Contacts of the helix formed by residues 1599 - 1620 (chain A) in PDB entry 3CLY
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 THR1599 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1597A GLN 4.5 5.6 - - - +
1598A MET* 1.3 79.0 - - - +
1600A PHE* 1.3 66.7 + - - +
1601A LYS* 3.4 12.0 + - - +
1602A ASP* 2.5 47.7 + - - +
1603A LEU* 3.0 15.7 + - - +
1768A GLU* 5.0 5.4 + - - -
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Residues in contact with PHE1600 (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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1599A THR* 1.3 71.7 - - - +
1601A LYS* 1.3 61.5 + - - +
1603A LEU* 3.1 12.1 + - + +
1604A VAL* 3.0 38.3 + - + +
1697A PHE* 4.0 7.0 - + - -
1727A ASN* 3.8 21.8 - - + -
1729A THR* 3.4 33.7 - - + -
1732A LEU* 3.7 20.9 - - + -
1760A ILE* 5.1 3.6 - - + -
1764A THR* 3.5 36.8 - - + -
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Residues in contact with LYS1601 (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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1599A THR* 3.1 8.9 + - - +
1600A PHE* 1.3 81.1 - - - +
1602A ASP* 1.3 73.4 + - - +
1604A VAL* 3.2 5.8 + - - +
1605A SER* 2.8 29.5 + - - -
1761A LEU* 4.1 7.9 - - + +
1764A THR* 4.2 19.2 - - + +
1765A THR* 4.0 32.8 - - + +
1768A GLU* 3.7 34.7 + - - +
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Residues in contact with ASP1602 (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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1597A GLN 4.3 2.5 - - - +
1598A MET* 3.8 22.4 - - + -
1599A THR* 2.5 48.2 + - - +
1601A LYS* 1.3 90.1 + - - +
1603A LEU* 1.3 58.1 + - - +
1605A SER* 3.3 7.9 + - - -
1606A CYS* 2.9 32.8 + - - -
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Residues in contact with LEU1603 (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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1576A LEU* 4.2 1.3 - - + -
1598A MET* 3.5 27.4 - - + +
1599A THR 3.0 16.2 + - - +
1600A PHE* 3.1 12.5 + - + +
1602A ASP* 1.3 74.7 - - - +
1604A VAL* 1.3 64.2 + - - +
1606A CYS* 3.3 3.7 + - - +
1607A THR* 2.9 28.4 + - - -
1696A ILE* 3.7 22.6 - - + +
1697A PHE* 3.6 32.5 - - + -
1699A LEU* 3.7 31.6 - - + -
1727A ASN* 4.4 16.8 - - + +
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Residues in contact with VAL1604 (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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1600A PHE* 3.0 49.8 + - + +
1601A LYS* 3.2 7.6 + - - +
1603A LEU* 1.3 75.9 - - - +
1605A SER* 1.3 53.7 + - - +
1607A THR* 3.2 7.3 + - - -
1608A TYR* 2.8 32.7 + - - +
1697A PHE* 4.4 2.7 - - + -
1732A LEU* 4.2 11.0 - - + -
1757A LEU* 4.3 12.6 - - + +
1760A ILE* 4.1 11.0 - - + -
1761A LEU* 3.8 37.9 - - + +
1764A THR* 4.6 1.8 - - - +
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Residues in contact with SER1605 (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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1601A LYS* 2.8 18.8 + - - -
1602A ASP* 3.5 9.9 - - - -
1604A VAL* 1.3 77.7 - - - +
1606A CYS* 1.3 62.8 + - - +
1608A TYR* 3.3 2.3 + - - +
1609A GLN* 3.0 45.9 + - - +
1761A LEU* 4.1 23.5 - - - +
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Residues in contact with CYS1606 (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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1572A LEU* 4.8 7.6 - - + -
1575A TYR* 4.8 2.9 - - - -
1576A LEU* 5.0 1.1 - - - -
1598A MET* 3.7 22.7 - - - -
1602A ASP 2.9 19.5 + - - -
1603A LEU 3.6 7.4 - - - +
1605A SER* 1.3 75.7 + - - +
