Contacts of the helix formed by residues 382 - 405 (chain A) in PDB entry 5DO7
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 ASN 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER* 4.6 9.7 - - - -
190A LEU* 5.6 4.8 - - - +
378A ASN* 3.9 18.6 + - - +
379A LEU* 4.0 8.6 - - - +
380A VAL 3.0 6.4 + - - -
381A ARG* 1.3 77.9 - - - +
383A LYS* 1.3 67.8 - - - +
384A LEU* 3.1 30.8 - - - +
385A ALA* 2.8 31.2 + - + +
386A VAL* 3.2 10.6 + - - +
441A LEU* 5.9 1.4 - - - +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL 4.7 6.3 - - - +
381A ARG* 4.5 22.6 - - - +
382A ASN* 1.3 74.3 + - - +
384A LEU* 1.3 71.3 + - + +
385A ALA 3.0 1.2 + - - -
386A VAL* 4.9 3.8 - - - +
387A ILE* 3.4 30.3 + - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LEU* 4.5 26.7 - - + -
382A ASN* 3.1 23.3 - - - +
383A LYS* 1.3 81.0 - - + +
385A ALA* 1.3 63.2 + - - +
387A ILE* 4.1 8.7 - - - +
388A THR* 3.8 9.9 + - - +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 4.7 5.6 - - + +
382A ASN* 2.8 35.5 + - + +
384A LEU* 1.3 71.1 - - + +
386A VAL* 1.3 67.9 + - - +
387A ILE 3.2 2.0 - - - -
388A THR* 2.3 29.8 + - - -
389A ARG* 3.3 7.9 + - - +
441A LEU* 4.4 29.2 - - + -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 2.8 36.6 - - + +
380A VAL* 3.8 22.7 - - + +
382A ASN 3.2 10.6 + - - +
383A LYS* 4.4 4.0 - - - +
385A ALA* 1.3 77.4 - - - +
387A ILE* 1.3 70.1 + - + +
389A ARG* 2.8 22.6 + - - +
390A LEU* 3.3 32.9 - - + +
474A PHE* 4.0 18.2 - - + -
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Residues in contact with ILE 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 3.4 22.4 - - + +
384A LEU 4.1 4.3 - - - +
385A ALA 3.2 0.2 - - - -
386A VAL* 1.3 81.1 - - + +
388A THR* 1.3 68.2 + - + +
390A LEU* 3.4 13.0 + - + +
391A LEU* 2.9 46.1 + - + +
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Residues in contact with THR 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A LEU 3.8 7.1 + - - +
385A ALA* 2.3 37.4 + - - -
387A ILE* 1.3 79.6 - - + +
389A ARG* 1.3 63.9 + - - +
391A LEU* 2.8 1.5 + - - +
392A GLN* 2.8 50.4 + - + +
436A LEU* 5.7 5.2 - - + -
437A ASN* 5.4 0.7 - - - -
441A LEU* 5.7 2.6 - - - +
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.5 37.4 - - - +
385A ALA 3.8 8.7 - - - +
386A VAL* 2.8 14.9 + - - +
388A THR* 1.3 73.6 - - - +
390A LEU* 1.3 62.8 - - + +
392A GLN* 3.2 18.5 + - - +
393A ASN 4.8 0.2 + - - -
437A ASN* 3.2 27.8 + - - +
441A LEU* 3.3 29.0 - - + +
467A TYR* 3.4 14.9 + - - -
470A HIS* 4.3 1.4 - - - -
471A VAL* 3.0 40.4 - - - +
474A PHE* 3.9 27.3 - - + +
475A SER* 5.1 0.7 - - - -
478A ALA* 3.2 15.7 - - - +
510A HIS* 4.3 6.1 + - - -
514A GLU* 3.1 14.6 + - - -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.3 37.7 - - + +
387A ILE* 3.6 12.8 - - + +
389A ARG* 1.3 76.3 - - + +
391A LEU* 1.3 71.4 + - + +
393A ASN* 4.4 1.0 + - - +
474A PHE* 3.8 24.0 - - + -
477A VAL* 3.2 31.0 - - + -
478A ALA* 3.1 31.3 - - - +
481A ILE* 3.6 20.9 - - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 2.9 34.4 + - + +
388A THR* 2.8 5.5 + - - -
390A LEU* 1.3 95.2 - - + +
392A GLN* 1.3 66.3 + - - +
393A ASN 3.1 2.0 - - - -
394A LEU* 2.8 31.7 + - + +
395A ILE* 3.1 19.5 + - + +
481A ILE* 4.2 17.3 - - + -
