Contacts of the helix formed by residues 343 - 367 (chain A) in PDB entry 5SYT
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 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A HIS 3.6 0.9 + - - -
340A TRP 3.0 16.2 + - - -
341A LYS 3.2 1.6 + - - -
342A LEU* 1.3 78.3 - - - +
344A HIS* 1.3 63.2 + - - +
345A THR* 3.3 3.1 - - - -
346A VAL* 3.1 16.4 + - - +
347A LYS* 3.0 28.9 + - - +
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Residues in contact with HIS 344 (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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338A GLY 4.5 0.4 - - - -
339A HIS* 3.0 39.8 + - + +
342A LEU* 3.3 35.4 - - + +
343A GLY* 1.3 77.2 - - - +
345A THR* 1.3 57.2 + - - +
347A LYS* 3.3 7.9 + - + +
348A ASN* 2.9 34.7 + - - +
414A PHE* 3.4 65.0 - + + +
417A GLN* 2.7 26.2 + - - -
418A ALA 4.3 0.9 - - - -
505A C8E 4.5 4.5 - - + -
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Residues in contact with THR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A HIS* 3.6 15.4 + - - +
340A TRP* 4.9 4.3 + - - -
343A GLY 3.3 1.0 - - - -
344A HIS* 1.3 79.4 - - - +
346A VAL* 1.3 64.3 + - + +
348A ASN* 3.5 1.7 + - - +
349A ILE* 3.1 35.7 + - + +
505A C8E 3.7 36.1 - - + +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY* 3.1 18.0 + - - +
345A THR* 1.3 78.5 - - + +
347A LYS* 1.3 66.6 + - + +
349A ILE* 3.3 12.1 + - + +
350A ILE* 3.0 42.5 + - + +
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Residues in contact with LYS 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU 3.4 22.2 + - - -
343A GLY* 3.0 16.7 + - - +
344A HIS* 3.6 10.8 - - - +
346A VAL* 1.3 78.6 - - + +
348A ASN* 1.3 57.7 + - - +
350A ILE* 3.3 9.3 + - + +
351A ILE* 2.9 40.1 + - + +
410A LEU* 6.0 0.2 - - + -
414A PHE* 3.8 29.1 - - + -
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Residues in contact with ASN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A HIS 2.9 16.6 + - - +
345A THR 3.8 2.0 - - - +
347A LYS* 1.3 75.3 - - - +
349A ILE* 1.3 58.7 + - - +
351A ILE* 3.4 13.4 + - - +
352A SER* 3.0 29.3 + - - -
407A LEU* 5.4 4.9 - - - +
410A LEU* 4.5 3.0 - - - +
414A PHE* 3.8 13.7 - - - -
505A C8E 3.1 84.6 - - - +
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A THR* 3.1 31.4 + - + +
346A VAL* 3.3 14.3 + - + +
348A ASN* 1.3 72.3 - - - +
350A ILE* 1.3 68.9 + - + +
352A SER* 2.9 20.0 + - - -
353A GLN* 3.1 14.6 + - + +
505A C8E 3.7 62.1 - - - +
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A VAL* 3.0 38.8 + - + +
347A LYS* 3.8 8.3 - - + +
349A ILE* 1.3 77.7 - - + +
351A ILE* 1.3 67.3 + - + +
353A GLN* 3.3 4.0 + - - +
354A MET* 2.9 43.7 + - + +
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Residues in contact with ILE 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LYS* 2.9 29.8 + - + +
348A ASN* 3.8 9.4 - - - +
350A ILE* 1.3 79.7 - - + +
352A SER* 1.3 59.0 + - - +
354A MET* 3.4 7.0 + - - +
355A ASN* 2.9 31.7 + - + +
403A LEU* 5.1 10.8 - - + -
407A LEU* 3.9 26.0 - - + -
410A LEU* 3.7 30.7 - - + -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN 3.0 13.7 + - - -
349A ILE* 2.9 23.0 + - - -
351A ILE* 1.3 78.9 - - - +
353A GLN* 1.3 63.3 + - - +
355A ASN* 3.5 8.9 + - - +
356A SER* 2.9 27.0 + - - -
504A CXE 5.6 0.2 - - - +
505A C8E 4.0 22.0 - - - -
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Residues in contact with GLN 353 (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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201A TRP* 3.0 33.7 + - + +
