Contacts of the helix formed by residues 139 - 160 (chain A) in PDB entry 5UU1
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 LYS 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 1.3 74.8 - - - +
140A LYS* 1.3 60.6 + - - +
141A SER* 4.4 5.6 - - - +
142A THR* 2.8 33.9 + - - +
143A VAL* 2.9 10.6 + - - +
324A ASP* 4.3 14.8 + - + +
326A SER 6.2 1.1 - - - +
327A THR* 4.9 14.4 + - + +
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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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138A PHE 3.5 2.0 + - - -
139A LYS* 1.3 71.0 - - - +
141A SER* 1.3 64.6 + - - +
143A VAL* 3.3 4.3 + - - +
144A LEU* 3.2 39.3 + - + +
244A LEU* 3.6 27.3 - - + +
283A SER* 4.8 12.3 - - - -
284A SER* 2.7 47.6 + - - +
287A GLU* 2.8 34.4 + - - -
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 3.1 5.6 + - - +
140A LYS* 1.3 81.5 - - - +
142A THR* 1.3 61.5 + - - +
144A LEU* 3.6 8.3 + - - +
145A GLN* 3.3 21.8 + - - +
324A ASP* 5.9 4.5 - - - -
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 4.5 4.3 - - + -
139A LYS* 2.8 16.3 + - - +
141A SER* 1.3 75.2 - - - +
143A VAL* 1.3 68.4 + - - +
145A GLN* 3.2 5.7 + - - +
146A LEU* 3.0 36.8 + - + +
323A LEU* 4.0 19.5 - - + -
324A ASP* 2.7 40.1 + - - +
325A PHE* 3.8 29.6 - - + -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A PHE* 3.6 21.1 - - + +
139A LYS 2.9 17.8 + - - +
140A LYS* 3.5 8.7 - - - +
142A THR* 1.3 76.6 - - - +
144A LEU* 1.3 66.0 + - + +
146A LEU* 3.4 10.5 + - - +
147A GLY 3.2 17.0 + - - -
240A MET* 3.7 45.0 - - + +
243A TRP* 3.7 27.8 - - + -
244A LEU* 4.1 7.2 - - + +
288A ILE* 4.3 10.1 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 3.2 44.3 + - + +
141A SER* 4.0 6.5 - - - +
142A THR 3.2 0.4 - - - -
143A VAL* 1.3 79.3 - - + +
145A GLN* 1.3 64.6 + - - +
147A GLY* 3.3 2.9 + - - -
148A ILE* 3.2 28.1 + - + +
240A MET* 4.9 2.2 - - - -
244A LEU* 6.0 0.7 - - + -
287A GLU* 4.1 21.5 - - + +
288A ILE* 4.6 14.4 - - + -
313A LEU* 3.5 48.5 - - + +
315A PRO* 5.7 1.1 - - + -
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Residues in contact with GLN 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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141A SER 3.3 11.6 + - - +
142A THR* 3.2 7.6 + - - +
144A LEU* 1.3 76.4 - - - +
146A LEU* 1.3 65.7 + - - +
148A ILE* 3.3 10.6 + - - +
149A ARG* 3.0 49.3 + - + +
180A ASP 4.5 6.1 + - - -
320A LEU* 3.7 27.6 - - + +
321A GLY 3.2 32.6 + - - +
322A PRO 4.0 5.9 - - - +
323A LEU* 3.7 27.8 - - + +
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Residues in contact with LEU 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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128A LEU* 3.6 33.2 - - + -
138A PHE* 4.9 8.7 - - + -
142A THR* 3.0 35.6 + - + +
143A VAL* 3.7 5.2 - - - +
145A GLN* 1.3 76.9 - - - +
147A GLY* 1.3 58.5 + - - +
149A ARG* 3.3 4.8 + - - +
150A MET* 2.9 35.2 + - - +
172A LEU* 4.8 3.8 - - + -
182A VAL* 3.8 27.6 - - + -
243A TRP* 3.9 31.6 - - + -
323A LEU* 4.0 17.3 - - + -
325A PHE* 5.0 2.0 - - + -
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Residues in contact with GLY 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 VAL 3.2 7.9 + - - -
144A LEU 3.3 4.2 + - - -
145A GLN 3.2 0.4 - - - -
146A LEU* 1.3 78.3 - - - +
148A ILE* 1.3 55.5 + - - +
150A MET* 3.2 3.6 + - - +
151A LEU* 2.8 31.9 + - - +
