
103F ALA* 3.5 5.2 - - - +
104F GLU 3.1 0.2 - - - -
105F CYS* 1.3 77.0 - - - +
107F ARG* 1.3 62.2 + - - +
109F ASN* 3.2 7.1 + - - +
110F LEU* 3.1 20.8 + - - +
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Residues in contact with ARG 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 2.8 55.9 + - - +
14F THR* 4.0 2.4 - - - +
81F TYR* 6.2 1.8 - - - -
103F ALA 3.5 6.3 + - - +
104F GLU* 2.9 26.7 + - - +
106F PHE* 1.3 78.9 - - - +
108F ARG* 1.3 76.1 + - - +
110F LEU* 3.0 35.4 + - + +
111F ASP* 4.8 0.3 + - - +
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Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F VAL* 4.5 10.1 + - - +
104F GLU* 3.0 18.4 + - - +
105F CYS* 3.5 38.1 - - - +
107F ARG* 1.3 92.1 - - - +
109F ASN* 1.3 69.7 + - - +
111F ASP* 3.0 14.8 - - - +
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Residues in contact with ASN 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F GLY* 3.4 25.2 + - - -
41F THR* 3.5 26.6 + - - +
44F CYS* 3.4 13.3 - - - -
105F CYS* 2.7 29.0 + - - +
106F PHE 3.2 4.5 + - - +
107F ARG 3.0 0.8 - - - -
108F ARG* 1.3 88.8 - - - +
110F LEU* 1.3 63.3 + - - +
111F ASP* 3.0 7.3 + - - -
112F THR* 3.1 19.5 + - - +
113F TYR 3.4 7.4 + - - -
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Residues in contact with LEU 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU 5.0 0.2 - - - +
14F THR* 4.1 25.6 - - - +
16F LYS* 3.8 33.4 - - + +
22F TYR* 3.8 14.6 - - - +
41F THR* 5.2 0.4 - - - -
106F PHE 3.1 10.1 + - - +
107F ARG* 3.0 26.7 + - + +
108F ARG 3.5 0.4 - - - -
109F ASN* 1.3 77.2 - - - +
111F ASP* 1.3 63.7 + - - +
113F TYR* 3.2 22.9 + - + +
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Residues in contact with ASP 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F ARG 4.9 0.2 - - - +
108F ARG 3.0 24.3 - - - +
109F ASN* 3.6 3.3 - - - -
110F LEU* 1.3 76.2 + - - +
112F THR* 1.3 74.8 + - - +
113F TYR 3.3 3.0 + - - +
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Residues in contact with THR 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F ASP* 3.6 16.8 + - - +
40F GLY* 4.6 10.4 + - - -
41F THR* 5.0 0.7 + - - -
109F ASN* 3.1 20.7 + - - +
111F ASP* 1.3 89.1 + - + +
113F TYR* 1.3 67.6 + - - +
114F ASN* 3.0 8.5 + - - +
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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