Contacts of the helix formed by residues 134 - 156 (chain A) in PDB entry 5JRE
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 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLU* 2.9 48.5 + - - +
130A LEU* 4.1 3.8 + - - +
132A LYS* 3.4 4.9 - - + +
133A GLY* 1.3 74.0 - - - +
135A ILE* 1.3 61.0 + - - +
136A GLU* 3.6 10.0 + - - +
137A TYR* 3.3 37.2 + - - +
138A ALA* 3.9 2.8 + - - +
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Residues in contact with ILE 135 (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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130A LEU* 4.1 22.2 - - + -
133A GLY* 3.3 13.8 + - - +
134A ASN* 1.3 71.1 - - - +
136A GLU* 1.3 64.0 + - - +
138A ALA* 3.1 5.2 + - - +
139A LYS* 3.0 36.4 + - + +
180A ILE* 4.8 8.1 - - + +
183A LYS* 4.2 25.6 - - + +
184A SER* 3.6 25.4 - - - +
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Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASN* 3.3 8.8 + - - +
135A ILE* 1.3 79.2 - - - +
137A TYR* 1.3 62.3 + - - +
139A LYS* 3.4 26.7 + - - +
140A LYS* 3.0 25.1 + - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.6 25.0 - + - -
93A ILE* 4.0 11.8 - - + +
122A ILE 5.1 0.9 - - - -
125A LYS* 3.3 42.5 - - + +
126A SER* 4.0 18.8 - - - -
129A GLU* 3.6 24.5 - - + -
134A ASN* 3.3 29.6 + - - +
135A ILE 3.3 0.8 - - - -
136A GLU* 1.3 77.0 - - - +
138A ALA* 1.3 60.3 + - - +
140A LYS* 3.3 13.5 + - + +
141A ALA* 2.9 28.9 + - + +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 4.4 8.7 - - - +
130A LEU* 3.9 38.1 - - + -
134A ASN 3.9 1.0 + - - +
135A ILE 3.1 9.0 + - - +
137A TYR* 1.3 78.1 - - - +
139A LYS* 1.3 60.3 + - - +
141A ALA* 3.3 8.6 + - - +
142A LYS* 2.9 28.1 + - - +
176A LEU* 3.8 12.7 - - + +
180A ILE* 3.7 12.6 - - + +
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Residues in contact with LYS 139 (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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135A ILE* 3.0 24.5 + - + +
136A GLU* 3.7 30.4 + - - +
137A TYR 3.3 0.2 - - - -
138A ALA* 1.3 72.5 - - - +
140A LYS* 1.3 65.0 + - - +
142A LYS* 3.4 6.7 + - + +
143A GLN* 3.2 30.5 + - - +
180A ILE* 4.0 26.9 - - + -
184A SER* 3.8 23.6 + - - -
131C ILE* 6.2 4.3 - - - -
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Residues in contact with LYS 140 (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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92A TYR* 4.2 4.8 + - - +
96A ASN* 2.6 39.4 + - - +
136A GLU* 3.0 17.3 + - - +
137A TYR* 3.6 17.0 - - + +
139A LYS* 1.3 74.3 - - - +
141A ALA* 1.3 65.4 + - - +
143A GLN* 3.2 16.2 + - + +
144A ASP* 2.8 55.0 + - - +
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Residues in contact with ALA 141 (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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92A TYR* 3.6 16.1 + - - +
122A ILE* 3.9 15.9 - - + +
126A SER* 3.2 27.4 - - - +
137A TYR* 2.9 19.2 + - + +
138A ALA 3.6 4.9 - - - +
140A LYS* 1.3 75.3 - - - +
142A LYS* 1.3 57.1 + - - +
144A ASP* 3.3 1.7 + - - +
145A LEU* 2.8 34.0 + - - +
176A LEU* 3.9 6.5 - - + -
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Residues in contact with LYS 142 (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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138A ALA 2.9 14.3 + - - +
139A LYS* 3.5 10.5 - - - +
140A LYS 3.2 0.2 - - - -
141A ALA* 1.3 76.8 - - - +
143A GLN* 1.3 62.2 + - + +
145A LEU* 3.3 4.4 + - - +
146A GLU* 2.7 66.4 + - - +
