Contacts of the helix formed by residues 44 - 69 (chain B) in PDB entry 5JRE
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 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER* 2.9 19.1 + - - +
42B ARG* 3.2 8.4 - - + +
43B GLU* 1.3 72.7 - - - +
45B TYR* 1.3 57.3 + - - +
46B LYS* 3.6 8.3 + - - +
47B SER* 2.7 36.2 + - - -
48B ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.6 42.7 + - + -
43B GLU* 3.2 49.5 + - + +
44B ASP* 1.3 71.4 - - - +
46B LYS* 1.3 61.8 + - - +
48B ALA* 3.9 3.8 - - + -
49B ASP* 3.0 43.0 + - - +
90B TYR* 6.5 0.2 - - + -
93B ILE* 3.8 18.0 - - + +
94B LYS* 6.3 1.6 - - - -
125B LYS* 4.8 1.7 + - - -
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 3.3 7.8 - - - +
45B TYR* 1.3 78.6 - - - +
47B SER* 1.3 63.2 + - - +
49B ASP* 3.5 5.6 + - - +
50B LYS* 3.3 29.5 + - + +
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 3.6 15.0 - - - -
44B ASP* 2.7 32.2 + - - -
46B LYS* 1.3 75.4 - - - +
48B ALA* 1.3 67.6 + - - +
50B LYS* 3.2 13.2 + - - +
51B TYR* 3.0 37.1 + - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.2 21.4 - - + +
39B SER* 3.8 10.7 - - - -
40B MET* 3.5 35.2 - - + +
44B ASP 3.0 16.8 + - - +
45B TYR* 3.7 6.3 - - - +
47B SER* 1.3 77.3 - - - +
49B ASP* 1.3 57.3 + - - +
51B TYR* 3.3 2.2 + - - -
52B LYS* 2.8 28.1 + - - +
90B TYR* 4.6 2.5 - - + -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 3.0 28.4 + - - +
46B LYS* 3.9 6.1 - - - +
48B ALA* 1.3 75.0 - - - +
50B LYS* 1.3 62.7 + - - +
52B LYS* 3.8 6.4 - - - +
53B GLU* 3.1 25.9 + - - +
90B TYR* 2.7 33.1 + - - -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 3.3 20.9 + - + +
47B SER* 3.2 14.0 + - - +
49B ASP* 1.3 77.2 - - - +
51B TYR* 1.3 65.6 + - + +
53B GLU* 3.3 8.1 + - - +
54B GLU* 3.1 33.9 + - - +
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS* 4.3 11.8 + - - -
32B LEU* 3.8 24.6 - - + +
35B SER* 3.7 33.5 + - - -
36B LEU* 4.0 17.9 - - + +
39B SER* 3.3 25.4 - - - -
47B SER* 3.0 32.1 + - - +
48B ALA 3.7 4.0 - - - +
50B LYS* 1.3 79.1 - - + +
52B LYS* 1.3 58.3 + - - +
54B GLU* 3.4 13.7 + - - +
55B LEU* 2.8 32.8 + - - +
150D LEU* 6.0 1.6 - - - +
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Residues in contact with LYS 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.9 19.2 - - + +
48B ALA 2.8 21.4 + - - +
49B ASP* 3.8 7.2 - - - +
50B LYS 3.3 0.2 - - - -
51B TYR* 1.3 73.6 - - - +
53B GLU* 1.3 56.5 + - - +
55B LEU* 3.8 1.7 - - - +
56B THR* 2.7 47.8 + - - +
87B LEU* 3.7 23.1 - - + -
90B TYR* 3.4 40.8 + - + +
91B TYR* 3.4 25.7 + - - -
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Residues in contact with GLU 53 (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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49B ASP 3.1 18.1 + - - +
50B LYS* 3.6 7.3 - - - +
52B LYS* 1.3 78.1 - - - +
54B GLU* 1.3 64.4 + - + +
56B THR* 3.8 4.9 - - - -
57B ASN* 3.1 43.2 + - - +
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Residues in contact with GLU 54 (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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32B LEU* 4.0 26.9 - - + +
