Contacts of the helix formed by residues 223 - 244 (chain D) in PDB entry 6WVM
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 THR 223 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TYR* 4.9 2.2 - - - -
221D THR* 3.9 14.4 - - + +
222D PRO* 1.3 77.3 - - - +
224D TYR* 1.3 63.2 + - - +
225D GLY* 3.1 14.3 + - - -
226D ASP* 2.7 35.2 + - - +
227D LEU* 3.2 17.0 + - - +
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Residues in contact with TYR 224 (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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11D GLN* 5.5 2.5 - - - -
15D GLN* 5.0 4.3 - - - +
177D VAL* 5.8 2.6 - - - +
179D ASP* 2.9 26.5 + - - -
206D ASN* 3.9 12.0 - - - +
210D TYR* 3.9 20.5 + + - -
223D THR* 1.3 73.8 - - - +
225D GLY* 1.3 56.6 + - - +
227D LEU* 3.3 10.3 + - + +
228D ASN* 2.9 37.3 + - - +
501D GDP 3.1 73.8 + + - +
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Residues in contact with GLY 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 6.0 0.2 - - - +
19D LYS* 3.8 12.8 + - - -
223D THR* 3.1 10.2 + - - -
224D TYR* 1.3 76.7 - - - +
226D ASP* 1.3 60.4 + - - +
228D ASN* 3.7 10.4 + - - +
229D HIS* 3.4 21.3 + - - +
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Residues in contact with ASP 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D CYS* 4.6 2.2 - - - -
219D LEU* 4.3 19.2 - - + +
221D THR 4.2 1.9 - - - +
222D PRO* 3.7 9.7 - - + +
223D THR* 2.7 42.6 + - - +
225D GLY* 1.3 74.1 - - - +
227D LEU* 1.3 65.0 + - - +
229D HIS* 3.5 6.8 + - - +
230D LEU* 3.4 18.0 + - - +
502D TA1 3.5 32.1 - - + -
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Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ASN* 3.5 23.6 - - - +
209D LEU* 3.5 43.2 - - + +
210D TYR* 3.8 37.9 - - + -
213D CYS* 3.7 13.2 - - - -
222D PRO* 4.7 0.9 - - + -
223D THR 3.2 15.5 + - - +
224D TYR* 3.3 15.5 + - + +
226D ASP* 1.3 77.3 - - - +
228D ASN* 1.3 58.7 - - - +
230D LEU* 3.3 10.3 + - - +
231D VAL* 3.2 26.3 + - - +
501D GDP 4.1 10.1 - - - +
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Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D GLN* 3.6 22.4 + - - +
16D ILE* 3.3 21.0 - - + +
19D LYS* 3.7 20.1 - - + +
224D TYR 2.9 25.4 + - - +
225D GLY* 3.8 9.2 - - - +
226D ASP 3.4 0.2 - - - -
227D LEU* 1.3 75.6 - - - +
229D HIS* 1.3 50.4 + - - +
230D LEU 3.5 0.2 - - - -
231D VAL* 3.7 1.8 + - - +
232D SER* 2.7 36.6 + - - -
501D GDP 2.7 47.2 + - - -
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Residues in contact with HIS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 3.5 24.3 + - - +
23D VAL* 5.0 4.9 - - + -
225D GLY 3.4 11.0 + - - +
226D ASP* 3.5 12.2 + - - +
228D ASN* 1.3 75.0 - - - +
230D LEU* 1.3 62.9 + - - +
232D SER* 3.3 7.7 + - - -
233D ALA* 3.2 25.2 + - + +
502D TA1 2.8 97.8 + + + +
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Residues in contact with LEU 230 (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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209D LEU* 3.7 26.7 - - + +
212D ILE* 3.7 35.7 - - + -
213D CYS* 3.7 26.2 - - - -
217D LEU* 4.6 2.7 - - + -
226D ASP 3.4 8.0 + - - +
227D LEU* 3.3 8.8 + - - +
229D HIS* 1.3 76.1 - - - +
231D VAL* 1.3 65.4 + - - +
233D ALA* 3.7 9.8 + - + +
234D THR 3.8 5.4 + - - -
272D PHE* 5.6 0.9 - - + -
275D LEU* 3.8 28.7 - - + -
302D MET* 3.5 27.3 - - + +
502D TA1 4.2 12.6 - - + -
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 4.2 32.1 - - + -
