Contacts of the helix formed by residues 463 - 485 (chain E) in PDB entry 5U8T
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 ALA 463 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462E SER* 1.3 77.2 - - - +
464E GLN* 1.3 62.2 + - - +
465E LYS 3.2 0.9 - - - -
466E LEU* 3.2 24.3 - - + +
467E THR* 3.2 20.8 - - + +
621E ARG* 6.2 1.6 - - - +
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Residues in contact with GLN 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 5.1 10.7 - - - +
462E SER* 3.0 7.3 - - - +
463E ALA* 1.3 78.1 - - - +
465E LYS* 1.3 60.0 + - + +
467E THR* 2.6 38.1 + - - +
468E ASN* 2.9 27.4 + - + +
471E LYS* 5.5 3.3 - - - +
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Residues in contact with LYS 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E SER* 3.5 26.9 - - - +
463E ALA 3.2 0.6 - - - -
464E GLN* 1.3 79.2 - - + +
466E LEU* 1.3 57.9 + - - +
468E ASN* 3.5 7.7 - - - +
469E LEU* 2.9 27.7 + - - +
574E GLU* 6.3 2.9 - - - -
575E ASN* 4.8 13.9 - - - +
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Residues in contact with LEU 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E SER 4.5 0.4 + - - +
463E ALA* 3.2 29.1 - - + +
465E LYS* 1.3 77.2 - - - +
467E THR* 1.3 67.6 + - + +
469E LEU* 3.4 15.5 - - + +
470E ARG* 2.9 65.1 + - + +
575E ASN* 4.2 21.7 - - + +
578E THR* 3.9 22.2 - - + -
621E ARG* 5.0 5.8 - - - +
631E GLU* 3.7 20.4 - - - +
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Residues in contact with THR 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E GLU* 6.0 1.1 - - - +
69E ARG* 4.9 16.6 - - - +
463E ALA* 3.2 17.3 - - + +
464E GLN* 2.6 45.0 + - - +
466E LEU* 1.3 86.9 - - + +
468E ASN* 1.3 59.4 + - - +
470E ARG* 3.9 15.9 - - - +
471E LYS* 2.9 31.1 + - - +
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Residues in contact with ASN 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464E GLN* 2.9 26.8 + - + +
465E LYS* 3.5 9.1 - - - +
467E THR* 1.3 77.7 + - - +
469E LEU* 1.3 57.4 + - - +
471E LYS* 3.2 31.7 + - - +
472E ARG* 2.9 24.4 + - - +
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Residues in contact with LEU 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465E LYS 2.9 17.5 + - - +
466E LEU* 3.4 16.8 - - + +
467E THR 3.1 0.2 - - - -
468E ASN* 1.3 74.8 - - - +
470E ARG* 1.3 63.3 + - + +
471E LYS 3.0 0.9 - - - -
472E ARG* 2.8 36.3 + - - +
473E TRP* 2.9 52.5 + - + +
540E ARG* 3.8 36.6 - - + +
575E ASN* 5.2 2.7 - - - +
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Residues in contact with ARG 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E PHE* 3.4 44.3 - - + +
63E GLY* 5.1 5.2 - - - -
66E GLU* 5.9 2.0 + - - +
466E LEU* 2.9 49.1 + - + +
467E THR* 3.9 16.2 - - - +
469E LEU* 1.3 78.7 - - + +
471E LYS* 1.3 57.3 + - - +
473E TRP* 3.0 20.1 + - + +
474E VAL* 2.9 32.9 + - - +
623E ASP* 3.8 28.2 + - - +
631E GLU* 2.8 36.8 + - - -
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Residues in contact with LYS 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LYS* 4.6 10.3 - - - +
185A LYS* 3.5 47.1 - - + +
186A ASP* 3.2 5.4 - - - +
464E GLN* 5.5 3.6 - - - +
467E THR 2.9 18.7 + - - +
468E ASN* 3.2 33.4 + - - +
470E ARG* 1.3 78.6 - - - +
472E ARG* 1.3 48.8 + - - +
