Contacts of the helix formed by residues 334 - 356 (chain B) in PDB entry 3M0V
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 ASP 334 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B THR* 1.3 73.4 - - - +
335B PRO* 1.3 67.7 - - - +
336B ILE* 2.9 10.7 + - - +
337B GLU* 2.9 39.0 + - + +
338B SER* 3.0 10.9 + - - -
406B TYR* 2.7 30.6 + - - -
412B ARG* 2.9 41.1 + - - +
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Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLY 3.4 15.5 - - - +
59B VAL 3.2 26.9 - - - +
60B GLY 3.7 17.7 - - - +
61B THR* 3.8 17.5 - - - +
74B GLU* 5.2 2.0 - - - +
330B HIS* 4.0 16.8 - - + +
333B THR 3.1 9.4 - - - +
334B ASP* 1.3 87.2 - - - +
336B ILE* 1.3 56.3 + - - +
338B SER* 3.4 1.7 + - - -
339B LEU* 3.0 37.1 + - - +
412B ARG* 4.2 8.7 - - - +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 5.0 5.2 - - + +
84B ASP* 3.9 31.2 - - + +
87B VAL* 4.0 7.4 - - + -
88B ILE* 3.9 23.7 - - + +
334B ASP* 2.9 8.2 + - - +
335B PRO* 1.3 76.7 - - + +
337B GLU* 1.3 56.8 + - - +
339B LEU* 3.4 2.0 + - - +
340B ILE* 2.9 45.8 + - + +
406B TYR* 3.5 28.7 - - + +
411B TYR* 3.7 25.8 - - + -
412B ARG* 3.6 21.8 - - - +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ASP* 2.9 28.1 + - + +
336B ILE* 1.3 75.7 - - - +
338B SER* 1.3 63.5 + - - +
340B ILE* 3.3 6.2 + - - +
341B ASN* 3.0 21.8 + - - +
403B VAL* 3.9 17.8 - - + +
406B TYR* 3.4 28.4 - - + -
407B ARG* 2.7 57.8 + - - +
371C LEU* 3.6 25.6 - - + +
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Residues in contact with SER 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 2.8 27.0 + - - +
330B HIS* 3.2 25.4 - - - -
333B THR* 2.5 31.3 + - - +
334B ASP 3.0 5.4 + - - -
335B PRO 3.8 4.0 - - - -
337B GLU* 1.3 78.3 - - - +
339B LEU* 1.3 54.4 + - - +
341B ASN* 3.4 1.3 + - - -
342B SER* 2.7 38.3 + - - -
371C LEU* 3.7 6.6 - - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.6 22.2 - - + -
55B PRO* 4.1 4.9 - - + -
58B GLY* 3.7 14.8 - - - +
59B VAL* 3.7 16.2 - - + -
88B ILE* 3.5 36.8 - - + +
95B THR* 5.4 0.3 - - - +
326B ILE* 3.7 35.1 - - + +
328B GLN* 4.2 0.7 - - - +
330B HIS* 3.6 20.6 - - + +
335B PRO 3.0 21.1 + - - +
338B SER* 1.3 75.7 - - - +
340B ILE* 1.3 62.4 + - - +
342B SER* 3.8 2.6 - - - -
343B ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 4.1 15.7 - - + -
91B LEU* 4.1 26.5 - - + -
92B THR* 3.6 19.6 - - + +
336B ILE* 2.9 38.3 + - + +
337B GLU* 3.4 11.7 - - - +
339B LEU* 1.3 78.9 - - - +
341B ASN* 1.3 68.0 + - - +
343B ALA* 3.3 2.4 + - - +
344B ASN* 3.0 33.6 + - - +
402B PRO* 3.2 33.0 - - + +
403B VAL* 4.1 3.8 - - + +
406B TYR* 4.4 11.0 - - + -
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 5.4 3.4 - - + +
337B GLU 3.0 8.6 + - - +
338B SER* 4.1 2.7 - - - +
340B ILE* 1.3 78.5 - - - +
342B SER* 1.3 60.0 + - - +
344B ASN* 3.4 18.6 - - - +
345B GLU* 2.9 32.3 + - + +
402B PRO* 5.2 0.7 - - - +
403B VAL* 3.4 29.1 + - - +
371C LEU* 4.0 23.8 - - + +
374C THR* 6.3 0.8 - - - +
375C GLU* 4.3 23.1 + - - +
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ASP* 3.3 16.3 - - - +
294B ALA* 4.0 7.5 - - - +
