Contacts of the helix formed by residues 3399 - 3427 (chain D) in PDB entry 6X34
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 PHE3399 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3398D GLU* 1.3 78.3 - - + +
3400D SER* 1.3 59.5 + - - +
3402D LEU* 3.9 5.3 - - - +
3403D CYS* 3.0 31.9 + - - +
3452D PHE* 6.4 2.2 - - + -
3455D GLU* 3.7 38.0 - - + +
3456D GLU* 5.6 1.4 - - - -
3459D PHE* 4.6 3.8 - - + +
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Residues in contact with SER3400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398D GLU 3.3 5.0 - - - +
3399D PHE* 1.3 78.9 - - - +
3401D VAL* 1.3 57.9 + - - +
3403D CYS 3.6 0.2 + - - -
3404D ARG* 3.1 28.9 + - - +
3459D PHE* 3.7 39.3 - - - -
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Residues in contact with VAL3401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398D GLU* 3.6 12.5 + - - +
3399D PHE 3.4 0.2 - - - -
3400D SER* 1.3 79.4 - - - +
3402D LEU* 1.3 61.1 + - - +
3404D ARG* 4.0 4.7 - - - +
3405D ASP* 3.1 25.3 + - - +
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Residues in contact with LEU3402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3398D GLU 3.1 18.9 + - - +
3399D PHE* 3.9 6.7 - - - +
3400D SER 3.3 0.2 - - - -
3401D VAL* 1.3 76.0 - - - +
3403D CYS* 1.3 59.9 + - - +
3405D ASP* 3.5 4.1 + - - +
3406D LEU* 3.0 28.1 + - - +
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Residues in contact with CYS3403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3399D PHE 3.0 19.2 + - - +
3402D LEU* 1.3 74.5 - - - +
3404D ARG* 1.3 64.4 + - - +
3406D LEU* 3.4 7.5 + - - +
3407D TYR* 3.3 20.8 + - - +
3456D GLU* 4.3 17.0 - - + +
3459D PHE* 3.6 32.5 - - + -
3460D VAL* 5.4 3.4 - - + +
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Residues in contact with ARG3404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3400D SER 3.1 18.4 + - - +
3401D VAL* 4.0 7.2 - - - +
3402D LEU 3.3 0.2 - - - -
3403D CYS* 1.3 78.1 - - - +
3405D ASP* 1.3 61.1 + - - +
3407D TYR* 3.4 14.8 + - - +
3408D ALA* 3.5 11.1 + - - +
3459D PHE* 4.6 10.7 - - + -
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Residues in contact with ASP3405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3401D VAL 3.1 18.3 + - - +
3402D LEU* 4.0 3.8 - - - +
3404D ARG* 1.3 74.3 - - - +
3406D LEU* 1.3 59.9 + - - +
3408D ALA* 3.4 7.1 + - - +
3409D LEU* 3.0 28.5 + - - +
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Residues in contact with LEU3406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3402D LEU 3.0 18.4 + - - +
3403D CYS* 3.7 9.4 - - - +
3404D ARG 3.2 0.2 - - - -
3405D ASP* 1.3 78.7 - - - +
3407D TYR* 1.3 57.4 + - - +
3409D LEU* 3.4 5.9 + - - +
3410D TYR* 2.9 30.0 + - - +
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Residues in contact with TYR3407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3403D CYS 3.3 10.7 + - - +
3404D ARG* 3.7 10.1 - - - +
3405D ASP 3.3 0.4 - - - -
3406D LEU* 1.3 79.5 - - - +
3408D ALA* 1.3 60.9 + - - +
3410D TYR* 3.4 6.1 + - - +
3411D PRO* 3.1 23.9 - - - +
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Residues in contact with ALA3408 (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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3404D ARG 3.5 8.0 + - - +
3405D ASP* 3.4 10.2 + - - +
3406D LEU 3.3 0.4 - - - -
3407D TYR* 1.3 78.1 - - - +
3409D LEU* 1.3 61.8 + - - +
3411D PRO* 3.5 5.6 - - - +
3412D LEU* 3.1 23.7 + - - +
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Residues in contact with LEU3409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3405D ASP 3.0 17.6 + - - +
3406D LEU* 3.9 7.4 - - - +
3407D TYR 3.3 0.2 - - - -
3408D ALA* 1.3 74.5 - - - +
3410D TYR* 1.3 60.1 + - - +
3412D LEU* 3.5 5.3 + - - +
3413D LEU* 3.0 30.5 + - - +
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Residues in contact with TYR3410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3406D LEU 2.9 16.9 + - - +
3407D TYR* 3.8 7.2 - - - +
3409D LEU* 1.3 78.7 - - - +
3411D PRO* 1.3 58.1 - - - +
3413D LEU* 3.5 4.2 + - - +
3414D ILE* 3.0 29.1 + - - +
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Residues in contact with PRO3411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3407D TYR 3.1 17.0 - - - +
3408D ALA* 3.8 6.5 - - - +
3409D LEU 3.4 0.2 - - - -
3410D TYR* 1.3 77.7 - - - +
3412D LEU* 1.3 59.8 + - - +
3414D ILE* 3.4 5.1 + - + +
3415D ARG* 3.1 23.9 + - - +
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Residues in contact with LEU3412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3408D ALA 3.1 17.2 + - - +
3409D LEU* 4.0 5.8 - - - +
3411D PRO* 1.3 77.2 - - - +
3413D LEU* 1.3 58.3 + - - +
3415D ARG* 3.5 5.3 + - - +
3416D TYR* 3.0 29.2 + - - +
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Residues in contact with LEU3413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3409D LEU 3.0 19.2 + - - +
3410D TYR* 4.0 5.4 - - - +
3412D LEU* 1.3 74.3 - - - +
3414D ILE* 1.3 59.9 + - - +
3416D TYR* 3.5 6.3 + - - +
3417D VAL* 3.0 28.8 + - - +