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Residues in contact with GLN 392 (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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388A THR* 2.8 45.4 + - + +
389A ARG* 3.2 11.7 + - - +
391A LEU* 1.3 70.8 - - - +
393A ASN* 1.3 71.3 + - - +
395A ILE* 2.5 31.4 + - + +
396A MET* 2.9 8.3 + - - +
433A THR* 3.8 25.8 + - + -
436A LEU* 3.2 33.4 - - + +
437A ASN* 2.7 30.0 + - - +
510A HIS* 4.3 3.8 - - - -
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Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU 4.4 0.8 + - - +
391A LEU 3.0 1.0 + - - -
392A GLN* 1.3 88.1 - - - +
394A LEU* 1.3 56.8 + - - +
396A MET* 2.8 27.7 + - - +
430A THR* 3.7 24.7 - - - +
433A THR* 4.1 10.4 - - - +
478A ALA* 4.2 13.0 - - + +
479A THR* 4.0 21.4 + - - +
482A PHE* 3.0 30.8 - - + +
506A LEU 4.5 1.6 + - - -
510A HIS* 3.2 38.7 + - + +
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Residues in contact with LEU 394 (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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390A LEU 4.6 1.0 + - - -
391A LEU* 2.8 18.9 + - + +
393A ASN* 1.3 74.3 - - - +
395A ILE* 1.3 80.2 + - + +
397A GLY* 2.8 3.8 + - - -
398A LEU* 2.8 56.7 + - + -
481A ILE* 3.3 35.4 - - + +
482A PHE* 3.6 16.7 - - - +
485A VAL* 3.7 27.8 - - + -
486A CYS* 4.4 0.4 - - - -
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Residues in contact with ILE 395 (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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391A LEU* 3.3 34.1 - - + +
392A GLN* 2.5 23.3 + - + +
394A LEU* 1.3 85.1 - - + +
396A MET* 1.3 65.9 + - + +
398A LEU* 3.3 6.4 + - + +
399A PHE* 2.8 30.4 + - + +
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Residues in contact with MET 396 (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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392A GLN 2.9 5.1 + - - +
393A ASN* 2.8 25.1 + - - +
395A ILE* 1.3 80.0 - - + +
397A GLY* 1.3 56.0 + - - +
399A PHE* 3.3 8.9 + - + +
400A LEU* 3.0 47.9 + - + +
425A GLN* 4.9 6.5 - - + -
426A PHE* 4.9 7.9 - - + -
429A ALA* 3.8 33.7 - - + -
430A THR* 6.2 0.9 - - + -
432A TYR* 6.2 2.2 - - + -
433A THR* 5.1 11.7 - - + -
482A PHE* 4.4 1.3 - - + -
568B ASN* 4.3 23.8 - - - +
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Residues in contact with GLY 397 (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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393A ASN 3.3 3.2 + - - -
394A LEU 2.8 7.9 + - - -
396A MET* 1.3 78.3 - - - +
398A LEU* 1.3 58.6 + - - -
400A LEU* 3.7 2.2 - - - +
401A LEU* 2.8 29.8 + - - +
426A PHE* 4.3 9.6 - - - -
482A PHE* 3.7 11.8 - - - -
486A CYS* 3.5 24.5 - - - +
490A LEU* 5.3 1.9 - - - +
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Residues in contact with LEU 398 (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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394A LEU* 2.8 49.7 + - + +
395A ILE* 3.7 10.5 - - + +
397A GLY* 1.3 71.4 - - - +
399A PHE* 1.3 56.8 + - - +
401A LEU* 2.7 34.9 + - + +
402A PHE* 2.8 14.6 + - - +
485A VAL* 3.8 22.7 - - + -
486A CYS* 4.2 1.3 - - - -
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Residues in contact with PHE 399 (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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395A ILE* 2.8 27.8 + - + +