169D PHE* 5.2 0.7 - - + -
171D VAL* 5.0 2.2 - - + -
204D ILE* 3.7 33.0 - - + -
209D LEU* 3.7 25.1 - - + -
227D LEU 3.2 13.0 + - - +
228D ASN 3.9 6.7 - - - +
230D LEU* 1.3 75.5 - - - +
232D SER* 1.3 62.3 + - - +
234D THR* 2.9 26.0 + - - -
235D MET* 3.2 25.2 + - + +
302D MET* 4.7 3.4 - - - -
501D GDP 5.5 0.4 - - - +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE 4.2 2.9 - - - -
19D LYS* 3.8 6.9 - - - +
20D PHE* 3.5 37.5 - - - -
23D VAL* 3.8 13.6 - - - +
228D ASN 2.7 23.9 + - - -
229D HIS* 3.3 12.5 + - - -
231D VAL* 1.3 72.2 - - - +
233D ALA* 1.3 58.3 + - - +
235D MET* 3.6 11.3 - - - +
236D SER* 2.9 30.3 + - - -
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 5.1 2.1 - - - +
229D HIS* 3.2 20.3 + - + +
230D LEU* 3.8 9.4 - - + +
231D VAL 3.3 0.2 - - - -
232D SER* 1.3 75.8 + - - +
234D THR* 1.3 55.6 + - - +
236D SER* 3.5 3.6 + - - -
237D GLY* 3.0 23.4 + - - -
272D PHE* 4.0 21.7 - - + -
376D THR* 4.1 2.4 + - - -
502D TA1 3.7 39.8 - - + -
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Residues in contact with THR 234 (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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169D PHE* 4.6 9.1 - - - -
204D ILE* 4.9 1.9 - - - +
230D LEU 4.0 0.8 + - - +
231D VAL* 2.9 19.7 + - - -
233D ALA* 1.3 71.8 - - - +
235D MET* 1.3 61.7 + - - +
238D VAL* 3.2 30.6 + - - +
270D PRO* 4.0 23.6 - - + +
271D GLY 3.4 27.4 - - - +
272D PHE* 4.1 6.3 - - + -
302D MET* 3.7 30.4 - - + -
376D THR* 3.9 12.3 - - + +
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Residues in contact with MET 235 (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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6D HIS* 4.0 13.7 - - + +
16D ILE* 4.8 3.1 - - - +
20D PHE* 3.7 41.9 - - + -
52D TYR* 4.1 5.9 + - - -
136D GLN* 4.4 7.4 + - + +
138D THR* 3.4 34.5 - - + -
169D PHE* 3.7 41.7 - - + -
231D VAL* 3.2 25.1 + - + +
232D SER* 3.3 9.8 + - - +
234D THR* 1.3 75.7 - - - +
236D SER* 1.3 64.2 + - - +
237D GLY 3.4 0.2 + - - -
238D VAL* 3.8 11.1 + - - +
239D THR* 4.0 11.1 + - - +
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Residues in contact with SER 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D PHE* 4.3 2.1 - - - -
23D VAL* 4.1 4.5 - - - -
24D ILE* 4.0 20.0 - - - -
27D GLU* 2.8 26.5 + - - -
232D SER 2.9 16.8 + - - -
233D ALA 3.6 4.9 - - - -
235D MET* 1.3 75.2 - - - +
237D GLY* 1.3 60.3 + - - +
239D THR* 3.8 1.9 + - - -
240D THR* 3.0 11.9 + - - -
243D ARG* 2.9 24.7 + - - +
320D ARG* 3.8 1.7 + - - -
502D TA1 3.3 22.5 - - - -
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Residues in contact with GLY 237 (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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233D ALA 3.0 11.0 + - - -
234D THR 3.3 2.4 + - - -
235D MET 3.2 1.2 - - - -
236D SER* 1.3 75.7 - - - +
238D VAL* 1.3 62.2 + - - +
240D THR* 3.1 24.9 + - - -
272D PHE* 5.9 0.2 - - - -
318D ILE* 3.9 10.9 - - - +
320D ARG* 5.1 7.5 - - - -
376D THR* 3.4 28.3 - - - -
502D TA1 5.2 0.6 - - - -
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Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D GLN* 4.8 0.4 - - - +
167D ASN* 4.8 0.4 - - - +
169D PHE* 3.9 26.0 - - + -
202D TYR* 4.1 17.9 - - + +
234D THR* 3.2 13.1 + - - +
235D MET 4.0 5.2 - - - +
236D SER 3.6 0.2 - - - -
237D GLY* 1.3 74.5 - - - +
239D THR* 1.3 64.2 + - + +
240D THR 3.4 0.4 + - - -
