Contacts of the helix formed by residues 56 - 78 (chain c) in PDB entry 5GJQ
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 LEU 56 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3c ILE* 3.7 33.1 + - + +
4c MET* 4.7 1.2 - - - -
6c TYR* 4.1 15.5 - - + -
7c ASN* 3.7 15.9 - - - +
55c GLY* 1.3 71.6 - - - -
57c ALA* 1.3 67.2 + - - +
58c THR* 3.2 13.0 - - - +
59c ASP* 2.9 26.9 + - + +
60c VAL* 2.9 18.2 + - - +
104c TYR* 2.8 36.8 + - + +
92d LEU* 5.4 6.5 - - + -
93d ARG* 5.2 3.4 - - - +
121d LEU* 4.5 15.7 - - + -
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Residues in contact with ALA 57 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7c ASN* 3.1 23.2 + - + +
28c PHE* 3.8 19.5 - - + -
39c PHE* 3.7 26.7 - - + -
55c GLY 3.2 4.8 + - - -
56c LEU* 1.3 70.3 - - - +
58c THR* 1.3 63.7 + - - +
60c VAL* 3.1 11.6 + - - +
61c GLN* 3.0 28.3 + - - +
123d ALA* 4.2 6.5 - - + -
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Residues in contact with THR 58 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7c ASN* 4.9 0.4 + - - -
56c LEU* 4.6 11.3 - - - +
57c ALA* 1.3 79.8 - - - +
59c ASP* 1.3 70.5 + - - +
61c GLN* 4.6 2.0 - - - -
62c THR* 2.9 31.4 + - - +
85d ARG* 2.9 16.6 + - - +
89d ALA* 4.5 7.9 - - + +
92d LEU* 4.0 14.6 - - + -
121d LEU* 2.4 46.3 + - - +
122d ALA 3.6 14.4 - - - +
123d ALA* 3.8 2.7 + - - +
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Residues in contact with ASP 59 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56c LEU* 2.9 18.1 + - - +
58c THR* 1.3 86.8 - - - +
60c VAL* 1.3 61.3 + - - +
62c THR* 3.8 7.7 + - - -
63c VAL* 2.9 33.1 + - - +
103c TYR* 3.6 21.6 - - + -
104c TYR* 2.8 42.7 + - - +
105c THR* 4.3 3.7 - - - +
93d ARG* 3.0 32.5 + - - -
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Residues in contact with VAL 60 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39c PHE* 4.8 6.1 - - + -
40c GLN 4.2 11.4 - - - +
41c LYS* 4.6 2.5 - - + -
43c PHE* 4.0 17.3 - - + -
53c LEU* 3.5 48.2 - - + +
54c ALA* 4.0 14.1 - - - -
55c GLY 4.2 1.8 - - - +
56c LEU 2.9 17.8 + - - +
57c ALA* 3.1 15.5 + - - +
59c ASP* 1.3 76.8 - - - +
61c GLN* 1.3 61.9 + - + +
64c ALA* 2.9 29.5 + - - +
105c THR* 4.2 3.6 - - - +
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Residues in contact with GLN 61 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39c PHE* 3.5 22.8 - - + -
40c GLN 5.5 0.9 - - - +
43c PHE* 5.2 8.1 - - + -
57c ALA 3.0 10.5 + - - +
58c THR 3.8 0.9 - - - +
60c VAL* 1.3 80.4 - - + +
62c THR* 1.3 56.8 + - - +
64c ALA* 3.6 5.0 - - - +
65c GLN* 2.9 42.2 + - - +
85d ARG* 3.6 25.3 + - - +
122d ALA 3.9 0.2 - - - +
123d ALA* 3.5 9.7 - - - -
124d LEU* 2.9 53.2 + - - +
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Residues in contact with THR 62 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58c THR* 2.9 20.9 + - - +
59c ASP* 4.1 7.9 + - - -
61c GLN* 1.3 73.1 - - - +
63c VAL* 1.3 67.5 + - - +
65c GLN* 3.1 6.8 + - - +
66c ARG* 2.9 32.2 + - - +
103c TYR* 3.7 30.1 - - + +
85d ARG* 2.7 25.2 + - - +
86d ARG* 3.8 22.8 + - - +
89d ALA* 4.2 3.9 - - + +
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Residues in contact with VAL 63 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53c LEU* 4.0 21.8 - - + -
59c ASP 2.9 21.3 + - - +
60c VAL 4.2 0.7 - - - +
62c THR* 1.3 72.9 - - - +
64c ALA* 1.3 69.7 + - - +
66c ARG* 4.4 1.6 - - - +
