Contacts of the helix formed by residues 137 - 159 (chain J) in PDB entry 5JKL
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 TYR 137 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J GLU* 4.2 7.2 - - - -
65J HIS* 2.7 54.3 + + + -
68J LYS* 3.4 19.5 - - + +
69J LEU* 3.3 23.1 + - + +
114J LEU* 4.0 35.2 - - + -
132J PHE* 3.4 36.1 - + - -
133J ILE* 3.0 15.1 + - + +
135J THR 3.7 0.4 - - - -
136J HIS* 1.3 96.5 - - + +
138J LEU* 1.3 67.4 + - - +
139J ASN 3.3 2.5 - - - -
140J GLU* 3.3 5.8 + - + +
141J GLN* 3.0 28.8 + - - +
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Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ASN* 4.2 7.8 - - - +
114J LEU* 3.9 22.9 - - + +
115J LEU* 4.0 18.4 - - + -
118J HIS* 4.3 1.1 - - + -
133J ILE* 3.0 36.1 + - + +
134J GLU* 3.8 21.6 + - + +
137J TYR* 1.3 76.6 - - - +
139J ASN* 1.3 58.3 + - - +
141J GLN* 3.4 6.4 + - - +
142J VAL* 3.0 31.4 + - - +
127L PRO* 3.7 36.6 - - + -
128L HIS* 3.8 23.8 - - + +
131L ASP* 6.2 0.4 - - + -
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Residues in contact with ASN 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J GLU 4.0 9.7 + - - +
135J THR 5.7 2.4 + - - +
137J TYR 4.8 0.2 - - - +
138J LEU* 1.3 78.0 - - - +
140J GLU* 1.3 61.7 + - - +
142J VAL* 4.0 7.7 - - - +
143J LYS* 2.9 55.3 + - - +
75L GLN* 4.5 7.7 + - - +
128L HIS* 2.9 30.9 + - + +
131L ASP* 5.0 8.0 + - - +
136L HIS* 6.1 1.2 + - - -
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Residues in contact with GLU 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J GLU* 5.0 7.4 - - - +
65J HIS* 5.0 22.3 + - + +
135J THR 5.6 1.6 - - - +
136J HIS* 3.4 24.5 - - - +
137J TYR* 3.3 9.5 + - - +
139J ASN* 1.3 77.3 + - - +
141J GLN* 1.3 59.3 - - - +
143J LYS* 3.0 32.6 + - - +
144J ALA* 3.0 28.5 + - - +
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Residues in contact with GLN 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J HIS* 4.7 6.4 - - - -
107J GLU* 2.8 53.8 + - - +
110J VAL* 3.9 10.6 - - - +
111J ASN* 3.4 26.5 - - + +
114J LEU* 3.5 32.8 - - + +
137J TYR* 3.0 13.1 + - - +
138J LEU 3.6 4.9 - - - +
140J GLU* 1.3 76.1 - - - +
142J VAL* 1.3 60.3 + - - +
144J ALA* 3.2 3.8 + - - +
145J ILE* 2.9 36.6 + - - +
201J FE 3.8 15.9 - - - -
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Residues in contact with VAL 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ASN* 5.1 10.5 - - - +
138J LEU 3.0 21.1 + - - +
139J ASN* 3.8 7.2 - - - +
141J GLN* 1.3 75.5 - - - +
143J LYS* 1.3 64.3 + - - +
145J ILE* 3.9 6.2 - - + +
146J LYS* 3.0 23.6 + - - +
75L GLN* 3.8 38.7 - - + +
76L ARG* 3.9 15.9 - - - +
128L HIS* 3.6 37.9 - - + +
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Residues in contact with LYS 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ASN* 2.9 42.3 + - - +
140J GLU* 3.0 38.0 + - - +
142J VAL* 1.3 79.2 - - - +
144J ALA* 1.3 56.2 + - - +
146J LYS* 3.5 5.3 + - - +
147J GLU* 3.0 30.0 + - - +
75L GLN* 4.0 20.0 - - - +
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Residues in contact with ALA 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 5.9 0.2 - - - +
58J GLN* 5.9 2.9 - - - +
107J GLU* 4.0 26.2 - - + +
140J GLU 3.0 18.7 + - - +
141J GLN* 3.7 4.7 - - - +
143J LYS* 1.3 76.1 - - - +
145J ILE* 1.3 59.2 + - - +
147J GLU* 3.4 7.1 + - - +
