Contacts of the helix formed by residues 81 - 102 (chain A) in PDB entry 1V40
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY 3.4 0.2 - - - -
80A ASN* 1.3 83.0 - - + +
82A GLU* 1.3 61.1 + - - +
83A MET* 3.7 8.5 + - - +
84A GLU* 2.6 39.9 + - - +
85A GLN* 2.9 35.9 + - - +
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Residues in contact with GLU 82 (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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81A THR* 1.3 74.6 - - - +
83A MET* 1.3 61.6 + - + +
85A GLN* 3.2 15.6 + - - +
86A CYS 3.0 17.7 + - - -
670D TYR* 3.6 30.6 - - + +
673D LYS* 3.9 29.4 + - + +
674D ASN* 2.5 35.1 + - - +
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Residues in contact with MET 83 (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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81A THR* 3.2 8.4 + - - +
82A GLU* 1.3 79.6 - - + +
84A GLU* 1.3 57.1 + - + +
86A CYS* 3.0 19.7 + - - +
87A HIS* 3.0 26.1 + - - +
656D VAL* 4.1 19.3 - - + +
659D LEU* 4.0 34.1 - - + -
661D LEU* 3.8 30.7 - - + -
670D TYR* 3.4 34.8 - - + +
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Residues in contact with GLU 84 (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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79A GLY* 4.4 1.1 - - - -
80A ASN* 3.7 21.7 + - - +
81A THR* 2.6 48.7 + - - +
83A MET* 1.3 76.4 - - + +
85A GLN* 1.3 60.4 + - - +
87A HIS* 3.2 12.8 + - + +
88A VAL* 2.9 32.8 + - - +
142A ILE* 3.6 10.3 - - + +
143A GLY* 3.5 12.6 - - - -
144A MET* 5.9 0.3 - - - +
3002A GOL 3.1 38.6 + - - -
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Residues in contact with GLN 85 (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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78A ALA* 3.2 36.3 - - + +
79A GLY 3.0 18.9 + - - +
80A ASN 4.7 1.0 - - - -
81A THR* 2.9 21.7 + - - +
82A GLU* 3.2 16.2 + - - +
84A GLU* 1.3 76.8 - - - +
86A CYS* 1.3 62.2 + - - +
88A VAL* 3.4 3.2 + - - +
89A ASP* 3.0 30.1 + - - +
673D LYS* 2.9 37.8 - - - +
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Residues in contact with CYS 86 (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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82A GLU 3.0 12.3 + - - +
83A MET 3.1 12.8 - - - +
85A GLN* 1.3 78.2 - - - +
87A HIS* 1.3 54.3 + - - +
89A ASP* 3.2 8.3 + - - +
90A ALA* 2.8 27.3 + - - +
661D LEU* 3.9 31.9 - - + -
662D HIS 4.8 2.5 - - - -
666D ALA* 3.5 31.0 - - - -
667D ILE* 4.1 4.5 - - - -
670D TYR* 3.9 20.0 - - + -
673D LYS* 5.6 1.3 - - - +
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Residues in contact with HIS 87 (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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83A MET* 3.0 28.6 + - + +
84A GLU* 3.2 15.0 + - + +
86A CYS* 1.3 73.3 - - - +
88A VAL* 1.3 66.1 + - - +
90A ALA* 3.2 5.5 + - - +
91A ILE* 2.9 29.6 + - - +
134A TYR* 3.7 16.3 + + - +
142A ILE* 3.7 16.6 - - + -
3002A GOL 3.9 22.2 - - - -
659D LEU* 5.7 6.2 - - + +
660D THR 3.6 15.9 + - - -
661D LEU* 3.3 31.9 - - + +
662D HIS* 5.5 6.8 + - - -
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Residues in contact with VAL 88 (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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78A ALA 3.7 17.0 - - - +
79A GLY* 4.5 0.4 - - - -
84A GLU 2.9 18.5 + - - +
85A GLN 3.5 7.9 - - - +
86A CYS 3.2 0.2 - - - -
87A HIS* 1.3 77.3 - - - +
89A ASP* 1.3 64.0 + - - +
91A ILE* 3.9 1.4 - - - +
92A VAL* 3.0 24.5 + - + +
142A ILE* 3.9 20.6 - - + -
147A THR* 3.7 24.2 - - + +
148A TRP* 3.4 40.4 - - + +
149A ALA* 4.0 12.6 - - + +
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Residues in contact with ASP 89 (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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69A ARG* 2.8 35.9 + - - +
85A GLN* 3.0 19.9 + - - +
86A CYS* 3.2 9.5 + - - +
88A VAL* 1.3 79.0 - - - +
90A ALA* 1.3 56.4 + - - +
92A VAL* 3.3 6.5 + - - +
93A ASP* 2.9 33.6 + - - +
148A TRP* 3.8 10.6 + - - -
666D ALA* 3.7 16.7 - - + +
669D ARG* 3.1 30.2 + - - +
673D LYS* 4.8 5.0 + - - -
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Residues in contact with ALA 90 (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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86A CYS* 2.8 21.0 + - - +
87A HIS* 3.2 7.2 + - - +
89A ASP* 1.3 73.6 - - - +
91A ILE* 1.3 62.7 + - - +
93A ASP 3.2 1.6 + - - -
94A THR* 2.9 26.7 + - - -
662D HIS* 3.4 51.6 - - + +