241D CYS* 4.9 1.4 + - - +
242D LEU* 4.9 0.3 - - - +
250D ALA 4.6 8.0 - - - +
252D LEU* 3.8 23.8 - - + +
255D LEU* 3.9 17.0 - - + +
270D PRO* 6.2 0.9 - - + -
318D ILE* 4.6 10.9 - - + +
376D THR* 3.9 13.5 - - + -
378D ILE* 3.7 27.8 - - + -
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Residues in contact with THR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 3.9 14.6 - - + -
52D TYR* 2.9 29.9 + - - +
136D GLN* 3.6 22.4 - - - +
235D MET 4.0 5.0 + - - +
236D SER 3.8 5.1 + - - -
237D GLY 3.3 0.2 - - - -
238D VAL* 1.3 77.5 - - + +
240D THR* 1.3 65.7 + - - +
241D CYS 3.2 2.7 - - - -
242D LEU* 3.0 34.3 + - - +
243D ARG* 3.1 21.8 + - - +
252D LEU* 4.1 12.1 - - + -
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Residues in contact with THR 240 (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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236D SER 3.0 16.9 + - - -
237D GLY 3.1 14.2 + - - -
238D VAL 3.4 0.4 - - - -
239D THR* 1.3 76.5 + - - +
241D CYS* 1.3 57.7 + - - +
243D ARG* 2.9 30.1 + - - +
244D PHE* 3.0 18.1 + - + +
318D ILE* 4.9 3.6 - - + -
320D ARG* 3.4 37.2 + - + +
356D CYS* 3.4 36.3 - - + -
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Residues in contact with CYS 241 (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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73C THR* 4.4 8.8 + - - -
2D ARG* 4.6 3.3 + - - -
238D VAL 4.9 1.1 + - - +
239D THR 3.1 1.0 + - - -
240D THR* 1.3 77.0 - - - +
242D LEU* 1.3 57.8 + - - +
244D PHE 3.8 13.8 - - - +
246D GLY* 5.8 0.9 - - - -
248D LEU 3.7 15.9 - - - -
249D ASN* 3.9 17.1 - - - +
250D ALA 3.2 45.3 + - - +
251D ASP 5.4 0.2 - - - -
318D ILE* 4.6 10.9 - - + +
354D ALA* 4.2 12.8 - - - -
355D VAL 4.8 0.7 - - - -
356D CYS* 4.5 19.3 - - - -
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Residues in contact with LEU 242 (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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73C THR* 5.6 1.3 - - - -
2D ARG* 3.6 68.2 + - + +
4D ILE* 4.1 11.9 - - + -
48D ARG* 3.8 9.0 + - - -
51D VAL* 3.6 31.8 - - + +
133D GLN* 5.3 6.3 - - + -
238D VAL 4.9 0.7 - - - +
239D THR* 3.0 39.6 + - - +
241D CYS* 1.3 76.7 - - - +
243D ARG* 1.3 58.1 + - - +
244D PHE 3.8 0.7 - - - -
250D ALA 5.0 0.7 - - - +
251D ASP* 4.5 8.7 - - - +
252D LEU* 4.3 26.7 - - + +
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Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ILE* 4.2 4.1 - - - +
27D GLU* 2.7 32.5 + - - -
28D HIS* 3.0 36.2 + - + +
42D LEU 4.2 4.9 - - - +
48D ARG* 3.2 27.7 - - - +
51D VAL* 3.7 19.7 - - + -
52D TYR* 3.3 33.3 - - - -
236D SER* 2.9 31.7 + - - +
239D THR* 3.1 21.9 + - - +
240D THR* 2.9 16.2 + - - +
242D LEU* 1.3 81.9 - - - +
244D PHE* 1.3 78.6 + - + +
320D ARG* 4.4 0.4 - - - +
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Residues in contact with PHE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 4.1 8.3 - - - +
27D GLU* 4.2 23.6 - - + -
28D HIS* 4.4 11.4 - + - -
42D LEU* 3.5 29.4 - - + -
43D GLN* 4.2 7.0 - - + -
48D ARG* 5.5 0.4 - - - -
240D THR* 3.0 17.4 + - + +
241D CYS* 3.8 16.1 - - - +
242D LEU 3.8 0.2 - - - -
243D ARG* 1.3 108.7 - - + +
245D PRO* 1.3 73.5 - - + +
249D ASN* 4.9 1.0 - - - +
320D ARG* 4.0 24.9 - - - -
356D CYS* 3.5 19.7 - - - -
358D ILE* 3.9 32.3 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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