1607A THR* 1.3 63.5 + - - +
1609A GLN* 3.3 5.2 + - - +
1610A LEU* 3.1 30.0 + - - +
1640A MET* 3.8 39.4 - - - +
1696A ILE* 4.5 14.6 - - + -
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Residues in contact with THR1607 (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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1603A LEU 2.9 13.9 + - - -
1604A VAL* 3.4 10.3 - - - -
1606A CYS* 1.3 77.7 - - - +
1608A TYR* 1.3 62.1 + - - +
1610A LEU* 3.2 4.1 + - - +
1611A ALA* 3.0 21.8 + - - +
1689A PHE* 3.7 15.0 - - + -
1693A MET* 3.9 23.1 - - + -
1696A ILE* 3.6 19.6 - - + +
1697A PHE* 3.6 17.5 - - + -
1757A LEU* 3.8 26.7 - - + -
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Residues in contact with TYR1608 (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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1604A VAL 2.8 21.0 + - - +
1605A SER* 3.3 5.4 + - - +
1607A THR* 1.3 73.6 - - - +
1609A GLN* 1.3 67.9 + - + +
1611A ALA* 3.2 4.0 + - - +
1612A ARG* 3.0 61.6 + - + +
1754A VAL* 3.7 21.6 - - + +
1757A LEU* 3.9 19.7 - - + +
1758A ASP* 3.6 52.4 + - + -
1761A LEU* 3.7 27.1 - - + -
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Residues in contact with GLN1609 (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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1545A LYS* 5.5 2.1 - - - -
1546A ASN* 3.2 36.1 + - - +
1605A SER* 3.0 41.2 + - - +
1606A CYS* 3.6 8.2 - - - +
1607A THR 3.3 0.2 - - - -
1608A TYR* 1.3 84.8 - - + +
1610A LEU* 1.3 58.9 + - - +
1612A ARG* 3.2 4.5 + - - +
1613A GLY 3.0 21.7 + - - -
1638A ASN 4.1 9.9 + - - -
1639A VAL* 3.7 8.3 - - - +
1640A MET* 3.0 37.0 + - + +
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Residues in contact with LEU1610 (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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1546A ASN* 5.2 1.3 - - + +
1572A LEU* 4.0 15.5 - - + -
1606A CYS 3.1 17.8 + - - +
1607A THR 3.2 4.2 + - - +
1609A GLN* 1.3 73.1 - - - +
1611A ALA* 1.3 60.8 + - - +
1613A GLY* 3.2 2.6 + - - +
1614A MET* 2.9 33.7 + - + +
1627A LEU* 5.6 0.2 - - + -
1632A VAL* 3.7 30.5 - - + -
1640A MET* 3.9 17.3 - - + +
1642A ILE* 4.0 21.5 - - + +
1689A PHE* 3.8 11.9 - - + -
1692A LEU* 3.8 23.1 - - + -
1696A ILE* 3.8 19.5 - - + -
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Residues in contact with ALA1611 (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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1607A THR 3.0 6.0 + - - +
1608A TYR 3.5 5.8 - - - +
1610A LEU* 1.3 76.6 - - - +
1612A ARG* 1.3 58.2 + - - +
1614A MET* 3.4 3.2 + - - +
1615A GLU* 2.8 30.1 + - - +
1689A PHE* 3.5 16.5 - - + -
1750A PHE* 4.4 4.7 - - + +
1753A LEU* 4.5 4.5 - - + -
1754A VAL* 3.4 19.6 - - + +
1757A LEU* 3.4 33.2 - - + -
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Residues in contact with ARG1612 (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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1544A HIS* 3.9 17.0 + - + +
1545A LYS* 6.4 0.6 - - - +
1546A ASN* 3.9 12.5 + - - +
1608A TYR* 3.0 63.2 + - + +
1609A GLN* 3.4 8.5 - - - +
1610A LEU 3.2 0.2 - - - -
1611A ALA* 1.3 74.3 - - - +
1613A GLY* 1.3 65.7 + - - +
1615A GLU* 3.2 9.4 + - - +
1616A TYR* 3.0 23.6 + - - +
1754A VAL* 3.9 16.4 - - + +
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Residues in contact with GLY1613 (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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1544A HIS* 3.8 17.4 - - - -
1546A ASN* 3.9 10.8 - - - -
1547A ILE* 4.0 6.2 - - - +
1609A GLN 3.0 11.1 + - - -
