Contacts of the helix formed by residues 422 - 442 (chain A) in PDB entry 4WMJ
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 GLY 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A PRO* 3.3 20.7 + - - +
419A ILE 3.1 9.7 + - - -
421A ASN* 1.3 75.2 - - - +
423A ALA* 1.3 64.1 + - - +
424A HIS 3.2 2.5 - - - -
425A HIS* 3.2 18.8 + - - +
426A LYS* 3.2 19.8 + - - +
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Residues in contact with ALA 423 (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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419A ILE 3.7 0.8 + - - -
420A ALA* 3.1 23.5 + - + +
421A ASN 3.3 2.3 + - - +
422A GLY* 1.3 79.9 - - - +
424A HIS* 1.3 64.6 + - - +
426A LYS* 3.6 7.4 + - - +
427A ILE* 3.4 29.7 + - + +
223B THR* 5.3 7.0 - - + -
533B GLN* 6.1 0.2 - - - -
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Residues in contact with HIS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ASN 5.7 0.9 - - - +
419A ILE* 3.4 34.5 + - + +
420A ALA* 4.0 8.1 - - + +
422A GLY 3.2 0.6 - - - -
423A ALA* 1.3 78.3 - - - +
425A HIS* 1.3 59.8 + - - +
427A ILE* 3.3 4.4 + - - +
428A LEU* 2.9 28.3 + - - +
190B ILE* 2.8 42.8 - - + +
192B GLY* 3.7 15.0 - - - +
223B THR* 3.6 15.7 - - + +
224B ASN* 3.1 31.3 + - - -
227B SER* 2.8 30.6 + - - -
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Residues in contact with HIS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PRO* 2.9 42.9 + - + -
413A ALA 3.5 20.3 + - - -
414A GLN* 3.8 2.0 - - - -
415A THR* 3.6 42.1 - - + -
422A GLY* 3.2 11.4 + - - +
424A HIS* 1.3 77.5 - - - +
426A LYS* 1.3 66.4 + - + +
428A LEU* 3.6 26.4 - - + +
429A LEU* 2.9 44.4 + - + +
191B ASP* 5.0 2.8 + - - -
192B GLY 5.7 1.7 + - - +
556B PHE* 5.5 0.2 - + - -
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Residues in contact with LYS 426 (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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422A GLY 3.2 16.2 + - - +
423A ALA* 3.9 7.9 - - - +
424A HIS 3.4 0.2 - - - -
425A HIS* 1.3 79.1 - - + +
427A ILE* 1.3 58.5 + - + +
429A LEU* 3.4 2.8 + - + -
430A ALA* 3.0 26.4 + - - +
529B GLU* 5.1 6.5 - - + +
532B LEU* 3.5 41.3 + - + +
533B GLN* 3.7 32.7 - - - +
556B PHE* 3.2 44.0 - - + -
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Residues in contact with ILE 427 (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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423A ALA* 3.4 18.1 + - + +
424A HIS 3.3 6.8 + - - +
425A HIS 3.3 0.4 - - - -
426A LYS* 1.3 75.3 - - + +
428A LEU* 1.3 67.2 + - - +
430A ALA* 3.2 6.6 + - - +
431A ASN* 2.9 43.1 + - - +
190B ILE* 3.7 20.6 - - + -
219B GLN* 3.6 37.2 - - + +
220B GLU* 4.9 2.9 - - + -
223B THR* 3.8 31.0 - - + +
529B GLU* 4.3 12.8 - - - +
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Residues in contact with LEU 428 (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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344A TYR* 3.3 49.5 - - + +
345A ASP* 6.0 0.2 - - - +
387A GLY 3.9 8.1 - - - +
388A THR* 4.1 2.2 - - + +
412A PRO* 5.5 0.2 - - + -
424A HIS 2.9 17.8 + - - +
425A HIS* 3.3 29.6 + - + +
427A ILE* 1.3 77.5 - - - +
429A LEU* 1.3 63.3 + - + +
431A ASN* 3.3 5.2 + - - +
432A PHE* 3.0 20.3 + - - +
189B ASN* 3.8 21.8 - - - +
190B ILE* 3.8 17.2 - - + +
191B ASP* 3.8 23.3 - - + +
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Residues in contact with LEU 429 (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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411A ALA* 3.9 22.4 - - + -
412A PRO* 3.6 17.3 - - + +
413A ALA 4.1 1.8 - - - +
