Contacts of the helix formed by residues 660 - 683 (chain B) in PDB entry 4MVX
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 660 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B PHE* 4.3 6.3 - - - -
655B TYR* 2.7 22.3 + - + +
656B TYR 4.7 0.2 - - - -
658B ILE* 4.2 18.9 - - + +
659B PRO* 1.3 77.1 - - - +
661B ILE* 1.3 62.8 + - - +
662B GLN* 3.4 9.2 + - - +
663B LYS* 3.0 54.1 + - + +
664B ALA 3.3 13.2 + - - -
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Residues in contact with ILE 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 4.0 26.9 - - + -
268B VAL* 3.5 26.9 - - + -
269B ILE* 4.3 11.9 - - + -
582B LEU* 4.1 19.5 - - + +
587B PHE* 4.1 17.8 - - + -
655B TYR 5.3 0.2 - - - -
656B TYR* 4.6 14.6 - - + -
659B PRO* 4.1 2.9 - - + -
660B ASP* 1.3 74.1 - - - +
662B GLN* 1.3 66.0 + - - +
664B ALA* 3.2 7.0 + - - +
665B ILE* 3.0 29.1 + - + +
716B ILE* 3.6 29.8 - - + -
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Residues in contact with GLN 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LEU 3.4 17.5 + - - +
583B ARG* 3.0 37.0 + - - +
584B GLU 3.6 7.7 + - - -
585B SER* 3.4 19.2 - - - +
586B GLY* 3.5 20.6 + - - +
587B PHE* 5.8 1.0 - - - -
589B ASP* 5.0 3.3 + - - +
660B ASP* 3.3 7.2 - - - +
661B ILE* 1.3 79.8 - - - +
663B LYS* 1.3 68.8 + - - +
665B ILE* 3.3 6.3 + - - +
666B ILE* 3.1 40.6 + - + +
802B GOL 4.5 5.7 + - - -
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Residues in contact with LYS 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 6.1 1.6 - - - -
677A ALA* 5.6 9.7 - - - +
655B TYR* 3.5 41.4 - - + +
658B ILE* 5.7 1.3 - - + -
660B ASP* 3.0 33.7 + - - +
662B GLN* 1.3 82.2 + - - +
664B ALA* 1.3 66.7 + - - +
666B ILE* 3.3 11.8 + - + +
667B ALA* 2.9 25.1 + - - +
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Residues in contact with ALA 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B ALA* 4.3 5.1 - - - +
655B TYR* 3.7 25.9 - - + +
656B TYR* 4.1 34.1 - - + +
660B ASP 3.3 7.2 + - - +
661B ILE* 3.2 13.8 + - - +
663B LYS* 1.3 78.8 - - - +
665B ILE* 1.3 62.2 + - + +
667B ALA* 3.3 3.4 + - - +
668B VAL* 3.1 28.0 + - - +
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Residues in contact with ILE 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B TYR* 3.5 29.4 - - + +
582B LEU* 3.7 39.9 - - + +
583B ARG* 3.8 17.9 - - + +
656B TYR* 5.6 0.4 - - - +
661B ILE* 3.0 24.2 + - + +
662B GLN* 3.6 5.4 - - - +
663B LYS 3.2 0.2 - - - -
664B ALA* 1.3 76.2 - - + +
666B ILE* 1.3 57.4 + - - +
668B VAL* 3.2 6.6 + - - +
669B PHE* 2.8 37.6 + - + -
713B LEU* 4.5 5.8 - - + -
716B ILE* 4.0 31.6 - - + -
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Residues in contact with ILE 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583B ARG* 3.5 42.8 - - - +
662B GLN* 3.1 30.7 + - + +
663B LYS* 3.3 11.4 + - + +
665B ILE* 1.3 76.2 - - - +
667B ALA* 1.3 52.1 - - - +
669B PHE* 3.1 6.5 + - - +
670B ASP* 2.7 50.8 + - - +
673B ARG* 4.6 5.6 - - - +
802B GOL 5.2 2.9 - - - +
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Residues in contact with ALA 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.7 10.3 - - + +
651B THR* 4.0 26.5 - - + -
652B ALA* 5.1 2.0 - - - +
655B TYR* 4.1 9.2 - - + -
663B LYS 2.9 16.3 + - - +
664B ALA* 3.5 5.6 - - - +
666B ILE* 1.3 76.2 - - - +
668B VAL* 1.3 63.9 + - - +
670B ASP* 3.2 18.7 + - - +