1610A LEU 3.2 3.1 + - - -
1612A ARG* 1.3 77.4 - - - +
1614A MET* 1.3 56.1 + - - +
1616A TYR* 3.2 5.5 + - - +
1617A LEU* 2.9 25.8 + - - +
1642A ILE* 3.5 17.7 - - - -
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Residues in contact with MET1614 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1610A LEU* 2.9 20.4 + - + +
1611A ALA 3.9 0.2 - - - +
1613A GLY* 1.3 73.4 - - - +
1615A GLU* 1.3 60.5 + - - +
1617A LEU* 3.6 24.0 - - + +
1618A ALA* 2.8 33.7 + - + +
1622A CYS 5.8 0.4 - - - +
1624A HIS* 4.2 7.0 - - + -
1627A LEU* 3.9 32.3 - - + -
1642A ILE* 3.6 19.7 - - + -
1685A ASP* 3.5 28.9 - - + +
1689A PHE* 4.5 1.3 - - + -
1750A PHE* 3.5 43.7 - - + -
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Residues in contact with GLU1615 (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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1611A ALA 2.8 19.3 + - - +
1612A ARG* 3.2 12.5 + - - +
1614A MET* 1.3 76.3 - - - +
1616A TYR* 1.3 59.0 + - - +
1618A ALA* 3.4 3.0 + - - +
1619A SER* 3.0 28.7 + - - -
1750A PHE* 3.5 15.4 - - + +
1751A LYS* 3.5 36.7 + - + +
1754A VAL* 3.6 30.3 - - + +
1755A GLU* 6.0 0.2 - - - +
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Residues in contact with TYR1616 (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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1541A ILE* 2.8 30.6 + - + -
1542A GLY* 3.7 12.3 - - - -
1543A LYS 3.6 18.1 + - - -
1544A HIS* 3.4 47.1 - + + +
1547A ILE* 3.7 11.9 - - + -
1612A ARG 3.0 8.9 + - - +
1613A GLY 3.4 7.0 - - - +
1615A GLU* 1.3 76.4 + - - +
1617A LEU* 1.3 69.8 + - - +
1619A SER* 2.6 28.0 + - - -
1620A GLN* 3.2 25.9 + - + +
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Residues in contact with LEU1617 (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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1537A MET* 5.5 0.4 - - - -
1541A ILE* 4.0 25.8 - - + -
1547A ILE* 4.6 6.7 - - + -
1613A GLY 2.9 14.2 + - - +
1614A MET* 3.6 24.5 - - + +
1616A TYR* 1.3 80.4 - - - +
1618A ALA* 1.3 58.8 + - - +
1620A GLN* 3.0 25.8 + - + +
1622A CYS* 3.5 32.7 + - + +
1623A ILE 4.5 0.9 - - - -
1624A HIS* 3.8 35.0 - - + +
1642A ILE* 5.3 2.0 - - + -
1645A PHE* 4.0 26.7 - - + -
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Residues in contact with ALA1618 (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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1614A MET* 2.8 21.7 + - + +
1615A GLU* 3.8 5.2 - - - +
1617A LEU* 1.3 73.3 - - - +
1619A SER* 1.3 57.7 + - - +
1620A GLN 3.0 0.2 - - - -
1621A LYS* 2.9 22.5 + - - +
1622A CYS 4.0 2.0 + - - +
1682A HIS* 3.6 34.5 + - + +
1750A PHE* 4.0 20.4 - - + -
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Residues in contact with SER1619 (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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1615A GLU* 3.0 16.3 + - - -
1616A TYR* 2.6 30.5 + - - -
1618A ALA* 1.3 76.2 - - - +
1620A GLN* 1.3 66.6 + - - +
1621A LYS* 3.1 6.7 + - - +
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Residues in contact with GLN1620 (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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1540A MET* 4.6 2.8 + - + +
1541A ILE* 2.5 43.8 + - + +
1542A GLY* 4.8 0.2 - - - -
1616A TYR* 3.2 37.2 + - + +
1617A LEU* 3.0 11.7 + - - +
1619A SER* 1.3 82.8 + - - +
1621A LYS* 1.3 61.6 + - - +
1622A CYS* 3.3 15.0 + - + -
1652A ASN* 2.9 22.7 + - - +
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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