425A HIS* 2.9 48.5 + - + +
426A LYS* 3.9 6.3 - - + +
428A LEU* 1.3 74.9 - - + +
430A ALA* 1.3 65.5 + - - +
432A PHE* 3.3 5.9 + - + +
433A LEU* 3.0 32.2 + - - +
532B LEU* 4.0 8.5 - - + -
552B LEU* 4.0 24.2 - - + -
556B PHE* 3.8 31.4 - - + -
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Residues in contact with ALA 430 (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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426A LYS 3.0 17.6 + - - +
427A ILE* 3.2 5.8 + - - +
429A LEU* 1.3 75.5 - - - +
431A ASN* 1.3 58.6 + - - +
433A LEU* 3.8 1.4 - - - +
434A ALA* 2.8 31.7 + - - +
525B ALA* 3.7 28.4 - - + +
528B ILE* 3.9 21.2 - - + +
529B GLU* 3.8 16.2 - - + +
532B LEU* 3.8 3.7 - - + +
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Residues in contact with ASN 431 (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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344A TYR* 4.0 6.7 - - + -
388A THR* 4.2 12.2 - - + +
391A GLN* 2.9 35.9 + - - +
427A ILE* 2.9 41.6 + - - +
428A LEU 3.6 6.5 - - - +
430A ALA* 1.3 74.1 - - - +
432A PHE* 1.3 66.3 + - - +
434A ALA* 4.4 1.8 - - - -
435A GLN* 2.9 32.5 + - - +
190B ILE* 5.0 0.2 - - - +
219B GLN* 4.7 4.0 + - - -
220B GLU* 4.6 8.9 + - - +
521B GLY 5.0 1.9 - - - +
522B LYS* 5.6 3.1 - - - +
525B ALA* 4.0 20.4 - - - +
529B GLU* 5.6 0.2 + - - -
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Residues in contact with PHE 432 (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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344A TYR* 3.6 27.4 - + + -
409A PHE* 3.5 43.3 - - + -
410A LEU 3.6 12.3 - - - -
411A ALA* 3.7 26.0 - - + -
428A LEU 3.0 13.6 + - - +
429A LEU* 3.4 15.7 - - + +
431A ASN* 1.3 76.5 - - - +
433A LEU* 1.3 84.4 + - + +
435A GLN 3.8 3.8 + - - -
436A THR* 3.9 16.3 + - - +
479A SER* 4.0 17.2 + - - -
480A ILE 4.0 4.5 - - - -
481A VAL* 3.8 27.1 - - + -
548B LEU* 4.9 1.8 - - + -
552B LEU* 4.6 4.7 - - + -
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Residues in contact with LEU 433 (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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61A LYS* 5.2 0.2 + - - -
429A LEU 3.0 23.4 + - - +
430A ALA 3.8 2.5 - - - +
432A PHE* 1.3 85.3 - - + +
434A ALA* 1.4 65.6 + - - +
436A THR* 3.2 9.1 + - - -
437A GLU* 3.1 22.0 + - - +
528B ILE* 3.8 25.8 - - + -
532B LEU* 4.1 6.7 - - + -
545B THR* 4.5 9.3 + - + +
548B LEU* 3.4 37.0 - - + -
549B ILE* 3.8 25.8 - - + +
552B LEU* 3.9 23.6 - - + -
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Residues in contact with ALA 434 (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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430A ALA 2.8 23.1 + - - +
431A ASN* 4.0 2.9 - - - +
433A LEU* 1.4 72.9 - - - +
435A GLN* 1.3 60.9 + - + +
437A GLU* 3.3 5.3 + - - +
438A ALA* 2.8 30.5 + - - +
521B GLY* 3.6 10.5 - - - +
524B LEU* 3.6 9.8 - - + +
525B ALA* 3.2 32.5 - - + +
528B ILE* 3.9 7.6 - - - -
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Residues in contact with GLN 435 (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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344A TYR* 3.8 4.5 - - - +
391A GLN* 3.5 36.8 - - - +
395A TYR* 3.2 16.9 - - + +
399A HIS* 2.8 32.1 + - - -
409A PHE* 3.7 21.1 - - + -
431A ASN* 2.9 22.5 + - - +
432A PHE 4.3 0.2 - - - +
433A LEU 3.2 0.2 - - - -
434A ALA* 1.3 78.4 - - + +
436A THR* 1.3 58.2 + - - +
438A ALA* 3.3 3.4 + - - +
439A LEU* 2.9 37.3 + - + +
518B VAL 5.3 1.8 + - - -
521B GLY* 3.7 26.5 + - - -
522B LYS* 4.8 1.0 - - - +