148J LEU* 3.0 36.6 + - + +
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Residues in contact with ILE 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J LEU* 3.7 18.2 - - + +
107J GLU* 3.9 34.3 - - + +
108J LYS* 4.0 9.2 - - + -
111J ASN* 3.9 14.4 - - + +
141J GLN 2.9 22.7 + - - +
142J VAL* 3.9 7.2 - - + +
144J ALA* 1.3 72.9 - - - +
146J LYS* 1.3 59.9 + - - +
148J LEU* 3.4 2.4 + - - -
149J GLY 2.9 25.1 + - - -
8L VAL* 3.6 40.4 - - + +
10L GLN* 3.8 22.0 - - + +
75L GLN 5.7 0.7 - - - +
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Residues in contact with LYS 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J VAL 3.0 18.3 + - - +
143J LYS* 3.8 6.5 - - - +
145J ILE* 1.3 76.2 - - - +
147J GLU* 1.4 57.2 + - - +
149J GLY* 3.4 1.2 + - - -
150J ASP* 2.9 63.9 + - - +
42K ASP* 2.7 38.0 + - - -
44K ASP* 3.9 16.4 - - + +
8L VAL* 4.1 7.6 - - + -
74L ASN* 3.4 32.1 - - - +
75L GLN* 4.1 24.2 + - + +
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Residues in contact with GLU 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54J TYR* 2.7 31.1 + - - +
58J GLN* 4.1 7.1 + - - -
143J LYS 3.0 18.1 + - - +
144J ALA* 3.8 7.6 - - - +
146J LYS* 1.4 74.8 - - - +
148J LEU* 1.3 65.0 + - - +
150J ASP* 3.3 11.8 + - - +
151J HIS* 3.0 46.6 + - + +
49K LYS* 5.6 5.8 + - - +
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Residues in contact with LEU 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 3.9 7.6 - - - +
54J TYR* 3.8 21.5 - - + +
55J PHE* 5.0 0.4 - - + -
100J MET* 3.7 30.3 - - - +
103J ALA* 3.6 31.4 - - + +
104J LEU* 3.7 16.4 - - + +
107J GLU* 3.5 32.5 - - + -
144J ALA* 3.0 20.5 + - + +
145J ILE* 3.8 4.3 - - - +
147J GLU* 1.3 77.4 - - - +
149J GLY* 1.3 57.6 + - - +
151J HIS* 3.2 4.6 + - - +
152J VAL* 2.9 35.5 + - - +
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Residues in contact with GLY 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J LEU* 4.3 5.2 - - - +
145J ILE 2.9 16.4 + - - -
146J LYS 3.8 1.3 - - - -
148J LEU* 1.3 73.6 - - - +
150J ASP* 1.3 65.0 + - - +
152J VAL* 3.3 2.3 + - - +
153J THR* 2.9 20.1 + - - -
44K ASP* 4.0 2.9 - - - -
7L GLN* 3.0 35.3 + - - -
8L VAL* 4.3 7.6 - - - -
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Residues in contact with ASP 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J LYS* 2.9 53.1 + - - +
147J GLU* 3.4 12.0 - - - +
149J GLY* 1.3 75.4 - - - +
151J HIS* 1.4 61.4 + - + +
153J THR* 3.3 2.3 + - - -
154J ASN* 2.9 37.8 + - - +
44K ASP* 3.3 16.3 - - - +
47K ALA* 3.8 22.2 - - + +
49K LYS* 4.3 21.0 - - - +
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Residues in contact with HIS 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J TYR* 3.7 22.6 + + - -
100J MET* 3.9 32.1 - - + -
147J GLU* 3.0 40.8 + - + +
148J LEU* 3.2 7.2 + - - +
150J ASP* 1.4 79.4 - - + +
152J VAL* 1.3 57.9 + - - +
154J ASN* 3.4 3.1 + - - +
155J LEU* 3.0 35.8 + - - +
170J PHE* 3.6 21.5 - + + -
174J THR* 3.7 22.9 - - + +
175J LEU* 3.9 10.7 - - + +
49K LYS* 6.3 3.4 - - - -
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Residues in contact with VAL 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J LEU* 3.8 14.8 - - + +
100J MET* 3.7 35.2 - - + +
101J GLU* 3.9 11.2 - - + +
104J LEU* 4.6 8.1 - - + -
148J LEU 2.9 21.4 + - - +