326B ILE* 4.3 6.3 - - - -
328B GLN* 3.0 38.4 + - - -
338B SER 2.7 26.8 + - - -
339B LEU* 3.8 5.4 - - - -
340B ILE 3.2 0.2 - - - -
341B ASN* 1.3 69.4 - - - +
343B ALA* 1.3 66.7 + - - +
344B ASN 3.1 0.2 - - - -
345B GLU* 3.2 8.3 + - - +
346B ILE* 3.0 29.6 + - - +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 4.2 8.7 - - + +
88B ILE* 5.3 0.2 - - + -
92B THR* 4.7 4.9 - - - +
94B ALA* 4.4 11.1 - - + +
95B THR* 3.9 27.1 - - + -
326B ILE* 4.0 9.1 - - + +
339B LEU 3.0 18.7 + - - +
340B ILE* 3.6 4.7 - - - +
342B SER* 1.3 76.2 - - - +
344B ASN* 1.3 62.7 + - - +
346B ILE* 3.3 7.8 + - - +
347B ARG* 3.0 27.2 + - - +
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Residues in contact with ASN 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.9 19.8 - - - +
94B ALA* 5.8 1.4 - - - +
340B ILE* 3.0 20.4 + - - +
341B ASN* 3.4 25.7 - - - +
343B ALA* 1.3 79.0 - - - +
345B GLU* 1.3 56.8 + - - +
347B ARG* 3.2 9.9 + - - +
348B ARG* 2.8 40.0 + - - +
386B GLU* 5.8 0.2 - - - +
389B LEU* 3.7 6.3 - - + +
393B ARG* 3.3 31.8 + - - +
402B PRO* 3.9 14.6 - - - +
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA 3.3 31.0 - - - +
295B GLY* 4.4 6.9 - - - +
296B ALA* 5.9 0.2 - - - -
299B PRO* 4.6 7.6 - - - +
302B LEU* 3.9 7.5 - - + +
341B ASN* 2.9 18.9 + - + +
342B SER 3.2 6.7 + - - +
344B ASN* 1.3 72.7 - - - +
346B ILE* 1.3 59.6 + - - +
348B ARG* 2.7 46.5 + - - +
349B ALA* 2.9 29.1 + - - +
378C LYS* 3.9 23.6 + - - +
382C ARG* 4.3 7.4 + - - -
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.6 18.2 - - + -
52B VAL* 4.2 8.3 - - + -
282B PHE* 3.6 40.8 - - + -
294B ALA* 4.0 15.5 - - + -
302B LEU* 4.4 9.6 - - + -
306B PHE* 3.5 25.4 - - + -
326B ILE* 3.7 25.6 - - + -
342B SER 3.0 14.6 + - - +
343B ALA* 3.6 7.9 - - - +
345B GLU* 1.3 75.6 - - - +
347B ARG* 1.3 63.1 + - - +
349B ALA* 3.4 3.3 + - - +
350B TYR* 3.1 21.3 + - - +
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Residues in contact with ARG 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.1 30.8 + - + +
48B GLU* 3.1 30.9 + - - +
50B PHE* 3.0 41.6 + - + -
51B PHE* 3.8 1.6 - - - -
52B VAL* 6.5 0.7 - - + -
92B THR 3.7 15.6 + - - -
93B ARG* 3.1 20.8 + - - +
94B ALA* 3.4 19.9 - - + +
343B ALA 3.0 14.5 + - - +
344B ASN* 3.2 11.4 + - - +
346B ILE* 1.3 74.9 - - + +
348B ARG* 1.3 60.5 + - - +
350B TYR* 3.6 7.7 - - + +
351B ALA* 2.9 30.8 + - - +
389B LEU* 3.7 15.3 + - + +
392B ALA* 4.3 11.5 - - - +
393B ARG* 4.8 8.4 - - - +
396B THR* 5.4 0.8 + - - -
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Residues in contact with ARG 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 6.5 0.2 - - - -
344B ASN* 2.8 24.4 + - - +
345B GLU* 2.7 45.6 + - - +
347B ARG* 1.3 78.2 - - - +
349B ALA* 1.3 62.1 + - - +
351B ALA* 3.3 2.9 + - - +
352B GLN* 3.0 45.1 + - - +
384B ASP* 4.4 0.8 + - - -
385B VAL* 3.6 14.3 - - + +
386B GLU* 2.9 41.4 + - - +
389B LEU* 3.4 19.5 - - + +
382C ARG* 3.5 42.5 - - - +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO 5.3 1.1 - - - +
302B LEU* 3.7 18.8 - - + -
303B PHE* 4.0 16.5 - - + +
306B PHE* 3.6 25.9 - - + +
345B GLU 2.9 14.8 + - - +