236A LEU* 3.6 13.4 - - - +
240A MET* 3.8 23.3 - - - -
243A TRP* 4.9 1.2 - - - -
313A LEU* 3.9 8.3 - - - -
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Residues in contact with ILE 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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144A LEU* 3.2 21.8 + - + +
145A GLN* 3.3 5.8 + - - +
147A GLY* 1.3 73.7 - - - +
149A ARG* 1.3 67.4 + - - +
151A LEU* 3.2 9.8 + - - +
152A ASP* 3.1 26.9 + - - +
310A LYS* 3.9 33.2 - - + +
313A LEU* 3.9 20.4 - - + +
314A ASN* 3.9 28.0 - - + +
320A LEU* 4.1 34.8 - - + -
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Residues in contact with ARG 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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95A LEU* 5.6 1.6 - - - +
96A ASP* 2.8 42.2 + - - -
97A TYR* 3.3 45.8 + - + +
99A GLY* 5.4 2.5 + - - +
145A GLN* 3.0 42.1 + - + +
146A LEU 3.7 4.0 - - - +
148A ILE* 1.3 79.9 - - - +
150A MET* 1.3 67.9 + - + +
152A ASP* 3.2 19.9 + - - +
153A VAL* 3.1 23.1 + - + +
180A ASP 5.4 1.6 + - - -
182A VAL* 3.8 22.4 - - + +
320A LEU* 3.5 35.6 + - - +
323A LEU* 6.0 0.4 - - + -
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Residues in contact with MET 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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99A GLY* 5.5 0.2 - - - -
146A LEU 2.9 21.0 + - - +
147A GLY 3.5 4.7 - - - +
149A ARG* 1.3 88.0 - - + +
151A LEU* 1.3 49.9 + - - +
153A VAL* 3.1 12.5 + - + +
154A LEU* 2.7 40.2 + - - +
167A ILE* 4.5 15.9 - - + -
172A LEU* 3.5 40.2 - - + -
182A VAL* 4.4 13.0 - - + +
183A TYR 4.7 0.4 - - - -
184A LEU* 4.0 34.5 - - + +
236A LEU* 3.8 27.1 - - + -
243A TRP* 5.2 0.7 - - + -
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Residues in contact with LEU 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 GLY 2.8 20.1 + - - +
148A ILE 3.2 4.9 + - - +
150A MET* 1.3 76.5 - - - +
152A ASP* 1.3 52.7 + - - +
154A LEU* 3.5 13.0 - - + +
155A GLU* 2.7 36.6 + - - +
233A VAL* 4.9 4.0 - - + -
236A LEU* 3.9 15.9 - - + -
291A PHE* 4.1 7.0 - - + -
306A TYR* 4.2 18.3 - - + +
309A LEU* 3.8 43.1 - - + -
310A LYS* 3.8 29.4 - - + +
313A LEU* 3.9 18.4 - - + -
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Residues in contact with ASP 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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89A TRP* 4.7 2.9 + - - -
95A LEU* 3.6 26.1 - - + +
97A TYR 5.5 1.9 - - - +
98A LEU* 3.5 21.7 - - + +
99A GLY 6.1 0.2 - - - +
148A ILE* 3.1 18.9 + - - +
149A ARG* 3.2 20.5 + - - +
151A LEU* 1.3 76.0 - - - +
153A VAL* 1.3 61.3 + - - +
155A GLU* 3.4 11.0 + - - +
156A TYR* 3.2 17.2 + - - +
310A LYS* 2.6 36.6 + - - +
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Residues in contact with VAL 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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98A LEU* 3.9 9.2 - - + -
99A GLY* 3.6 40.2 - - - +
100A ILE* 3.8 20.4 - - + -
149A ARG 3.1 12.7 + - - +
150A MET* 3.1 18.7 + - + +
152A ASP* 1.3 72.1 - - - +
154A LEU* 1.3 68.5 + - - +
156A TYR* 3.3 3.2 + - - +
157A ILE* 3.1 29.6 + - + +
184A LEU* 4.1 18.2 - - + -
187A TYR* 4.0 11.7 - - + +
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Residues in contact with LEU 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 MET 2.7 19.7 + - - +
151A LEU* 3.5 12.6 - - + +
153A VAL* 1.3 77.3 - - - +