50B LYS* 3.1 19.6 + - - +
51B TYR* 3.8 20.7 - - - +
53B GLU* 1.3 77.7 - - + +
55B LEU* 1.3 64.3 + - - +
57B ASN* 3.3 8.9 + - - +
58B LEU* 3.0 26.5 + - - +
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Residues in contact with LEU 55 (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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29B MET* 3.6 42.6 - - + +
32B LEU* 4.1 14.5 - - + +
33B SER* 3.9 25.4 - - - -
36B LEU* 4.0 10.8 - - + -
51B TYR 2.8 22.2 + - - +
52B LYS* 3.8 3.4 - - - +
54B GLU* 1.3 73.0 - - - +
56B THR* 1.3 58.5 + - - +
58B LEU* 3.3 2.4 + - - +
59B ALA* 2.9 29.9 + - - +
83B TYR* 3.8 21.8 - - + -
86B ALA* 4.2 4.0 - - + -
87B LEU* 3.7 22.9 - - + -
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Residues in contact with THR 56 (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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52B LYS* 2.7 36.5 + - - +
53B GLU* 3.8 5.6 - - - -
55B LEU* 1.3 76.6 - - - +
57B ASN* 1.3 61.6 + - - +
59B ALA* 3.3 2.3 + - - +
60B LYS* 3.0 36.8 + - + +
83B TYR* 4.1 25.7 + - - +
87B LEU* 4.5 6.9 - - - +
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Residues in contact with ASN 57 (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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53B GLU* 3.1 38.8 + - - +
54B GLU* 3.6 8.0 - - - +
55B LEU 3.2 0.2 - - - -
56B THR* 1.3 76.4 - - - +
58B LEU* 1.3 67.0 + - + +
60B LYS* 3.3 9.5 + - - +
61B THR* 3.2 25.0 + - - -
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.7 16.7 - - + +
28B ARG* 3.3 47.8 - - + +
29B MET* 3.8 22.4 - - + +
32B LEU* 3.7 25.1 - - + -
54B GLU 3.0 15.0 + - - +
55B LEU 3.7 7.4 - - - +
57B ASN* 1.3 75.5 - - + +
59B ALA* 1.3 58.2 + - - +
61B THR* 3.2 8.8 + - - +
62B GLN* 2.8 30.5 + - - +
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Residues in contact with ALA 59 (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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29B MET* 3.7 20.1 - - + +
55B LEU 2.9 17.6 + - - +
56B THR 3.5 5.4 - - - +
58B LEU* 1.3 75.1 - - - +
60B LYS* 1.3 56.7 + - + +
62B GLN* 3.3 0.5 + - - +
63B ILE* 2.8 39.1 + - + +
80B LEU* 4.3 2.5 - - + -
83B TYR* 3.6 39.3 - - + +
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Residues in contact with LYS 60 (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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56B THR* 3.0 23.3 + - + +
57B ASN* 3.5 12.8 - - - +
59B ALA* 1.3 77.6 - - - +
61B THR* 1.3 63.6 + - - +
63B ILE* 3.5 8.1 + - + +
64B GLU* 3.2 29.2 + - - +
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.8 29.6 - - - +
57B ASN 3.2 12.4 + - - -
58B LEU* 3.2 11.5 + - - +
60B LYS* 1.3 77.3 - - - +
62B GLN* 1.3 60.1 + - - +
64B GLU* 3.4 5.6 + - - +
65B GLU* 2.9 33.6 + - + +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.1 44.6 + - - +
25B ARG* 2.8 39.9 + - - +
26B SER* 3.6 17.2 - - - +
29B MET* 3.9 14.2 - - - -
58B LEU 2.8 20.5 + - - +
59B ALA* 3.7 4.5 - - - +
61B THR* 1.3 72.9 - - - +
63B ILE* 1.3 63.0 + - - +