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Residues in contact with ILE3414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3410D TYR 3.0 18.8 + - - +
3411D PRO* 3.8 6.5 - - + +
3412D LEU 3.3 0.2 - - - -
3413D LEU* 1.3 78.1 - - - +
3415D ARG* 1.3 61.3 + - - +
3417D VAL* 3.3 16.9 + - - +
3418D ASP* 3.9 4.9 + - - +
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Residues in contact with ARG3415 (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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3411D PRO 3.1 17.6 + - - +
3412D LEU* 4.0 4.7 - - - +
3414D ILE* 1.3 77.6 - - - +
3416D TYR* 1.3 61.7 + - - +
3417D VAL 3.4 0.3 + - - -
3418D ASP* 3.5 18.4 + - - +
3419D ASN* 4.5 1.9 + - - +
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Residues in contact with TYR3416 (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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3412D LEU 3.0 19.1 + - - +
3413D LEU* 3.8 7.4 - - - +
3414D ILE 3.3 0.2 - - - -
3415D ARG* 1.3 73.6 - - - +
3417D VAL* 1.3 60.6 + - - +
3418D ASP 3.2 1.0 + - - -
3419D ASN* 3.3 6.2 + - - +
3420D ASN* 2.9 29.5 + - + +
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Residues in contact with VAL3417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3413D LEU 3.0 17.7 + - - +
3414D ILE* 3.6 10.8 - - - +
3415D ARG 3.2 1.2 - - - -
3416D TYR* 1.3 75.1 - - - +
3418D ASP* 1.3 64.4 + - - +
3419D ASN 3.2 0.4 + - - -
3420D ASN* 3.6 14.3 + - - +
3421D ARG* 3.8 12.6 + - - +
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Residues in contact with ASP3418 (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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3414D ILE 3.9 5.0 + - - +
3415D ARG* 3.5 14.4 + - - +
3416D TYR 3.2 1.0 - - - -
3417D VAL* 1.3 79.4 - - - +
3419D ASN* 1.3 57.7 + - + +
3421D ARG* 4.7 6.4 + - - +
3422D ALA* 5.2 2.3 + - - +
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Residues in contact with ASN3419 (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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3415D ARG 4.5 1.7 + - - +
3416D TYR* 3.3 7.1 + - - +
3418D ASP* 1.3 77.2 - - + +
3420D ASN* 1.3 63.8 + - - +
3421D ARG 3.2 2.9 - - - -
3422D ALA* 3.6 8.6 + - + +
3423D HIS* 3.2 22.3 + - - +
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Residues in contact with ASN3420 (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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3416D TYR* 2.9 19.0 + - + +
3417D VAL* 3.6 10.9 + - - +
3419D ASN* 1.3 75.9 - - - +
3421D ARG* 1.3 59.6 + - - +
3423D HIS* 3.8 5.8 - - - +
3424D TRP* 2.9 32.2 + - - +
3429D ASN* 4.4 8.0 + - - +
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Residues in contact with ARG3421 (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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3417D VAL 3.8 11.5 + - - +
3418D ASP 4.9 4.9 - - - +
3419D ASN 3.2 0.8 - - - -
3420D ASN* 1.3 79.8 - - - +
3422D ALA* 1.3 61.5 + - - +
3424D TRP* 4.2 3.5 - - - +
3425D LEU* 3.4 20.6 + - - +
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Residues in contact with ALA3422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3418D ASP 5.2 1.7 + - - +
3419D ASN* 3.6 10.7 + - - +
3420D ASN 3.4 0.2 - - - -
3421D ARG* 1.3 77.1 - - - +
3423D HIS* 1.3 64.4 + - - +
3425D LEU* 3.6 16.2 + - - +
3426D THR* 3.9 10.2 + - - +
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Residues in contact with HIS3423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3419D ASN 3.2 18.2 + - - +
3420D ASN* 4.0 5.6 - - - +
3421D ARG 3.3 0.2 - - - -
3422D ALA* 1.3 75.9 - - - +
3424D TRP* 1.3 62.2 + - - +
3426D THR* 2.9 19.7 + - - -
3427D GLU 2.9 15.2 - - - +
3429D ASN* 4.2 17.5 - - - +
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Residues in contact with TRP3424 (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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3420D ASN 2.9 19.1 + - - +
3421D ARG* 4.2 3.8 - - - +
3423D HIS* 1.3 75.0 - - - +
3425D LEU* 1.3 64.5 + - - +
3426D THR 3.6 0.2 + - - -
3427D GLU* 3.4 20.4 + - - +
3428D PRO* 4.1 7.2 - - + +
3429D ASN* 3.9 13.2 - - - +
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Residues in contact with LEU3425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1215B ALA* 6.3 3.8 - - + -
3421D ARG 3.4 13.2 + - - +
3422D ALA* 3.7 12.8 - - - +
3423D HIS 3.2 0.8 - - - -
3424D TRP* 1.3 80.7 - - - +
3426D THR* 1.3 64.2 + - + +
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Residues in contact with THR3426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3422D ALA 3.9 7.9 + - - +
3423D HIS* 2.9 19.4 + - - -
3425D LEU* 1.3 79.7 - - + +
3427D GLU* 1.3 62.1 + - - +
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Residues in contact with GLU3427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423D HIS 2.9 16.8 - - - +
3424D TRP* 3.4 8.6 - - - -
3425D LEU 3.5 0.4 - - - -
3426D THR* 1.3 86.1 + - - +
3428D PRO* 1.3 79.1 - - + +
3429D ASN* 4.3 2.1 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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