Contacts of the helix formed by residues 100 - 121 (chain B) in PDB entry 5JTP
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 ALA 100 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B HIS* 3.3 12.6 + - + +
98B LEU 3.5 1.2 - - - -
99B GLY* 1.3 81.2 - - - +
101B TYR* 1.3 59.9 + - - +
102B CYS 3.6 0.9 - - - -
103B PRO* 3.5 5.8 - - - +
104B ASN* 3.1 28.1 + - - +
133B PHE* 3.4 39.1 - - - +
134B ASP* 3.8 13.0 - - - +
137B PHE* 4.0 15.0 - - + -
461F PHE* 4.8 0.2 - - + -
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Residues in contact with TYR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B MET* 6.2 2.2 - - + -
11B PHE* 3.5 40.8 - + - -
96B HIS* 3.0 24.5 + + + +
97B CYS* 3.5 9.0 - - - +
100B ALA* 1.3 73.2 - - - +
102B CYS* 1.3 64.1 + - - +
104B ASN* 3.1 16.7 + - - +
105B ILE* 3.2 28.2 + - + +
134B ASP* 3.4 26.0 - - - +
104D ASN* 5.8 2.9 + - - -
130D PRO* 3.5 30.4 + - + +
131D VAL 5.5 1.7 - - - -
132D ASN* 5.7 1.0 + - - +
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Residues in contact with CYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.9 13.9 - - - -
58B VAL* 3.7 17.9 - - + -
84B PHE* 3.6 26.9 - - + -
97B CYS* 2.9 37.9 + - - +
98B LEU* 3.6 23.3 - - - -
101B TYR* 1.3 72.2 - - - +
103B PRO* 1.4 67.2 - - + +
105B ILE* 3.5 14.7 + - - +
106B LEU* 3.3 22.0 + - - +
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Residues in contact with PRO 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 3.6 32.1 - - + -
58B VAL* 3.9 9.6 - - + -
60B LEU* 3.1 25.5 - - + +
98B LEU 3.6 20.2 - - - +
99B GLY 4.3 1.3 - - - +
100B ALA* 3.5 21.1 - - - +
102B CYS* 1.4 91.5 - - + +
104B ASN* 1.3 56.5 + - - +
106B LEU* 3.0 22.7 + - + -
107B PHE* 3.0 12.1 + - - +
133B PHE* 4.4 12.1 - - + -
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ALA 3.1 20.6 + - - +
101B TYR* 3.1 14.0 + - - +
103B PRO* 1.3 75.5 - - - +
105B ILE* 1.3 59.1 + - - +
107B PHE* 3.7 15.2 - - - +
108B PRO* 3.9 4.9 - - - +
131B VAL 3.8 15.2 - - - +
132B ASN* 4.7 9.8 + - - +
133B PHE* 3.8 17.2 - - + -
134B ASP* 3.0 21.7 + - - +
108D PRO* 4.4 11.7 - - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.6 31.4 - - + -
13B ILE* 3.6 18.4 - - + -
16B ILE* 3.8 12.8 - - + -
84B PHE* 3.9 14.8 - - + -
101B TYR* 3.2 24.8 + - + +
102B CYS* 3.6 7.2 - - - +
103B PRO 3.2 0.4 - - - -
104B ASN* 1.3 76.9 - - + +
106B LEU* 1.3 60.7 + - - +
108B PRO* 3.3 13.0 - - - +
109B TYR* 3.6 11.8 - - - -
108D PRO* 4.9 2.7 - - + -
111D ARG* 3.3 31.3 + - - +
130D PRO* 3.8 20.9 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.8 22.9 - - + -
58B VAL* 3.6 22.4 - - + +
60B LEU* 3.8 17.3 - - + +
80B GLN* 3.3 34.8 - - + +
81B GLY 3.4 21.5 - - - +
82B GLY* 3.9 3.1 - - - +
84B PHE* 3.8 21.5 - - + -
102B CYS 3.3 20.4 - - - +
103B PRO* 3.0 8.0 + - + +
105B ILE* 1.3 76.2 - - - +
107B PHE* 1.4 64.0 + - - +
108B PRO* 3.6 1.1 - - - -
109B TYR* 3.3 7.9 + - - +
110B ALA 3.2 17.5 + - - -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.2 2.2 - - + -