671B VAL* 3.3 15.9 + - - +
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Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.8 18.1 - - + +
652B ALA* 4.8 4.0 - - + -
656B TYR* 6.1 0.9 - - + -
664B ALA 3.1 15.0 + - - +
665B ILE 3.5 7.6 - - - +
667B ALA* 1.3 75.7 - - - +
669B PHE* 1.3 58.7 + - - +
671B VAL* 3.0 6.9 + - - +
672B LEU* 3.0 25.6 + - + +
709B THR* 3.7 26.6 - - + +
712B LEU* 4.0 28.0 - - + +
713B LEU* 3.6 35.7 - - + -
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Residues in contact with PHE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B TYR* 3.6 31.9 - + - -
583B ARG* 6.1 1.6 - - - +
605B GLU* 3.4 35.4 - - + -
606B LEU* 4.1 15.5 - - + -
609B THR* 3.9 14.1 - - + -
610B LEU* 4.4 5.8 - - + -
665B ILE* 2.8 34.4 + - + +
666B ILE* 3.8 3.8 - - - +
668B VAL* 1.3 74.2 - - - +
670B ASP* 1.3 60.6 + - - +
672B LEU* 3.5 24.1 - - + +
673B ARG* 2.8 57.6 + - - +
713B LEU* 3.8 24.0 - - + -
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Residues in contact with ASP 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ASP* 5.5 4.3 - - - +
644B LEU* 5.5 1.0 - - - +
666B ILE* 2.7 30.7 + - - +
667B ALA* 3.2 13.1 + - - +
669B PHE* 1.3 74.4 - - - +
671B VAL* 1.3 58.5 + - + +
673B ARG* 2.9 29.0 + - - +
674B ALA* 3.1 26.2 + - - +
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Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 5.2 1.3 - - + -
644B LEU* 4.1 24.2 - - + +
645B ILE* 4.2 22.0 - - + +
648B LEU* 3.8 23.3 - - + -
667B ALA 3.3 13.2 + - - +
668B VAL 3.0 8.1 + - - +
670B ASP* 1.3 74.4 - - + +
672B LEU* 1.3 62.2 + - - +
674B ALA* 3.1 7.0 + - - +
675B ILE* 2.8 45.1 + - + +
709B THR* 3.8 13.7 - - + -
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Residues in contact with LEU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B THR* 3.8 11.4 - - + -
610B LEU* 4.0 30.3 - - + -
613B LEU* 4.0 20.2 - - + +
668B VAL* 3.0 13.3 + - + +
669B PHE* 3.2 49.8 + - + +
671B VAL* 1.3 76.5 - - - +
673B ARG* 1.3 62.2 + - - +
675B ILE* 3.2 8.0 + - + +
676B ASN* 3.0 28.4 + - - +
706B VAL* 5.3 2.5 - - + -
709B THR* 3.6 25.6 - - + +
713B LEU* 4.2 10.1 - - + -
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Residues in contact with ARG 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B ARG* 5.9 3.2 - - - +
605B GLU* 4.7 11.7 - - - +
609B THR* 4.3 16.4 + - + +
666B ILE* 4.0 9.7 + - - +
669B PHE* 2.8 41.5 + - - +
670B ASP* 2.9 42.1 + - - +
672B LEU* 1.3 72.8 - - - +
674B ALA* 1.3 62.7 + - - +
676B ASN* 3.2 10.2 + - - +
677B ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A TYR* 5.5 1.1 - - - +
641B LEU* 4.1 9.1 - - + +
644B LEU* 3.8 28.9 - - + -
670B ASP 3.1 15.8 + - - +
671B VAL 3.1 7.8 + - - +
673B ARG* 1.3 76.8 - - - +
675B ILE* 1.3 57.5 + - - +
677B ALA* 3.3 8.5 + - - +
678B TYR* 3.0 27.7 + - - +
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Residues in contact with ILE 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 3.6 18.6 - - + -
641B LEU* 4.0 27.8 - - + -
645B ILE* 4.9 1.3 - - + -
671B VAL* 2.8 38.8 + - + +
672B LEU* 3.6 15.7 - - + +
674B ALA* 1.3 75.0 - - - +
676B ASN* 1.3 57.8 + - - +
678B TYR* 3.3 3.1 + - - +
679B VAL* 2.9 27.6 + - + +
701B ILE 5.7 0.2 - - - +
702B THR* 3.9 32.3 - - + +
705B GLY* 3.9 32.5 - - - +
706B VAL 4.3 0.7 - - - +
709B THR* 4.4 2.9 - - + -