396A MET* 3.5 10.8 - - + +
398A LEU* 1.3 73.1 - - - +
400A LEU* 1.3 60.0 + - + +
402A PHE* 3.7 12.2 - + - +
403A PHE* 3.1 40.6 - + - -
565B ALA* 4.0 13.0 - - + -
568B ASN* 3.6 41.5 - - + -
569B SER* 3.8 28.5 - - - -
572B LEU* 4.1 10.3 - - + -
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Residues in contact with LEU 400 (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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396A MET* 3.0 25.3 + - + +
397A GLY* 3.7 3.6 - - - +
399A PHE* 1.3 75.0 - - + +
401A LEU* 1.3 67.6 + - - +
402A PHE 2.9 2.5 - - - -
403A PHE* 2.8 16.3 + - - +
404A VAL* 2.8 26.6 + - + +
422A LEU* 4.5 13.0 - - + +
425A GLN* 3.8 30.7 - - + -
426A PHE* 3.5 38.6 - - + -
490A LEU* 5.9 0.7 - - + -
568B ASN* 5.8 1.1 - - - +
572B LEU* 3.7 37.2 - - + -
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Residues in contact with LEU 401 (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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397A GLY 2.8 20.0 + - - +
398A LEU* 2.7 29.2 + - + +
400A LEU* 1.3 72.2 - - - +
402A PHE* 1.3 52.0 + - - +
404A VAL* 3.6 8.5 - - - -
405A LEU* 2.8 45.9 + - - +
485A VAL* 5.0 2.7 - - + -
486A CYS* 4.9 5.8 - - - -
489A THR* 3.8 36.8 - - + +
490A LEU* 3.3 28.0 - - + +
584B TRP* 5.6 0.3 + - - -
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Residues in contact with PHE 402 (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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398A LEU 2.8 14.2 + - - +
399A PHE* 3.7 11.7 - + + +
400A LEU 2.8 0.4 + - - -
401A LEU* 1.3 76.5 - - - +
403A PHE* 1.3 87.3 + + - +
584B TRP* 3.7 41.2 - + - +
586B VAL* 3.1 43.4 - - + +
587B PRO 5.3 0.4 - - - -
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Residues in contact with PHE 403 (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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399A PHE* 3.1 47.1 - + - -
400A LEU 2.8 9.4 + - - +
402A PHE* 1.3 94.2 - + - +
404A VAL* 1.3 63.5 + - + +
405A LEU* 3.2 7.1 + - - +
569B SER* 3.2 42.8 - - - -
572B LEU* 3.5 26.5 - - + -
573B ALA* 4.3 4.7 - - - -
578B ILE* 4.3 12.3 - - + -
583B LEU* 3.5 20.6 - - + +
584B TRP 4.5 0.5 + - - -
587B PRO* 3.9 26.9 - - + +
590B ILE* 4.1 21.1 - - + -
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Residues in contact with VAL 404 (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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400A LEU* 2.8 34.0 + - + +
401A LEU* 3.6 9.9 - - - -
403A PHE* 1.3 69.8 - - + +
405A LEU* 1.3 96.7 + - - +
406A ARG 3.4 5.8 - - - +
418A ASP* 4.6 18.7 - - + +
422A LEU* 3.9 32.1 - - + +
490A LEU* 4.7 3.4 - - + -
572B LEU* 6.0 1.1 - - + -
578B ILE* 3.3 34.3 - - + -
582B SER 5.4 0.5 - - - +
583B LEU* 5.1 1.3 - - - -
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU* 2.8 37.9 + - - +
402A PHE 4.3 0.2 + - - -
403A PHE 3.2 3.3 - - - +
404A VAL* 1.3 104.8 - - - +
406A ARG* 1.3 72.7 + - - +
408A ARG* 5.1 5.6 - - + +
418A ASP* 5.3 3.6 - - - +
490A LEU* 4.1 3.3 - - - +
582B SER* 4.4 17.7 - - - +
583B LEU* 3.6 15.7 - - - +
584B TRP* 3.4 49.1 - - + +
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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