Contacts of the helix formed by residues 101 - 122 (chain D) in PDB entry 3UYT
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 SER 101 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LYS 4.3 0.2 + - - -
100D PHE* 1.3 77.7 - - - +
102D LEU* 1.3 66.3 + - - +
103D LYS* 3.1 10.1 + - - +
104D THR* 3.2 20.4 + - - -
105D VAL* 3.4 9.8 + - - +
289D ASP* 2.6 31.9 + - - -
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PHE 3.8 0.6 + - - -
101D SER* 1.3 72.8 - - - +
103D LYS* 1.3 63.1 + - - +
105D VAL* 3.1 7.4 + - + +
106D LEU* 3.1 32.1 + - + +
207D ASN* 4.4 7.9 - - - +
244D TYR* 6.1 1.1 - - + -
245D PRO* 3.8 22.0 - - + -
248D PHE* 3.7 35.9 - - + -
276D LEU* 4.5 1.8 - - + -
280D GLN* 3.5 42.0 - - + +
282D PHE* 4.0 10.3 - - + -
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Residues in contact with LYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D SER* 3.1 9.5 + - - +
102D LEU* 1.3 79.1 - - - +
104D THR* 1.3 64.4 + - - +
106D LEU* 3.2 4.7 + - - +
107D LEU* 3.2 28.2 + - + +
277D PHE* 4.0 3.9 - - + -
282D PHE* 3.5 47.8 - - + -
283D SER* 3.2 29.4 + - - +
285D ASP* 3.0 34.2 + - - -
287D VAL* 3.8 20.5 + - - +
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Residues in contact with THR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PHE* 3.7 28.9 - - + -
101D SER* 3.2 10.3 + - - -
103D LYS* 1.3 79.6 - - - +
105D VAL* 1.3 63.2 + - - +
107D LEU* 3.4 8.1 + - - +
108D LEU* 3.2 28.1 + - + +
287D VAL 4.7 1.6 + - - -
288D PHE* 3.8 10.0 - - + -
289D ASP* 2.9 39.0 + - - +
290D TRP* 3.9 22.0 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D PHE* 4.0 9.9 - - + +
101D SER 3.4 12.8 + - - +
102D LEU* 3.1 8.2 + - - +
104D THR* 1.3 77.3 - - - +
106D LEU* 1.3 63.3 + - - +
108D LEU* 3.3 10.1 + - - +
109D ALA* 3.1 20.3 + - + +
203D LEU* 4.0 21.0 - - + +
206D PHE* 3.6 25.6 - - + -
207D ASN* 3.2 21.3 - - - +
248D PHE* 3.6 34.1 - - + -
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Residues in contact with LEU 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU* 3.1 25.6 + - + +
103D LYS 3.2 3.1 + - - +
105D VAL* 1.3 77.3 - - - +
107D LEU* 1.3 60.9 + - - +
109D ALA* 3.3 13.2 + - + +
110D ASP* 3.3 13.9 + - - +
248D PHE* 4.0 14.4 - - + -
273D PHE* 3.8 39.1 - - + +
276D LEU* 3.9 24.0 - - + +
277D PHE* 3.4 53.6 - - + +
282D PHE* 4.2 6.5 - - + -
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D LYS* 3.2 39.0 + - + +
104D THR* 3.8 4.5 - - - +
105D VAL 3.3 0.2 - - - -
106D LEU* 1.3 76.8 - - - +
108D LEU* 1.3 63.6 + - - +
110D ASP* 3.6 10.5 + - - +
111D GLN* 3.8 19.7 + - - +
277D PHE* 3.9 13.2 - - + -
284D TYR* 3.7 47.7 + - + -
285D ASP* 4.6 0.2 - - - +
286D TYR* 4.1 25.4 - - + +
287D VAL 4.2 8.7 - - - +
288D PHE* 3.7 28.9 - - + -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D LEU* 3.6 31.9 - - + -
100D PHE* 3.9 20.2 - - + -
104D THR* 3.2 21.4 + - + +
105D VAL* 3.5 6.5 - - - +
107D LEU* 1.3 78.4 - - - +
109D ALA* 1.3 63.3 + - - +
110D ASP 3.3 0.5 + - - -