474E VAL* 3.4 7.9 + - + +
475E SER* 2.3 37.8 + - - -
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Residues in contact with ARG 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433E GLU 4.0 19.8 + - - -
434E VAL* 4.9 1.4 - - - +
436E ASN* 3.4 52.0 - - + +
468E ASN 2.9 13.4 + - - +
469E LEU* 2.8 21.0 + - - +
471E LYS* 1.3 76.1 - - - +
473E TRP* 1.3 90.0 + - - +
475E SER* 3.1 12.3 + - - +
476E ASN* 2.9 30.1 + - - +
537E ASP 5.6 3.6 + - - -
538E LEU* 6.3 1.0 - - - +
540E ARG* 6.4 0.4 - - - +
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Residues in contact with TRP 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 6.1 8.2 - - + +
62E PHE* 3.7 37.0 - + + -
432E LEU* 3.9 24.1 + - - +
433E GLU* 4.7 6.0 + - - +
469E LEU* 2.9 31.4 + - + +
470E ARG* 3.0 16.8 + - + +
472E ARG* 1.3 110.3 - - - +
474E VAL* 1.3 56.7 + - - +
476E ASN* 3.2 6.2 + - + +
477E PHE* 2.9 25.6 + - - +
537E ASP 5.0 2.0 + - - -
540E ARG* 3.1 39.9 - - + -
541E ASN* 3.4 24.7 - - + +
542E PRO* 3.4 19.1 - - + -
580E LEU* 5.3 1.6 - - + -
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Residues in contact with VAL 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS 5.4 0.4 - - - +
186A ASP* 3.8 13.9 - - + +
33E CYS* 5.8 0.7 - - - -
60E PRO* 3.1 46.2 - - + +
61E ILE 4.4 2.0 - - - +
62E PHE* 3.6 31.6 - - + +
470E ARG 2.9 12.7 + - - +
471E LYS* 3.7 12.1 - - + +
473E TRP* 1.3 75.6 - - - +
475E SER* 1.3 62.7 + - - +
477E PHE* 3.0 20.9 - - + +
478E TRP* 3.4 9.5 - - - -
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Residues in contact with SER 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LYS* 3.7 12.6 - - - -
186A ASP* 2.7 25.5 + - - +
471E LYS* 2.3 29.5 + - - -
472E ARG* 3.1 14.8 - - - -
473E TRP 3.1 0.2 - - - -
474E VAL* 1.3 77.4 - - - +
476E ASN* 1.3 60.1 + - - +
477E PHE 3.3 0.7 + - - -
478E TRP* 3.3 19.8 + - - +
479E LEU* 4.1 2.1 + - - +
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Residues in contact with ASN 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E LEU* 2.3 40.7 + - - +
432E LEU 4.7 3.4 - - - +
433E GLU 4.8 0.2 - - - -
434E VAL 2.3 35.8 + - - +
435E GLY* 3.0 24.3 - - - +
436E ASN* 3.7 10.8 - - + +
472E ARG* 2.9 16.5 + - + +
473E TRP* 3.2 5.4 + - + +
475E SER* 1.3 74.0 - - - +
477E PHE* 1.3 64.9 + - - +
478E TRP 3.2 0.4 - - - -
479E LEU* 3.4 25.2 + - - +
480E SER* 3.5 6.2 + - - -
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Residues in contact with PHE 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 3.4 32.1 - - + -
33E CYS 3.6 11.9 - - - -
34E LEU* 5.0 8.7 - - + -
39E LEU* 3.3 35.9 - - + -
60E PRO* 3.8 25.1 - - + -
432E LEU* 4.9 12.8 - - + +
473E TRP 2.9 9.9 + - - +
474E VAL* 3.0 20.2 - - + +
476E ASN* 1.3 78.0 - - - +
478E TRP* 1.3 88.4 + + - +
480E SER* 2.9 24.3 + - - -
481E TRP* 3.0 20.9 + + + -
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Residues in contact with TRP 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.1 50.0 + - - +
186A ASP* 3.2 29.8 + - + +
188A GLN* 3.3 32.5 - - + -
31E VAL* 5.8 0.4 - - + -
58E ILE* 3.3 34.3 - - + -
59E VAL 5.5 0.2 - - - -
60E PRO* 3.2 36.3 - - + +
474E VAL 3.4 20.0 - - - -
475E SER 3.3 10.2 + - - +
476E ASN 3.2 0.6 - - - -
477E PHE* 1.3 85.8 - + - +
479E LEU* 1.3 62.9 + - - +
480E SER 3.0 1.8 - - - -