204A THR* 5.1 0.9 + - - -
205A LEU* 3.5 43.9 + - + +
208A SER* 4.4 7.3 + - - -
349A ILE* 3.1 18.3 + - + +
350A ILE* 4.1 3.8 - - - +
352A SER* 1.3 85.9 + - - +
354A MET* 1.3 59.7 + - - +
356A SER* 4.1 6.8 + - - -
357A PHE* 2.9 24.1 + - - +
505A C8E 4.1 34.7 + - - -
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Residues in contact with MET 354 (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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350A ILE* 2.9 36.9 + - + +
351A ILE* 3.8 6.5 - - - +
353A GLN* 1.3 73.8 - - + +
355A ASN* 1.3 66.2 + - - +
357A PHE* 3.2 8.2 + - - +
358A LEU* 3.0 24.1 + - - +
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Residues in contact with ASN 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 2.9 20.1 + - + +
352A SER* 3.7 8.5 + - - +
354A MET* 1.3 77.2 - - - +
356A SER* 1.3 62.7 + - - +
358A LEU* 3.2 4.1 + - - +
359A CYS* 3.0 24.9 + - - -
399A TYR* 2.4 46.7 + - - +
403A LEU* 3.2 19.1 - - + +
504A CXE 3.1 35.4 + - - -
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Residues in contact with SER 356 (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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201A TRP* 3.4 15.7 - - - -
204A THR* 3.8 13.7 + - - -
352A SER 2.9 19.1 + - - -
353A GLN* 3.7 12.9 + - - -
354A MET 3.2 0.4 - - - -
355A ASN* 1.3 76.0 - - - +
357A PHE* 1.3 61.7 + - - +
359A CYS* 3.5 1.4 + - - +
360A PHE* 3.1 30.1 + - - -
504A CXE 3.7 31.4 - - - -
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Residues in contact with PHE 357 (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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197A PHE* 4.5 18.1 - + - -
198A ILE* 4.4 19.3 - - + -
201A TRP* 3.4 49.3 - + + +
353A GLN 2.9 17.6 + - - +
354A MET* 3.2 8.0 + - - +
356A SER* 1.3 78.0 - - - +
358A LEU* 1.3 65.3 + - - +
360A PHE* 3.4 1.6 + - - +
361A PHE* 3.0 31.8 + + + +
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Residues in contact with LEU 358 (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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354A MET 3.0 15.9 + - - +
355A ASN* 3.7 5.2 - - - +
357A PHE* 1.3 82.9 - - + +
359A CYS* 1.3 57.7 + - - +
361A PHE* 3.3 13.7 + - + +
362A LEU* 3.0 48.1 + - + +
399A TYR* 3.8 33.2 - - + +
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Residues in contact with CYS 359 (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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355A ASN* 3.0 40.1 + - - +
356A SER* 4.0 3.1 - - - +
358A LEU* 1.3 77.2 - - - +
360A PHE* 1.3 60.8 + - - +
362A LEU* 3.4 1.3 + - - -
363A PHE* 2.8 30.3 + - - +
392A PHE* 3.7 18.6 - - + -
396A PHE* 3.6 32.4 - - + -
399A TYR* 3.9 16.4 - - - -
504A CXE 4.4 11.9 - - - +
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Residues in contact with PHE 360 (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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185A LEU* 4.4 8.7 - - + -
189A ILE* 4.7 3.1 - - + -
196A PHE* 5.5 0.4 - + - -
197A PHE* 3.4 30.8 - - + +
200A ALA* 3.7 26.5 - - + -
201A TRP* 3.8 15.7 - - + -
204A THR* 3.7 39.3 - - + -
356A SER* 3.1 31.7 + - - +
357A PHE 4.0 2.7 - - - +
359A CYS* 1.3 72.7 - - - +
361A PHE* 1.3 66.6 + - - +
363A PHE* 3.4 13.7 + + - +
364A ALA 3.0 17.2 + - - -
388A LEU* 4.6 13.2 - - + -
392A PHE* 4.2 15.9 - + - -