60B LEU* 3.6 13.7 - - + -
62B VAL* 4.9 9.9 - - + -
103B PRO 3.0 9.9 + - - +
104B ASN* 3.7 14.8 - - - +
106B LEU* 1.4 76.7 - - - +
108B PRO* 1.4 63.9 - - + +
110B ALA* 3.3 3.7 + - - +
111B ARG* 3.0 33.5 + - + +
128B LEU* 3.6 36.8 - - + -
129B ALA 3.2 28.0 - - - -
130B PRO* 3.7 8.3 - - + -
131B VAL* 4.0 14.4 - - + -
133B PHE* 4.2 23.3 - + + -
109D TYR* 3.3 29.2 - + - -
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN 3.9 5.4 - - - +
105B ILE 3.3 14.4 - - - +
106B LEU 3.7 0.7 - - - -
107B PHE* 1.4 94.4 - - + +
109B TYR* 1.3 57.1 + - + +
111B ARG* 3.4 6.9 - - + +
112B GLU* 3.1 22.3 + - - +
108D PRO* 3.7 29.2 - - + +
109D TYR* 3.7 39.2 - - + +
112D GLU* 3.6 32.2 - - + +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 5.1 0.2 + - - -
16B ILE* 3.5 38.4 - - + +
80B GLN* 3.3 24.9 + - - +
105B ILE 3.6 25.8 - - - -
106B LEU 3.5 4.9 - - - +
107B PHE 3.3 0.2 - - - -
108B PRO* 1.3 74.4 - - + +
110B ALA* 1.4 60.3 + - - +
112B GLU* 3.4 3.4 + - - +
113B CYS* 3.0 31.7 + - - +
108D PRO 4.6 1.8 - - - -
111D ARG* 3.2 39.1 - - - +
112D GLU* 3.7 29.2 - - + -
115D THR* 3.4 31.3 + - + -
116D SER* 6.5 0.2 - - - -
125D GLN* 5.2 2.2 - - - -
127D ASN* 4.3 2.3 + - - -
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Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.5 2.9 - - + -
62B VAL* 3.9 27.1 - - + -
78B VAL* 4.0 16.8 - - + +
80B GLN* 3.7 21.6 - - + +
106B LEU 3.2 5.5 + - - +
107B PHE* 3.5 12.6 - - + +
109B TYR* 1.4 76.9 - - - +
111B ARG* 1.4 57.0 + - - +
113B CYS* 3.5 2.6 + - - +
114B ILE* 3.1 35.9 + - - +
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.0 19.9 + - + +
108B PRO* 3.4 10.5 - - + +
110B ALA* 1.4 76.2 - - - +
112B GLU* 1.4 57.4 + - - +
114B ILE* 3.2 11.3 + - - +
115B THR* 2.9 36.2 + - - +
126B LEU* 6.0 0.2 - - - +
127B ASN* 2.9 37.3 + - - +
128B LEU* 3.7 41.9 + - + +
130B PRO* 5.6 2.2 - - - +
119C SER* 4.0 4.0 + - - -
120C ARG* 5.0 3.8 + - - +
122C THR* 3.7 19.2 - - - +
16D ILE* 3.9 18.6 + - - +
109D TYR* 3.2 40.5 + - - -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.0 29.7 + - - +
108B PRO 3.1 16.7 + - - +
109B TYR* 3.4 4.4 + - - +
111B ARG* 1.4 76.1 - - - +
113B CYS* 1.3 55.8 + - - +
115B THR* 3.6 8.4 + - - -
116B SER* 3.0 24.1 + - - -
112C GLU* 3.9 2.9 - - - +
116C SER* 3.4 16.5 + - - +
119C SER* 6.0 3.1 - - - +
120C ARG* 3.0 41.0 + - + +
112D GLU* 3.7 12.8 - - - +
116D SER* 3.3 5.9 + - - -
120D ARG* 3.1 12.8 + - - -
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.4 39.2 - - - +
18B THR* 3.5 19.7 - - - -
21B ILE* 3.5 20.4 - - - -
78B VAL* 3.7 19.1 - - + -
80B GLN* 4.6 0.2 - - - -
109B TYR 3.0 17.1 + - - +
110B ALA 3.7 4.9 - - - +
111B ARG 3.2 0.2 - - - -
112B GLU* 1.3 74.2 - - - +
114B ILE* 1.4 63.6 + - - +
116B SER* 3.4 2.8 - - - -
117B MET* 3.1 29.0 + - - +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.5 43.1 - - + +
64B VAL* 3.7 17.7 - - + -
76B CYS* 3.3 30.3 - - + +
78B VAL* 3.5 17.7 - - + +
110B ALA 3.1 20.0 + - - +