67c LEU* 3.0 30.8 + - + +
91c VAL* 5.3 7.4 - - + -
94c LEU* 4.1 17.1 - - + +
95c LEU* 4.1 7.2 - - + -
103c TYR* 3.6 38.6 - - + -
105c THR* 3.9 15.5 - - + -
107c PRO* 6.0 0.2 - - + -
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Residues in contact with ALA 64 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43c PHE* 3.7 41.7 - - + -
45c MET* 4.9 3.6 - - - +
51c ILE* 5.9 1.6 - - + -
53c LEU* 3.7 9.6 - - + +
60c VAL 2.9 19.1 + - - +
61c GLN 3.6 4.0 - - - +
63c VAL* 1.3 80.2 - - - +
65c GLN* 1.4 59.2 + - + +
67c LEU* 3.5 6.6 - - - +
68c LYS* 2.9 29.9 + - - +
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Residues in contact with GLN 65 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 4.3 10.8 - - + +
102D GLN* 3.1 51.9 - - - +
61c GLN* 2.9 24.8 + - - +
62c THR 3.1 3.8 + - - +
64c ALA* 1.4 74.3 - - + +
66c ARG* 1.3 60.9 + - - +
68c LYS* 3.3 7.0 + - - +
69c PHE* 2.9 25.6 + - - +
82d ASN* 3.6 9.1 + - - -
85d ARG* 3.0 30.2 + - - +
86d ARG* 3.1 15.4 + - - +
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Residues in contact with ARG 66 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 4.5 23.1 - - + +
62c THR* 2.9 20.9 + - + +
63c VAL 4.4 0.7 - - - +
65c GLN* 1.3 74.7 - - - +
67c LEU* 1.3 66.1 + - - +
69c PHE* 3.1 10.7 - - + +
70c ARG* 3.1 34.9 + - - +
94c LEU* 3.9 22.3 - - + +
98c LYS* 5.9 4.4 - - - +
103c TYR* 3.6 26.8 + - - -
86d ARG* 4.3 17.8 - - - +
90d ASP* 4.6 6.7 + - - -
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Residues in contact with LEU 67 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45c MET* 3.6 22.9 - - + -
51c ILE* 3.5 32.3 - - + -
63c VAL* 3.0 25.0 + - + +
64c ALA* 3.5 5.4 - - - +
66c ARG* 1.3 78.0 - - - +
68c LYS* 1.3 57.7 + - - +
70c ARG* 3.4 2.1 + - + -
71c LEU* 2.8 30.5 + - - +
87c LEU* 4.1 7.4 - - + -
90c MET* 4.1 26.0 - - + -
91c VAL* 3.6 30.3 - - + -
94c LEU* 4.2 13.8 - - + +
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Residues in contact with LYS 68 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLU* 4.5 6.5 + - - -
95D GLN* 4.8 0.2 - - - -
98D LEU* 5.4 6.3 - - + -
102D GLN* 6.2 2.7 - - - +
44c PRO* 3.6 20.6 - - - +
45c MET* 3.7 28.2 - - + +
46c GLY 5.6 0.4 - - - +
64c ALA 2.9 17.1 + - - +
65c GLN* 3.3 7.6 + - - +
67c LEU* 1.3 75.7 - - - +
69c PHE* 1.3 58.0 + - - +
71c LEU* 4.1 5.1 - - + +
72c ASN* 2.9 66.5 + - - +
75c GLU* 5.8 0.6 + - - -
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Residues in contact with PHE 69 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LEU* 4.6 13.0 - - + -
95D GLN* 3.5 47.6 - - + +
96D ARG* 3.9 16.8 - - + -
98D LEU* 6.0 1.1 - - - +
99D LEU* 4.2 20.6 - - + -
65c GLN 2.9 13.6 + - - +
66c ARG* 3.1 14.8 - - + +
68c LYS* 1.3 79.3 - - - +
70c ARG* 1.3 79.2 + - + +
72c ASN* 3.3 3.3 + - - +
73c LEU* 3.2 42.0 + - + +
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Residues in contact with ARG 70 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C VAL* 5.7 2.2 - - - +
100C TYR* 5.5 1.8 + - - +
66c ARG* 3.1 19.3 + - - +
67c LEU* 4.0 3.1 - - - +
69c PHE* 1.3 93.9 - - + +
71c LEU* 1.3 63.1 + - - +
73c LEU* 3.4 7.7 + - + +
74c TYR* 3.0 22.3 + - - +
90c MET* 4.1 26.0 + - + +
93c ASN* 3.2 28.9 - - - +
94c LEU* 3.8 34.2 - - - +
97c GLU* 2.7 30.2 + - - -
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Residues in contact with LEU 71 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45c MET* 3.4 53.4 - - + +