155A GLU* 1.3 62.9 + - - +
156A TYR 3.2 0.2 + - - -
157A ILE* 3.5 13.1 - - + +
158A HIS* 2.9 38.9 + - + +
164A HIS* 4.6 3.1 - - + -
167A ILE* 3.9 22.2 - - + -
184A LEU* 5.3 3.6 - - + -
232A ASP* 3.5 56.5 - - + +
233A VAL* 4.3 6.1 - - + +
236A LEU* 4.4 15.5 - - + -
306A TYR* 4.6 4.3 - - + -
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Residues in contact with GLU 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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89A TRP* 3.9 22.7 - - + -
151A LEU 2.7 20.6 + - - +
152A ASP* 3.8 14.1 - - - +
153A VAL 3.3 0.2 - - - -
154A LEU* 1.3 73.6 - - - +
156A TYR* 1.3 61.7 + - - +
158A HIS* 4.0 1.2 - - - +
159A GLU* 3.1 23.9 + - + +
303A LYS* 5.0 8.4 + - - +
306A TYR* 3.4 52.1 - - + +
310A LYS* 5.3 3.6 + - - +
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Residues in contact with TYR 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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80A VAL* 2.7 36.7 + - + -
85A CYS* 3.6 20.1 - - + +
86A ILE* 3.5 24.6 - - + +
89A TRP* 3.4 54.5 - + + +
98A LEU* 3.8 13.5 - - + -
100A ILE* 3.6 21.1 - - + -
152A ASP 3.2 11.0 + - - +
153A VAL* 3.7 7.2 - - - +
155A GLU* 1.3 79.4 - - - +
157A ILE* 1.3 63.0 + - + +
159A GLU* 3.4 1.7 + - - +
160A ASN* 2.8 49.8 + - - -
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Residues in contact with ILE 157 (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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76A PHE* 3.7 34.8 - - + -
80A VAL* 4.3 3.4 - - + -
100A ILE* 3.9 17.9 - - + -
153A VAL* 3.1 19.6 + - + +
154A LEU* 3.5 21.8 - - + +
156A TYR* 1.3 74.8 - - - +
158A HIS* 1.3 69.2 + - + +
160A ASN* 3.0 14.0 + - - +
162A TYR* 3.0 29.6 + - - +
163A VAL 4.4 0.9 - - - -
164A HIS* 3.8 37.9 - - + +
184A LEU* 5.5 0.2 - - + -
187A TYR* 4.7 9.4 - - + -
232A ASP* 4.4 0.2 - - - +
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Residues in contact with HIS 158 (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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154A LEU* 2.9 31.5 + - + +
155A GLU 4.0 1.3 - - - +
157A ILE* 1.3 78.1 - - + +
159A GLU* 1.3 62.7 + - - +
160A ASN 3.0 0.2 - - - -
161A GLU* 3.0 9.9 + - - -
162A TYR 3.2 18.6 - - - -
163A VAL* 3.9 10.8 - - + +
193A TYR* 2.8 21.5 + - - -
229A ARG* 3.5 43.9 - - + +
232A ASP* 2.7 34.6 + - + +
233A VAL* 4.9 1.1 - - + -
304A PRO* 4.8 1.3 - - + -
306A TYR* 2.6 35.8 + + - +
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 4.1 22.4 - - + -
155A GLU* 3.1 19.3 + - + +
156A TYR 3.7 6.1 - - - +
157A ILE 3.3 0.2 - - - -
158A HIS* 1.3 75.3 - - - +
160A ASN* 1.4 62.9 + - - +
161A GLU* 3.4 5.7 + - - +
303A LYS* 6.4 0.4 - - - +
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Residues in contact with ASN 160 (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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79A ARG* 4.8 4.5 - - - +
80A VAL* 3.5 33.0 - - + +
85A CYS* 6.1 0.5 - - - +
89A TRP* 5.5 1.6 - - - -
156A TYR* 2.8 52.8 + - - +
157A ILE 3.0 8.2 + - - +
158A HIS 3.0 1.2 - - - -
159A GLU* 1.4 83.2 - - - +
161A GLU* 1.4 68.1 + - - +
162A TYR* 3.4 13.5 + - - -
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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
------------------------------------------------------------
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