111B ARG* 3.2 10.5 + - - +
113B CYS* 1.4 73.7 - - - +
115B THR* 1.3 64.8 + - - +
117B MET 3.1 3.3 + - - -
118B VAL* 3.0 30.1 + - + +
126B LEU* 4.1 24.7 - - + -
128B LEU* 5.3 4.0 - - + -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 2.9 23.5 + - - +
112B GLU* 3.8 8.9 - - - -
114B ILE* 1.3 77.5 - - - +
116B SER* 1.4 57.2 + - - +
118B VAL* 3.5 7.8 + - + +
119B SER* 3.0 29.4 + - - -
125B GLN* 3.4 16.2 - - - +
126B LEU* 2.8 23.0 + - - +
127B ASN* 4.9 0.3 + - - -
115C THR* 5.6 0.4 - - + +
119C SER* 3.2 31.8 + - - +
125C GLN* 3.9 11.0 + - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 3.2 24.9 + - - -
112B GLU* 3.0 20.3 + - - -
113B CYS 3.4 8.1 - - - -
114B ILE 3.2 0.2 - - - -
115B THR* 1.4 75.7 - - - +
117B MET* 1.3 60.4 + - - +
119B SER* 3.2 8.7 + - - -
120B ARG* 2.9 61.1 + - - +
112C GLU* 3.7 8.3 + - - +
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Residues in contact with MET 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.4 22.2 - - + -
113A CYS* 4.8 6.3 - - - +
117A MET* 5.3 5.4 - - + -
120A ARG* 4.5 15.9 - - - -
21B ILE* 3.6 41.5 - - + -
23B PHE* 3.6 28.5 - - + -
76B CYS* 3.7 16.4 - - - -
78B VAL* 5.1 0.4 - - + -
113B CYS 3.1 20.2 - - - +
114B ILE 3.1 5.7 + - - +
116B SER* 1.3 80.4 - - - +
118B VAL* 1.3 61.3 + - - +
120B ARG* 3.4 29.1 + - - +
121B GLY 3.0 20.6 + - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 3.9 7.0 - - - -
74B PHE* 3.5 36.8 - - + -
76B CYS* 4.0 9.6 - - + -
114B ILE* 3.0 24.4 + - + +
115B THR* 3.8 7.4 - - - +
117B MET* 1.3 74.5 - - - +
119B SER* 1.3 60.9 + - - +
121B GLY 3.3 2.3 + - - -
122B THR 3.2 4.0 + - - -
123B PHE* 3.0 43.5 + - + +
124B PRO 3.3 26.2 - - - +
126B LEU* 4.4 10.5 - - + +
125C GLN* 5.2 2.2 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR 3.0 15.3 + - - -
116B SER* 3.3 12.1 - - - -
118B VAL* 1.3 75.4 - - - +
120B ARG* 1.3 61.0 + - - +
122B THR* 3.1 17.7 + - - -
123B PHE 4.7 0.9 - - - -
111C ARG* 3.6 13.9 + - - -
112C GLU* 5.8 4.4 - - - +
115C THR* 3.2 13.9 - - - +
125C GLN* 3.0 27.4 + - - +
127C ASN* 2.9 23.5 + - - +
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE 4.4 0.5 - - - +
17A TYR* 3.1 12.3 - - - +
18A THR* 3.0 40.2 + - + +
21A ILE* 3.8 0.7 - - - -
109A TYR 5.0 0.2 + - - -
112A GLU* 3.0 42.4 + - - -
113A CYS* 3.4 40.3 + - - +
116A SER* 3.3 22.0 + - - -
120A ARG* 4.4 1.6 - - - +
116B SER* 2.9 41.4 + - - +
117B MET* 3.4 30.2 - - - +
118B VAL 3.3 0.2 - - - -
119B SER* 1.3 76.2 - - - +
121B GLY* 1.4 55.3 + - - +
122B THR* 3.2 2.3 + - - +
111C ARG* 4.9 4.8 + - - +
112C GLU* 3.3 13.4 + - + +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.7 6.2 - - - +
18A THR* 3.5 7.6 + - - -
23B PHE* 3.6 26.0 - - - -
32B PHE* 3.3 9.0 - - - -
117B MET 3.0 10.3 + - - -
118B VAL 3.3 2.9 + - - -
119B SER 3.2 0.6 - - - -
120B ARG* 1.4 73.5 - - - +
122B THR* 1.4 73.0 + - - +
123B PHE* 3.1 19.3 - - - -
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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