67c LEU 2.8 19.0 + - - +
68c LYS* 3.7 13.0 - - + +
70c ARG* 1.3 78.5 - - - +
72c ASN* 1.3 58.2 + - - +
74c TYR* 3.0 5.8 + - + +
75c GLU* 2.9 43.1 + - + +
82c ILE* 3.6 45.5 - - + -
87c LEU* 4.3 7.2 - - + -
90c MET* 4.2 6.2 - - + -
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Residues in contact with ASN 72 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D GLU* 3.2 26.2 + - - -
95D GLN* 3.0 38.7 + - - +
98D LEU* 3.5 12.3 - - - +
68c LYS* 2.9 45.2 + - - +
69c PHE 3.7 0.4 - - - +
71c LEU* 1.3 76.4 - - - +
73c LEU* 1.3 63.2 + - - +
75c GLU* 3.3 12.0 + - - +
76c LEU* 3.0 32.4 + - + +
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Residues in contact with LEU 73 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ASN* 5.4 4.3 - - - +
91D ARG* 3.7 36.3 - - + -
92D LEU* 4.0 21.3 - - + +
95D GLN* 4.0 15.5 - - + -
69c PHE* 3.2 38.9 + - + +
70c ARG* 3.6 10.1 - - + +
72c ASN* 1.3 77.6 - - - +
74c TYR* 1.3 58.0 + - - +
76c LEU* 3.2 4.4 + - + +
77c LYS* 2.9 40.4 + - + +
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Residues in contact with TYR 74 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 3.5 9.9 - + - -
100C TYR* 4.0 33.2 - + - +
102C GLU* 3.5 10.6 + - - -
112C ARG* 6.4 0.4 - - - -
70c ARG 3.0 14.0 + - - +
71c LEU* 3.0 8.9 + - - +
73c LEU* 1.3 77.0 - - - +
75c GLU* 1.3 61.8 + - + +
76c LEU 3.1 0.2 + - - -
77c LYS* 5.0 2.7 - - - -
78c GLU* 3.0 61.2 + - + +
80c ARG* 2.8 37.0 + - - -
82c ILE* 3.7 38.1 - - + +
83c LYS* 5.4 1.4 + - - +
86c THR* 3.9 10.6 + - + +
90c MET* 4.3 10.3 - - + -
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Residues in contact with GLU 75 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45c MET 4.1 7.3 - - - +
46c GLY* 4.5 5.4 - - - -
68c LYS* 5.8 0.5 + - - -
71c LEU* 2.9 43.9 + - + +
72c ASN* 3.3 10.9 + - - +
74c TYR* 1.3 76.3 - - + +
76c LEU* 1.3 57.9 + - + +
78c GLU 2.7 15.4 - - - +
79c GLY* 4.4 2.3 - - - -
80c ARG 3.6 24.8 + - - +
81c GLN* 3.9 20.2 - - + +
82c ILE 3.8 16.6 + - - +
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Residues in contact with LEU 76 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LYS* 3.0 53.2 - - + +
68D LEU 3.2 26.9 - - - +
69D ASN* 4.2 5.6 - - - +
70D GLU 5.5 0.2 - - - +
91D ARG* 3.3 37.9 + - + +
95D GLN* 4.9 8.7 - - - +
72c ASN* 3.0 24.1 + - + +
73c LEU* 3.7 6.5 - - + +
74c TYR 3.1 0.2 - - - -
75c GLU* 1.3 80.7 - - - +
77c LYS* 1.3 67.9 + - - +
78c GLU 3.3 4.9 + - - +
79c GLY* 5.0 1.2 - - - -
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Residues in contact with LYS 77 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLN* 2.9 24.5 + - - +
111C GLN* 4.1 22.5 + - - +
112C ARG* 4.1 43.5 - - - +
88D ASN* 3.5 34.7 + - - +
91D ARG* 4.1 19.1 - - - +
73c LEU* 2.9 25.0 + - + +
74c TYR* 4.2 2.9 - - + +
76c LEU* 1.3 77.7 - - - +
78c GLU* 1.3 62.0 + - + +
79c GLY 4.2 0.2 + - - -
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Residues in contact with GLU 78 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 2.7 26.0 + - - -
105C PRO* 3.6 3.4 - - - +
108C GLN* 3.3 36.5 - - - +
112C ARG* 5.7 0.2 + - - -
74c TYR* 2.9 36.8 + - + +
75c GLU 2.7 26.2 - - - +
76c LEU 3.4 3.4 - - - +
77c LYS* 1.3 79.7 - - + +
79c GLY* 1.3 58.8 + - - +
80c ARG* 2.7 56.3 + - + +
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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