173A ILE* 4.6 7.4 - - + +
176A LEU* 3.5 16.1 - - + +
177A ILE* 3.4 36.6 - - + -
180A ILE* 4.1 16.6 - - + -
128C GLU* 3.5 21.6 + - - -
131C ILE* 4.5 9.4 - - + +
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Residues in contact with GLN 143 (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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139A LYS* 3.2 18.9 + - - +
140A LYS* 3.2 16.4 + - + +
142A LYS* 1.3 80.6 - - + +
144A ASP* 1.3 61.6 + - - +
146A GLU* 3.3 16.7 + - - +
147A SER* 3.0 32.7 + - - -
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Residues in contact with ASP 144 (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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92A TYR* 2.6 34.0 + - + +
122A ILE* 5.9 0.7 - - + -
140A LYS* 2.8 44.3 + - - +
141A ALA 3.6 2.5 - - - +
143A GLN* 1.3 80.0 - - - +
145A LEU* 1.3 59.2 + - + +
147A SER* 3.3 2.2 + - - -
148A LEU* 3.0 23.9 + - - +
1B MET* 3.1 45.5 - - + +
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Residues in contact with LEU 145 (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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119A ALA* 3.8 29.8 - - + +
122A ILE* 3.9 32.8 - - + -
123A LEU 5.1 0.4 - - - +
141A ALA 2.8 19.6 + - - +
142A LYS* 3.9 2.2 - - - +
144A ASP* 1.3 70.5 - - - +
146A GLU* 1.3 60.4 + - - +
148A LEU* 3.3 15.7 + - + +
149A TYR* 2.8 29.3 + - - +
169A VAL* 4.0 4.2 - - + +
172A ILE* 3.7 29.8 - - + -
173A ILE* 3.7 22.3 - - + +
176A LEU* 4.0 21.8 - - + -
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Residues in contact with GLU 146 (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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142A LYS* 2.7 55.7 + - - +
143A GLN* 3.5 15.3 - - - +
145A LEU* 1.3 73.8 - - - +
147A SER* 1.3 64.5 + - - +
149A TYR* 3.3 4.8 + - - +
150A LEU* 3.0 28.3 + - - +
173A ILE* 4.0 20.8 - - + +
38C TYR* 3.7 29.6 + - + +
42C ARG* 5.6 3.4 - - - -
124C ARG* 3.1 20.6 + - - +
128C GLU* 3.6 1.6 - - - +
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Residues in contact with SER 147 (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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143A GLN* 3.0 15.9 + - - +
144A ASP* 3.3 9.8 + - - -
146A GLU* 1.3 77.2 - - - +
148A LEU* 1.3 56.7 + - - +
150A LEU* 3.2 10.8 + - - +
151A ASP* 2.9 35.5 + - - +
0B SER 4.0 21.6 + - - -
1B MET* 3.8 15.7 - - - +
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Residues in contact with LEU 148 (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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115A ILE* 4.0 16.4 - - + +
118A ILE* 3.8 32.5 - - + -
119A ALA 5.0 1.1 - - - +
122A ILE* 5.7 0.4 - - + -
144A ASP 3.0 15.1 + - - +
145A LEU* 3.3 24.2 + - + +
147A SER* 1.3 75.6 - - - +
149A TYR* 1.3 64.0 + - - +
151A ASP* 3.2 4.0 + - - +
152A LEU* 2.9 36.8 + - + +
169A VAL* 4.7 14.6 - - + -
1B MET* 3.8 14.7 - - + +
2B LEU* 3.7 33.9 - - + -
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Residues in contact with TYR 149 (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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145A LEU 2.8 16.6 + - - +
146A GLU* 3.4 6.1 - - - +
147A SER 3.3 0.2 - - - -
148A LEU* 1.3 77.1 - - - +
150A LEU* 1.3 59.0 + - + +
152A LEU* 3.3 6.1 + - - +
153A LEU* 2.9 51.5 + - + +
166A LEU* 3.5 39.7 - - + +
167A ASP* 5.4 0.6 + - - -
169A VAL* 4.0 17.2 - - + +
170A SER* 3.8 21.5 + - - -
173A ILE* 4.1 9.4 - - + -