65B GLU* 3.2 1.0 + - - +
66B LEU* 2.9 34.3 + - + +
76B GLY* 3.8 11.6 + - - +
80B LEU* 4.3 18.8 - - + -
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Residues in contact with ILE 63 (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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59B ALA* 2.8 29.1 + - + +
60B LYS* 3.8 9.0 - - + +
62B GLN* 1.3 77.2 - - - +
64B GLU* 1.3 78.0 + - - +
66B LEU* 3.5 4.9 + - - +
67B LYS* 3.2 39.3 + - + +
80B LEU* 3.8 22.7 - - + -
104B LEU 4.3 6.7 - - - +
105B GLY* 3.5 28.3 - - - +
106B VAL* 4.0 17.9 - - + -
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Residues in contact with GLU 64 (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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60B LYS* 3.2 17.4 + - + +
61B THR* 4.0 4.5 - - - +
62B GLN 3.3 0.2 - - - -
63B ILE* 1.3 90.6 - - - +
65B GLU* 1.3 65.7 + - - +
67B LYS* 3.3 34.0 + - - +
68B LYS* 3.3 33.2 + - - +
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Residues in contact with GLU 65 (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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18B LYS* 3.3 34.4 - - - +
21B GLU* 4.4 5.0 - - - +
22B ILE* 4.4 12.8 - - + +
25B ARG* 3.8 26.0 + - - +
61B THR* 2.9 29.6 + - + +
62B GLN 3.2 4.0 + - - +
64B GLU* 1.3 75.9 - - - +
66B LEU* 1.3 60.2 + - - +
68B LYS* 3.2 25.1 + - - +
69B TYR* 2.9 39.0 + - - +
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Residues in contact with LEU 66 (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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70A PRO* 5.3 4.0 - - - +
22B ILE* 3.8 28.0 - - + -
62B GLN* 2.9 21.1 + - + +
63B ILE* 4.0 4.0 - - - +
65B GLU* 1.3 75.3 - - - +
67B LYS* 1.3 61.1 + - - +
69B TYR 3.3 2.4 - - - -
70B PRO* 3.2 26.7 - - - +
72B PHE 3.4 27.4 - - - +
73B TYR* 3.8 39.6 - - + +
76B GLY* 4.3 8.3 - - - -
77B PHE* 5.5 0.4 - - - -
80B LEU* 3.6 31.9 - - + -
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Residues in contact with LYS 67 (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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70A PRO* 6.2 5.4 - - + -
63B ILE* 3.2 29.9 + - + +
64B GLU* 3.3 36.7 + - - +
65B GLU 3.2 0.4 - - - -
66B LEU* 1.3 78.6 - - - +
68B LYS* 1.3 62.9 + - + +
69B TYR 3.5 0.2 + - - -
70B PRO* 3.6 10.2 - - - +
105B GLY 5.3 2.4 + - - -
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLU* 3.3 19.6 + - - +
65B GLU* 3.2 27.9 + - - +
67B LYS* 1.3 78.4 - - + +
69B TYR* 1.3 89.0 + - + +
70B PRO* 3.4 6.3 - - - +
71B MET* 5.2 1.0 - - - +
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Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 4.7 9.4 - - + +
15B LEU* 3.6 29.8 - - + -
18B LYS* 3.5 52.3 - - + +
22B ILE* 4.4 6.3 - - + -
65B GLU* 2.9 32.4 + - - +
66B LEU* 3.3 8.6 - - - +
68B LYS* 1.3 103.2 - - + +
70B PRO* 1.3 60.8 - - - +
71B MET* 3.2 9.2 - - + -
72B PHE* 2.9 40.1 + - + +
73B TYR 3.9 2.3 + - - -
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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