111D GLN* 3.5 3.8 + - - +
112D MET* 3.0 37.9 + - - +
136D MET* 4.7 0.4 - - - -
145D VAL* 4.3 14.5 - - + +
203D LEU* 5.1 0.7 - - + -
206D PHE* 3.6 31.6 - - + -
288D PHE* 3.8 21.1 - - + -
290D TRP* 4.2 3.8 - - + -
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D VAL* 3.1 14.1 + - + +
106D LEU* 3.3 11.0 + - + +
108D LEU* 1.3 76.8 - - - +
110D ASP* 1.3 60.7 + - - +
112D MET* 3.9 5.4 - - - +
113D ILE* 3.0 33.8 + - + +
199D LEU* 5.1 0.9 - - - -
203D LEU* 3.7 32.1 - - + +
273D PHE* 3.9 22.2 - - + -
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU 3.3 9.0 + - - +
107D LEU 4.0 5.6 - - - +
108D LEU 3.3 1.0 - - - -
109D ALA* 1.3 81.0 - - - +
111D GLN* 1.3 61.5 + - - +
113D ILE* 4.8 1.1 - - - -
114D SER* 3.4 21.1 + - - -
270D ARG* 3.7 29.8 - - - +
273D PHE* 5.6 3.8 - - + +
274D ARG* 3.9 26.0 + - + +
284D TYR* 2.6 37.5 + - + +
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Residues in contact with GLN 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D LEU* 3.8 9.4 + - - +
108D LEU 3.5 3.2 + - - +
109D ALA 3.4 0.2 - - - -
110D ASP* 1.3 76.5 - - - +
112D MET* 1.3 66.1 + - - +
114D SER* 3.2 4.1 + - - -
115D ARG* 3.1 51.5 + - - +
143D ASN 3.0 24.4 + - - -
144D LEU* 3.6 7.7 - - - +
145D VAL* 2.6 49.4 + - + +
284D TYR* 4.6 9.6 - - - +
286D TYR* 4.1 19.8 - - + -
288D PHE* 4.5 5.9 - - - -
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Residues in contact with MET 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 3.7 17.7 - - + -
108D LEU* 3.0 42.3 + - - +
109D ALA* 3.9 2.0 - - - +
111D GLN* 1.3 74.1 - - - +
113D ILE* 1.3 66.5 + - - +
115D ARG* 3.5 2.8 + - - +
116D ILE* 3.3 25.1 + - - +
131D PRO* 5.5 0.2 - - + -
134D PHE* 3.4 51.0 - - + -
145D VAL* 4.4 7.9 - - + -
199D LEU* 3.5 44.2 - - + -
202D VAL* 4.1 19.1 - - + -
203D LEU* 4.8 3.1 - - - -
206D PHE* 5.0 0.9 - - - -
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D ALA 3.0 19.4 + - - +
110D ASP* 4.1 0.7 - - - +
111D GLN 3.3 0.4 - - - -
112D MET* 1.3 74.4 - - - +
114D SER* 1.3 59.6 + - - +
116D ILE* 3.2 8.6 + - - +
117D GLU* 3.1 24.3 + - - +
196D LEU* 4.5 13.5 - - + -
199D LEU* 3.5 19.5 - - + -
251D TYR* 4.3 6.1 - - + -
266D TYR* 4.2 19.1 - - + +
269D LEU* 4.0 17.0 - - + +
270D ARG* 3.6 50.0 - - + +
273D PHE* 4.2 15.9 - - + -
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Residues in contact with SER 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ASP* 3.4 7.5 + - - -
111D GLN* 3.2 11.0 + - - -
113D ILE* 1.3 76.7 - - - +
115D ARG* 1.3 74.7 + - - +
117D GLU* 3.4 2.2 + - - +
118D TYR* 3.0 23.6 + - - +
270D ARG* 2.8 37.6 + - - +
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Residues in contact with ARG 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D VAL* 3.5 32.9 + - - +
64D GLY* 3.5 18.9 - - - -
65D ILE* 5.4 2.7 - - - +
111D GLN* 3.1 55.2 + - - +
112D MET 3.9 5.2 - - - +
113D ILE 3.4 0.2 - - - -
114D SER* 1.3 87.4 + - - +
116D ILE* 1.3 63.0 + - - +
118D TYR* 3.3 7.3 + - - +