504A CXE 3.9 21.8 - - - -
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Residues in contact with PHE 361 (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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197A PHE* 3.7 39.6 - + + -
357A PHE* 3.0 27.1 + + + +
358A LEU* 3.5 16.4 - - + +
360A PHE* 1.3 77.2 - - - +
362A LEU* 1.3 67.9 + - + +
364A ALA* 3.0 19.2 + - - +
365A VAL* 3.0 32.1 + - + +
514A C8E 4.5 13.5 - - - -
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Residues in contact with LEU 362 (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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358A LEU* 3.0 42.3 + - + +
359A CYS* 5.2 1.3 - - - -
361A PHE* 1.3 83.3 - - + +
363A PHE* 1.3 67.0 + - - +
365A VAL* 3.2 19.7 + - + +
366A LEU* 2.9 34.7 + - + +
396A PHE* 3.6 26.0 - - + -
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Residues in contact with PHE 363 (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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189A ILE* 4.4 9.0 - - + -
196A PHE* 3.7 31.6 - + - -
359A CYS 2.8 22.5 + - - +
360A PHE* 3.5 12.1 - + - +
362A LEU* 1.3 73.4 - - - +
364A ALA* 1.3 57.8 + - - +
366A LEU 3.1 0.3 + - - -
367A ILE* 2.8 68.3 + - + +
384A THR* 4.5 10.8 - - + -
387A GLY 3.8 1.8 - - - -
388A LEU* 3.5 48.9 - - + -
391A ILE* 3.6 28.0 - - + -
392A PHE* 4.0 16.6 - + + -
396A PHE* 3.9 1.2 - - - -
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Residues in contact with ALA 364 (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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194A ASP 5.4 0.2 - - - +
196A PHE* 3.7 25.3 - - + -
197A PHE* 3.6 28.9 - - + -
360A PHE 3.0 11.9 + - - +
361A PHE 3.0 11.3 + - - +
363A PHE* 1.3 78.1 - - - +
365A VAL* 1.3 62.2 + - - +
366A LEU 3.4 0.2 + - - -
367A ILE* 3.8 11.9 + - - +
368A GLY 4.7 1.0 + - - -
514A C8E 4.0 20.6 - - - +
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Residues in contact with VAL 365 (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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361A PHE* 3.0 37.3 + - + +
362A LEU* 3.2 19.0 + - + +
364A ALA* 1.3 77.9 - - - +
366A LEU* 1.3 69.3 + - + +
368A GLY 4.6 1.0 + - - -
369A ARG* 4.8 2.1 - - - +
514A C8E 4.0 27.9 - - - +
519A GOL 3.6 20.0 + - - +
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Residues in contact with LEU 366 (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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362A LEU* 2.9 25.5 + - + +
363A PHE 3.1 0.2 + - - -
365A VAL* 1.3 84.4 - - + +
367A ILE* 1.3 66.1 + - - +
368A GLY 3.2 3.1 - - - -
369A ARG* 3.0 23.7 + - + +
372A LEU* 3.3 31.3 - - + +
391A ILE* 4.0 14.8 - - + -
395A ILE* 4.0 17.9 - - + -
396A PHE* 3.9 25.4 - - + -
513A C8E 4.3 24.2 - - - -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 4.6 7.6 - - + -
363A PHE* 2.8 50.9 + - + +
364A ALA* 4.0 10.8 - - - +
365A VAL 3.5 1.2 - - - -
366A LEU* 1.3 78.8 - - - +
368A GLY* 1.3 62.9 + - - +
369A ARG 3.2 0.6 + - - -
373A PHE* 3.8 32.6 - - + -
382A GLN* 5.4 1.3 - - + +
384A THR* 5.2 2.5 - - - -
387A GLY* 4.7 2.7 - - - -
391A ILE* 3.9 9.2 - - + -
518A GOL 3.3 39.3 - - - +
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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) + - + + + + + -
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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