481E TRP* 2.8 39.0 + + + +
482E ASP* 2.9 15.1 + - - +
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Residues in contact with LEU 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E LEU* 4.4 22.0 - - + -
435E GLY* 3.9 12.3 - - - +
436E ASN 5.3 2.0 - - - +
475E SER 4.1 1.6 + - - +
476E ASN* 3.4 30.1 + - - +
477E PHE 3.3 0.4 - - - -
478E TRP* 1.3 78.4 - - - +
480E SER* 1.3 56.8 + - - +
482E ASP* 3.7 4.1 + - - +
483E ALA* 2.9 25.3 + - - +
491E LEU* 3.7 29.9 - - + +
494E ARG* 4.5 17.5 - - - +
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Residues in contact with SER 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 5.0 10.9 - - - +
428E LEU* 3.3 35.0 + - - +
431E LEU* 3.5 27.6 - - - +
432E LEU* 4.3 10.2 - - - +
476E ASN 3.5 2.9 + - - -
477E PHE* 2.9 15.3 + - - -
479E LEU* 1.3 78.5 - - - +
481E TRP* 1.3 63.5 + - - +
483E ALA* 3.3 1.6 - - - +
484E LEU* 2.9 21.0 + - - +
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Residues in contact with TRP 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ASP* 5.9 0.6 + - - -
166A ARG* 3.8 20.4 - - - -
188A GLN* 3.5 19.7 - - - +
207A LYS* 5.9 1.5 - - - +
31E VAL* 5.5 4.3 - - + -
39E LEU* 3.7 15.3 - - + -
42E THR* 3.2 28.3 - - - -
43E LYS* 3.4 56.1 - - + +
46E SER* 4.0 17.0 - - - -
58E ILE* 5.5 9.0 - - + -
477E PHE* 3.0 20.8 + + + +
478E TRP* 2.8 33.7 + + + +
480E SER* 1.3 77.0 - - - +
482E ASP* 1.3 57.9 + - + +
484E LEU* 3.1 19.5 + - + +
485E ASP* 3.0 24.2 + - - +
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Residues in contact with ASP 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ARG* 5.6 4.7 - - - +
207A LYS* 5.7 7.9 - - + +
478E TRP 2.9 13.1 + - - +
479E LEU* 3.8 6.7 - - - +
481E TRP* 1.3 77.6 - - + +
483E ALA* 1.3 56.1 + - - +
484E LEU 3.1 2.7 - - - -
485E ASP* 2.9 46.2 + - - +
487E ARG* 4.2 12.4 - - - +
488E LYS* 3.5 15.8 + - - +
491E LEU* 3.2 27.9 - - + +
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Residues in contact with ALA 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E PHE* 3.4 21.0 - - - -
428E LEU* 4.2 6.6 - - + +
431E LEU* 3.4 23.6 - - + -
479E LEU 2.9 19.6 + - - +
480E SER* 3.0 10.4 + - - +
482E ASP* 1.3 73.9 - - - +
484E LEU* 1.3 61.7 + - - +
485E ASP 4.2 2.9 - - - +
488E LYS 5.4 0.2 - - - -
491E LEU* 3.5 17.0 - - + -
492E LEU* 4.4 15.8 - - + +
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Residues in contact with LEU 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 4.1 13.0 - - + +
40E CYS* 4.2 14.8 - - - +
43E LYS* 3.5 40.2 - - + -
271E TRP* 5.2 2.8 + - + +
272E LEU* 3.8 24.7 - - + -
275E LEU* 4.0 22.4 - - + -
424E PHE* 4.5 9.7 - - + -
428E LEU* 4.6 7.4 - - + -
480E SER 2.9 9.0 + - - +
481E TRP* 3.1 15.4 + - + +
483E ALA* 1.3 78.5 - - - +
485E ASP* 1.3 66.6 + - - +
486E ASP* 3.3 12.1 + - - +
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Residues in contact with ASP 485 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LYS* 3.5 33.2 + - - +
481E TRP* 3.0 20.5 + - - +
482E ASP* 2.9 42.1 + - - +
483E ALA 4.2 2.8 - - - +
484E LEU* 1.3 78.0 - - - +
486E ASP* 1.3 64.4 + - - +
487E ARG* 3.4 18.4 + - + +
488E LYS 3.5 11.4 + - - +
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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