119D ILE* 3.2 28.9 + - - +
134D PHE* 4.6 7.9 - - + -
144D LEU* 3.6 17.8 - - - +
145D VAL* 2.9 20.8 + - + +
147D ILE* 4.0 32.1 - - + +
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D MET 3.3 15.7 - - - +
113D ILE 3.2 6.9 + - - +
114D SER 3.2 0.6 - - - -
115D ARG* 1.3 73.7 - - - +
117D GLU* 1.3 65.6 + - - +
119D ILE* 3.4 9.0 + - + +
120D HIS* 3.2 50.6 + - + +
126D HIS* 5.7 1.1 - - + -
129D VAL* 4.0 23.6 - - + -
134D PHE* 4.8 2.9 - - + -
147D ILE* 4.7 11.2 - - + -
195D ASP* 3.5 34.3 - - + +
196D LEU* 3.8 20.2 - - + -
199D LEU* 4.3 12.1 - - + -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ILE 3.1 9.8 + - - +
114D SER* 3.4 5.8 + - - +
116D ILE* 1.3 77.1 - - - +
118D TYR* 1.3 65.3 + - - +
120D HIS* 3.2 4.6 + - - +
121D SER* 3.0 22.8 + - - -
263D LYS* 6.1 0.3 - - - -
266D TYR* 3.3 51.4 - - + +
267D SER* 5.6 0.9 + - - -
270D ARG* 2.6 36.6 + - - +
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Residues in contact with TYR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET 4.8 0.2 + - - -
59D MET* 3.2 47.2 + - + -
60D GLN 4.0 3.3 + - - -
61D GLY 4.4 0.7 - - - -
62D GLY* 3.4 25.6 + - - -
63D VAL 5.1 5.6 - - - +
65D ILE* 3.9 21.3 - - + -
114D SER 3.0 13.6 + - - +
115D ARG* 3.5 10.3 - - - +
117D GLU* 1.3 79.0 - - - +
119D ILE* 1.3 66.1 + - - +
121D SER* 2.8 34.0 + - - -
122D LYS* 3.4 25.6 + - + +
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Residues in contact with ILE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D MET* 3.8 13.2 - - + +
65D ILE* 4.8 7.0 - - + -
115D ARG 3.2 15.9 + - - +
116D ILE* 3.6 9.2 - - - +
117D GLU 3.3 0.2 - - - -
118D TYR* 1.3 78.1 - - - +
120D HIS* 1.3 63.9 + - + +
122D LYS* 3.0 14.2 + - - +
124D PHE* 3.3 41.9 + - + +
125D ILE* 4.1 12.6 - - - -
126D HIS* 3.7 27.4 - - + +
147D ILE* 3.8 16.2 - - + -
150D PHE* 3.6 33.4 - - + -
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Residues in contact with HIS 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ILE* 3.2 32.0 + - + +
117D GLU 3.2 6.8 + - - +
119D ILE* 1.3 78.8 - - + +
121D SER* 1.3 61.1 + - - +
123D ASN* 3.2 6.6 + - - +
124D PHE 3.0 23.1 - - - +
125D ILE* 3.6 9.6 - - + +
156D TYR* 2.5 25.2 + - - +
192D ARG* 3.2 47.1 - - + +
195D ASP* 2.7 24.7 + - - -
266D TYR* 2.7 35.6 + + + +
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Residues in contact with SER 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLU* 3.0 13.4 + - - -
118D TYR* 2.8 26.2 + - - -
120D HIS* 1.3 73.3 - - - +
122D LYS* 1.3 77.3 + - - +
123D ASN* 3.0 16.6 + - - +
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Residues in contact with LYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET* 3.8 35.6 - - + +
59D MET* 4.2 20.6 - - + -
118D TYR* 3.4 28.4 + - + +
119D ILE 3.0 9.7 + - - +
121D SER* 1.3 95.8 + - - +
123D ASN* 1.3 74.3 + - - +
124D PHE* 3.3 19.2 - - + -
155D LYS* 4.4 0.2 - - - -
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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