149J GLY 3.6 4.3 - - - +
151J HIS* 1.3 76.3 - - - +
153J THR* 1.3 56.6 + - - +
155J LEU* 3.3 1.3 + - - -
156J ARG* 2.9 69.7 + - - +
7L GLN* 3.7 9.0 - - - +
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Residues in contact with THR 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149J GLY 2.9 7.9 + - - -
150J ASP* 3.5 3.6 - - - -
152J VAL* 1.3 76.7 - - - +
154J ASN* 1.3 64.9 + - - +
156J ARG* 3.3 10.9 + - - +
157J LYS* 2.9 35.4 + - + +
44K ASP 2.7 22.5 + - - +
45K ASP* 3.6 33.6 - - - +
46K VAL 3.9 14.4 - - - +
47K ALA* 4.2 0.7 - - + -
7L GLN* 3.0 15.6 + - - -
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Residues in contact with ASN 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J ASP* 2.9 29.2 + - - +
151J HIS* 4.8 1.8 + - - +
152J VAL 3.3 0.2 - - - -
153J THR* 1.3 77.3 - - - +
155J LEU* 1.3 63.2 + - - +
157J LYS* 3.2 5.4 + - - +
158J MET* 2.9 30.5 + - - +
170J PHE* 3.8 23.1 - - + -
174J THR* 6.2 0.4 - - - +
46K VAL 4.6 2.3 - - - +
47K ALA* 3.0 33.0 + - - +
48K LEU* 3.9 10.2 - - - +
168K TYR* 3.4 27.7 - - + +
172K LYS* 5.0 1.0 + - - -
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J PHE* 4.2 4.5 - - + -
96J GLY 4.1 2.0 - - - +
97J LEU* 3.9 27.6 - - + +
100J MET* 3.9 26.5 - - + -
151J HIS 3.0 21.7 + - - +
152J VAL 3.8 2.7 - - - +
154J ASN* 1.3 76.2 - - - +
156J ARG* 1.3 62.3 + - - +
158J MET* 3.4 5.5 + - - +
159J GLY 3.3 5.0 + - - -
160J ALA* 2.9 35.0 + - + +
166J ALA 4.4 2.2 - - - +
167J GLU* 4.2 26.2 - - + -
170J PHE* 3.5 43.7 - - + -
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Residues in contact with ARG 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J LEU* 4.0 16.6 - - + +
101J GLU* 2.9 27.9 + - - +
152J VAL* 2.9 41.9 + - - +
153J THR* 3.6 8.0 + - - +
155J LEU* 1.3 76.6 - - - +
157J LYS* 1.3 65.2 + - + +
159J GLY* 3.1 15.1 + - - -
160J ALA 4.2 8.2 + - - +
7L GLN* 3.5 18.4 + - - +
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Residues in contact with LYS 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153J THR* 2.9 34.7 + - + +
154J ASN* 3.9 5.2 - - - +
156J ARG* 1.3 74.9 - - + +
158J MET* 1.3 60.0 + - + +
159J GLY* 3.4 1.0 + - - -
40K TYR* 5.8 1.2 + - - -
45K ASP 3.0 25.4 + - - -
46K VAL* 4.2 15.7 - - - +
94K GLU 5.9 0.8 + - - -
164K GLY* 3.5 36.3 + - - +
165K LEU 3.6 1.4 + - - -
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Residues in contact with MET 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ASN 2.9 20.3 + - - +
155J LEU* 3.7 5.2 - - - +
156J ARG 3.2 0.4 - - - -
157J LYS* 1.3 77.8 - - + +
159J GLY* 1.3 56.3 + - - +
160J ALA 3.7 0.2 - - - -
163J SER* 4.5 3.8 + - - -
166J ALA* 3.2 44.4 - - + +
169J LEU* 4.0 5.6 - - + -
170J PHE* 3.7 23.3 - - - +
164K GLY 4.8 0.7 - - - +
165K LEU* 3.8 41.4 - - + +
168K TYR* 3.5 58.3 - - + -
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Residues in contact with GLY 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J ARG 3.1 11.7 + - - -
157J LYS 3.2 1.5 - - - -
158J MET* 1.3 78.7 - - - +
160J ALA* 1.4 64.3 + - - +
162J GLU* 3.6 4.9 + - - +
163J SER* 3.0 28.8 + - - -
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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
------------------------------------------------------------
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