346B ILE 3.7 1.8 - - - +
347B ARG 3.3 0.2 - - - -
348B ARG* 1.3 76.8 - - - +
350B TYR* 1.3 57.6 + - - +
352B GLN* 3.4 12.3 + - - +
353B ALA* 3.0 28.9 + - - +
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Residues in contact with TYR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 3.8 27.2 + - - +
47B VAL* 4.4 9.6 - - + -
50B PHE* 3.7 45.4 - + + -
306B PHE* 3.8 29.1 - + + -
309B LEU* 6.4 0.4 - - + -
310B VAL* 4.3 10.5 - - + -
313B GLU* 5.2 6.9 + - - -
346B ILE 3.1 17.3 + - - +
347B ARG* 3.6 7.0 - - - +
349B ALA* 1.3 76.8 - - - +
351B ALA* 1.3 62.1 + - - +
353B ALA* 3.3 3.6 + - - +
354B LEU* 3.0 57.4 + - + +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.5 6.5 - - + +
47B VAL* 3.9 24.5 - - + -
347B ARG 2.9 17.7 + - - +
348B ARG 3.6 4.5 - - - +
350B TYR* 1.3 77.7 - - - +
352B GLN* 1.3 61.9 + - - +
354B LEU* 3.1 21.4 + - - +
355B LEU* 3.3 14.5 + - - +
385B VAL* 3.9 22.9 - - + -
388B ILE* 5.1 0.9 - - + -
389B LEU* 4.2 4.5 - - + -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 3.6 15.5 - - + +
348B ARG* 3.0 38.1 + - - +
349B ALA* 3.9 9.5 - - - +
350B TYR 3.3 0.2 - - - -
351B ALA* 1.3 75.3 - - - +
353B ALA* 1.3 63.0 + - - +
355B LEU* 3.0 15.6 + - - +
380B ALA* 3.3 37.8 - - - +
381B TYR* 3.1 43.9 + - - -
383B THR 3.2 12.1 + - - -
384B ASP* 5.1 0.6 - - - +
385B VAL* 3.8 16.1 - - + +
382C ARG* 6.4 0.2 - - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 3.6 12.0 - - + -
306B PHE* 3.6 22.2 - - + +
307B ASN* 4.0 7.2 - - - +
310B VAL* 3.5 25.8 - - + +
349B ALA 3.0 18.3 + - - +
350B TYR 3.5 2.5 - - - +
352B GLN* 1.3 76.2 - - - +
354B LEU* 1.3 62.4 + - - +
355B LEU 3.3 0.9 + - - -
356B VAL* 3.3 11.3 + - - +
358B ARG* 3.1 21.9 + - - -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 5.9 1.7 - - - +
43B VAL* 4.4 24.8 - - + +
46B LYS* 3.8 37.9 - - + +
47B VAL* 4.7 0.9 - - + -
310B VAL* 3.7 30.5 - - + -
350B TYR* 3.0 49.8 + - + +
351B ALA* 3.3 12.6 - - - +
352B GLN 3.1 0.4 - - - -
353B ALA* 1.3 78.9 - - - +
355B LEU* 1.3 60.2 + - - +
356B VAL 3.6 4.9 + - - +
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Residues in contact with LEU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.1 27.1 - - + -
36B ARG* 4.3 8.4 + - - +
38B VAL* 4.2 20.7 - - + +
43B VAL* 3.8 31.6 - - + -
351B ALA 3.4 13.2 - - - +
352B GLN* 3.0 9.6 + - - +
354B LEU* 1.3 77.6 - - - +
356B VAL* 1.3 64.9 + - - +
357B ASP* 3.3 4.0 + - - +
380B ALA* 3.9 13.7 - - + +
383B THR* 3.7 38.8 - - + +
385B VAL* 3.9 16.2 - - + -
388B ILE* 5.2 0.4 - - + -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 4.0 8.1 - - + -
307B ASN* 3.9 7.6 - - - +
352B GLN 3.5 3.5 + - - +
353B ALA 3.3 17.8 + - - +
354B LEU 4.2 4.7 - - - +
355B LEU* 1.3 77.5 - - - +
357B ASP* 1.3 69.4 + - - +
358B ARG* 3.0 35.0 + - - +
361B LEU* 4.1 11.2 - - + -
376B THR* 4.6 7.9 - - + -
377B LEU* 3.8 31.9 - - + -
380B ALA* 3.6 21.5 - - + -
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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
------------------------------------------------------------
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