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Residues in contact with ASN 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B ASP 4.9 1.6 - - - -
609B THR* 3.1 37.4 + - - +
612B ASN* 3.3 16.0 + - - -
613B LEU* 3.9 15.2 - - - +
616B ARG* 3.3 21.1 + - - +
672B LEU 3.0 23.4 + - - -
673B ARG* 3.5 9.1 - - - +
675B ILE* 1.3 76.0 - - - +
677B ALA* 1.3 57.1 + - - +
679B VAL* 3.2 7.5 + - - +
680B THR* 2.9 33.7 + - - +
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Residues in contact with ALA 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LYS* 5.2 11.9 - - - +
673B ARG 3.0 12.1 + - - +
674B ALA* 3.3 11.6 + - - +
676B ASN* 1.3 76.0 - - - +
678B TYR* 1.3 52.7 + - - +
680B THR* 3.2 6.8 + - - -
681B ASP* 2.8 44.3 + - - +
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Residues in contact with TYR 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 4.3 22.2 - - + -
638B ASP* 2.4 43.7 + - - -
641B LEU* 3.3 34.3 - - + -
674B ALA 3.0 9.2 + - - +
675B ILE* 3.4 9.0 - - + +
677B ALA* 1.3 76.0 - - - +
679B VAL* 1.3 57.5 + - - +
681B ASP* 3.2 5.6 + - - +
682B MET* 2.9 51.6 + - + +
698B VAL* 3.6 49.4 + - + +
701B ILE* 3.7 13.8 - - + +
702B THR* 4.2 10.3 - - - -
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Residues in contact with VAL 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B LEU* 4.1 8.1 - - + -
616B ARG* 3.6 39.3 - - + +
622B ILE* 6.4 0.2 - - + -
675B ILE* 2.9 18.4 + - + +
676B ASN* 3.6 6.7 - - - +
678B TYR* 1.3 77.5 - - + +
680B THR* 1.3 58.0 + - - +
682B MET* 3.3 2.1 + - - -
683B ALA* 2.9 26.7 + - - -
684B PRO* 3.3 25.6 - - + +
685B TRP* 4.2 4.1 - - + -
698B VAL* 5.3 1.6 - - + -
702B THR* 3.7 36.1 - - + +
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Residues in contact with THR 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ARG* 5.3 2.1 + - - -
616B ARG* 3.6 17.6 + - - +
676B ASN* 2.9 20.2 + - - +
677B ALA* 3.6 7.4 - - - -
679B VAL* 1.3 77.1 - - - +
681B ASP* 1.3 65.3 + - - +
683B ALA* 3.7 10.0 + - - +
685B TRP* 4.5 13.4 - - + -
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Residues in contact with ASP 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PRO* 5.6 3.5 - - - +
430A GLU* 3.4 17.3 + - + +
431A PHE* 4.9 1.4 + - - +
434A ARG* 3.0 23.9 + - - -
588A SER* 5.3 5.7 + - - -
663A LYS* 5.7 4.3 - - - -
637B GLU* 3.2 30.1 - - - +
677B ALA* 2.8 24.1 + - - +
678B TYR 3.4 8.3 - - - +
680B THR* 1.3 79.5 - - - +
682B MET* 1.3 61.7 + - - +
683B ALA 3.5 0.2 + - - -
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Residues in contact with MET 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLU* 3.3 43.1 - - - +
434A ARG* 3.9 5.7 + - - -
637B GLU* 4.8 8.1 - - - +
678B TYR* 2.9 42.1 + - + +
679B VAL 4.1 1.8 - - - +
681B ASP* 1.3 75.0 - - - +
683B ALA* 1.3 72.6 + - - +
684B PRO 3.4 0.3 - - - -
687B LEU* 3.5 17.2 - - + +
694B ARG* 3.3 42.4 - - + +
698B VAL* 3.8 34.1 - - + -
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Residues in contact with ALA 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ARG* 3.8 27.1 - - - +
679B VAL 2.9 12.2 + - - -
680B THR 4.3 4.5 - - - +
681B ASP 3.3 1.4 - - - -
682B MET* 1.3 79.2 - - - +
684B PRO* 1.3 68.2 - - - +
685B TRP* 3.1 31.9 - - + +
686B LYS* 3.0 22.0 + - + +
687B LEU* 3.4 6.6 + - - +
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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