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Residues in contact with THR 436 (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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61A LYS* 3.1 26.3 + - - +
409A PHE* 3.4 42.6 - - + -
432A PHE 3.9 6.0 + - - +
433A LEU* 3.2 11.1 + - - -
435A GLN* 1.3 74.4 - - - +
437A GLU* 1.3 66.3 + - - +
439A LEU* 3.4 5.4 + - - +
440A MET* 3.1 24.1 + - - +
475A ARG 5.2 0.2 - - - +
477A THR* 3.4 22.2 + - - +
479A SER* 3.6 14.8 + - - +
548B LEU* 4.7 1.9 - - - +
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Residues in contact with GLU 437 (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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61A LYS* 4.1 8.7 - - - +
433A LEU 3.1 10.4 + - - +
434A ALA 3.5 6.3 - - - +
436A THR* 1.3 82.1 + - - +
438A ALA* 1.3 56.9 + - - +
440A MET* 3.4 3.4 + - - +
441A LYS* 2.9 50.4 + - + +
524B LEU* 3.6 33.6 - - + +
528B ILE* 3.7 10.9 - - - +
541B HIS* 2.8 39.6 - - - +
542B ASP* 3.7 9.4 + - - +
545B THR* 3.5 17.0 - - + +
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Residues in contact with ALA 438 (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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399A HIS* 3.7 17.4 + - + -
434A ALA 2.8 17.7 + - - +
435A GLN 3.5 4.9 - - - +
436A THR 3.2 0.2 - - - -
437A GLU* 1.3 73.8 - - - +
439A LEU* 1.3 59.6 + - - +
441A LYS* 5.2 0.2 - - - -
442A GLY* 3.0 31.0 + - - +
471A PHE* 5.4 0.9 - - - +
473A GLY* 4.6 0.3 - - - -
520B LEU* 3.7 21.0 - - + +
521B GLY* 4.2 9.2 - - - +
524B LEU* 3.6 18.6 - - + +
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Residues in contact with LEU 439 (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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395A TYR* 5.8 1.3 - - + -
398A VAL* 3.7 42.2 - - + +
399A HIS* 3.6 26.5 - - + +
407A CYS* 5.0 1.1 - - - -
409A PHE* 4.0 19.7 - - + -
435A GLN* 2.9 21.5 + - + +
436A THR* 3.8 4.5 - - - +
438A ALA* 1.3 76.9 - - - +
440A MET* 1.3 58.5 + - - +
473A GLY* 3.2 15.1 - - - -
475A ARG* 3.0 49.4 + - + +
477A THR* 3.7 23.8 - - + -
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Residues in contact with MET 440 (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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29A ILE* 3.3 28.5 - - + -
30A LEU* 3.6 41.1 + - + +
33A PHE* 4.0 9.4 - - + -
61A LYS* 3.8 20.6 - - + -
436A THR 3.1 17.5 + - - +
437A GLU 3.7 2.7 - - - +
439A LEU* 1.3 76.8 - - - +
441A LYS* 1.3 72.7 + - + +
474A ASN* 3.0 23.2 + - - +
475A ARG 3.8 8.9 + - - +
542B ASP* 3.5 42.4 - - + +
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Residues in contact with LYS 441 (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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30A LEU* 3.9 30.0 - - + +
437A GLU* 2.9 39.0 + - + +
438A ALA 5.2 0.2 - - - +
440A MET* 1.3 93.0 - - + +
442A GLY* 1.3 74.8 + - - +
443A LYS 3.8 0.3 + - - -
444A THR* 5.7 2.9 - - - +
447A GLU* 3.6 24.5 + - - +
472A LYS 5.2 1.2 - - - +
473A GLY* 4.4 1.5 - - - -
520B LEU* 5.5 1.8 - - - -
524B LEU* 4.4 22.7 - - + -
542B ASP* 5.9 0.2 - - - +
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Residues in contact with GLY 442 (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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438A ALA 3.0 18.1 + - - -
440A MET 3.5 1.8 + - - -
441A LYS* 1.3 97.1 - - - +
443A LYS* 1.3 62.5 + - - +
447A GLU* 4.3 2.1 - - - +
471A PHE* 3.4 21.8 - - - -
473A GLY* 3.8 9.3 - - - -
520B LEU* 3.5 13.2 - - - +
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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