34C LYS* 3.6 30.9 + - + +
38C TYR* 4.2 32.1 - + + -
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Residues in contact with LEU 150 (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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146A GLU 3.0 16.7 + - - +
147A SER* 3.6 10.3 - - - +
149A TYR* 1.3 78.7 - - + +
151A ASP* 1.3 57.5 + - - +
153A LEU* 3.4 19.1 + - + +
154A TYR* 2.9 29.5 + - - +
35C SER* 6.3 0.7 - - - -
38C TYR* 3.6 55.2 - - + +
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Residues in contact with ASP 151 (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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147A SER 2.9 16.0 + - - +
148A LEU 3.4 7.9 - - - +
150A LEU* 1.3 78.3 - - - +
152A LEU* 1.3 61.6 + - - +
154A TYR* 3.2 13.0 + - - +
155A ILE* 3.2 18.1 + - - +
0B SER* 3.2 21.9 + - - -
1B MET* 2.5 33.4 + - - +
2B LEU* 3.0 28.4 + - + -
5B LEU* 3.7 23.1 - - + +
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Residues in contact with LEU 152 (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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112A LEU* 4.6 13.9 - - + +
115A ILE* 4.6 8.3 - - + -
116A GLY* 5.0 12.6 - - - +
148A LEU* 2.9 38.8 + - + +
149A TYR* 3.7 1.6 - - - +
151A ASP* 1.3 72.7 - - - +
153A LEU* 1.3 67.0 + - - +
155A ILE* 3.3 27.1 + - + +
156A GLU 3.8 2.9 + - - -
157A LEU* 3.8 24.6 + - + +
165A LYS* 5.5 0.7 - - + -
166A LEU* 3.5 26.0 - - + +
169A VAL* 4.3 20.0 - - + -
2B LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 153 (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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149A TYR* 2.9 39.8 + - + +
150A LEU* 3.6 17.9 - - + +
152A LEU* 1.3 75.7 - - - +
154A TYR* 1.3 64.2 + - - +
156A GLU* 3.1 13.7 + - - -
157A LEU 6.0 0.2 - - - +
166A LEU* 3.6 32.6 - - + +
31C LYS* 3.7 32.8 - - + +
34C LYS* 3.9 18.8 - - + +
35C SER* 3.9 36.6 - - - +
38C TYR* 5.4 0.7 - - + -
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Residues in contact with TYR 154 (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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150A LEU 2.9 15.4 + - - +
151A ASP* 3.2 10.3 + - - +
153A LEU* 1.3 76.4 - - - +
155A ILE* 1.3 63.8 + - - +
156A GLU* 3.1 4.3 - - - +
5B LEU* 3.5 33.4 - - + -
6B ASP* 2.5 29.9 + - - -
9B LYS* 3.0 57.7 + - + +
31C LYS* 5.0 5.4 - - - +
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Residues in contact with ILE 155 (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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112A LEU* 4.0 25.1 - - + -
151A ASP 3.2 15.0 + - - +
152A LEU* 3.5 16.8 - - + +
153A LEU 3.2 0.8 - - - -
154A TYR* 1.3 76.5 - - - +
156A GLU* 1.3 57.2 + - - +
157A LEU* 3.8 13.7 - - + -
2B LEU* 4.0 11.7 - - + -
5B LEU* 4.0 12.8 - - + -
8B LEU* 4.0 15.3 - - + -
9B LYS* 3.9 26.3 - - + +
12B TYR* 3.6 32.5 - - + -
13B GLN* 2.9 22.5 + - - -
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Residues in contact with GLU 156 (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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152A LEU 3.8 0.8 + - - -
153A LEU 3.1 13.2 + - - +
154A TYR 3.1 16.8 - - - +
155A ILE* 1.3 78.5 - - - +
157A LEU* 1.3 67.8 + - - +
158A LYS* 3.4 24.6 + - - +
9B LYS* 3.2 20.9 + - - +
13B GLN* 3.0 22.7 + - - +
28C ARG* 5.5 6.1 - - - +
31C LYS* 3.9 31.9 - - + +
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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