663D GLN* 3.4 14.0 - - - +
666D ALA* 3.6 0.9 - - + +
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Residues in contact with ILE 91 (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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87A HIS 2.9 20.5 + - - +
88A VAL 3.9 2.9 - - - +
90A ALA* 1.3 75.6 - - - +
92A VAL* 1.3 63.3 + - - +
94A THR* 3.3 4.5 + - - -
95A LEU* 3.1 37.3 + - + +
131A LEU* 4.8 8.3 - - + -
134A TYR* 3.4 34.3 - - + +
141A LEU* 4.0 24.7 - - + -
142A ILE* 3.8 18.6 - - + -
149A ALA* 4.3 8.1 - - + -
648D PHE* 3.7 29.2 - - + -
662D HIS* 4.5 3.4 - - + -
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Residues in contact with VAL 92 (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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65A LEU* 3.7 26.9 - - + -
69A ARG* 5.5 1.3 - - - +
88A VAL 3.0 23.4 + - - +
89A ASP* 3.7 4.5 - - - +
91A ILE* 1.3 76.5 - - + +
93A ASP* 1.3 58.2 + - - +
95A LEU* 3.3 1.7 + - - -
96A ASP* 2.8 26.0 + - - +
148A TRP* 3.7 42.2 - - + -
149A ALA* 3.9 24.2 - - - +
152A TYR* 3.6 22.0 - - + -
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Residues in contact with ASP 93 (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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65A LEU* 3.6 20.6 - - - +
69A ARG* 4.9 8.0 + - - -
89A ASP* 2.9 19.0 + - - +
90A ALA 3.8 0.4 - - - +
92A VAL* 1.3 74.9 - - - +
94A THR* 1.3 60.1 + - - +
96A ASP* 4.2 3.6 - - - -
97A ASP* 2.7 38.1 + - - +
3900A MG 4.3 12.1 - - - -
663D GLN* 3.5 26.8 - - + +
665D LEU* 4.1 25.5 - - - +
666D ALA* 4.5 6.4 + - - +
669D ARG* 5.4 3.5 + - - -
693D ASP* 5.1 5.2 - - - +
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Residues in contact with THR 94 (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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90A ALA 2.9 17.7 + - - -
91A ILE* 3.7 7.9 - - - -
93A ASP* 1.3 76.3 - - - +
95A LEU* 1.3 65.7 + - + +
97A ASP* 3.5 4.4 + - - +
98A PHE* 3.2 21.5 + - - +
127A LEU* 3.9 17.2 - - + +
131A LEU* 5.6 1.3 - - + -
648D PHE* 3.8 33.5 - - + +
662D HIS* 3.6 16.8 + - - -
663D GLN* 3.1 20.0 + - - +
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Residues in contact with LEU 95 (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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91A ILE* 3.1 35.9 + - + +
92A VAL 3.6 4.0 - - - +
94A THR* 1.3 78.1 - - + +
96A ASP* 1.3 62.3 + - - +
98A PHE* 3.2 6.1 + - - +
99A MET* 3.0 28.1 + - + +
127A LEU* 4.6 10.3 - - + -
128A MET* 5.8 0.4 - - + -
131A LEU* 3.8 33.0 - - + -
149A ALA 4.6 0.7 - - - +
152A TYR* 3.8 20.6 - - + +
153A TRP* 3.8 45.1 - - + +
156A CYS* 4.1 10.3 - - + -
160A LEU* 6.4 1.6 - - + -
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Residues in contact with ASP 96 (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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14A ARG* 2.9 28.2 + - - -
65A LEU* 3.5 25.0 - - + +
92A VAL 2.8 17.6 + - - +
93A ASP* 3.9 4.9 - - - +
95A LEU* 1.3 72.5 - - - +
97A ASP* 1.3 62.1 + - - +
99A MET* 3.3 3.3 + - - +
100A SER* 2.8 40.7 + - - -
152A TYR* 2.9 27.7 + - - +
3200A GSH 4.8 6.4 + - - +
3201A O16 3.8 4.0 - - - -
3900A MG 3.9 12.6 - - - -
697D ASP* 5.3 1.0 - - - +
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Residues in contact with ASP 97 (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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93A ASP* 2.7 27.3 + - - +
94A THR* 3.5 6.7 - - - +
96A ASP* 1.3 74.3 - - - +
98A PHE* 1.3 61.8 + - - +
100A SER* 3.4 6.7 + - - -
101A CYS* 3.3 25.7 + - - -
3900A MG 4.0 15.6 - - - -
663D GLN* 3.1 13.9 + - - -
696D ASP* 5.4 1.0 - - - +
700D SER* 5.8 0.2 + - - -
3800D GSH 2.8 35.3 + - - +
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Residues in contact with PHE 98 (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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94A THR 3.2 6.4 + - - +
95A LEU 3.6 7.2 - - - +
96A ASP 3.2 0.6 - - - -
97A ASP* 1.3 76.8 - - - +
99A MET* 1.3 64.8 + - - +
101A CYS* 2.8 32.8 + - + +
102A PHE* 3.3 33.4 - + - -
119A LEU* 3.6 30.7 - - + -
123A ASN* 3.6 27.6 - - + -
124A ALA* 3.7 19.1 - - + -
127A LEU* 3.6 32.3 - - + -
128A MET* 5.1 0.2 - - + -
160A LEU* 4.0 26.0 - - + -
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Residues in contact with MET 99 (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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95A LEU* 3.0 20.5 + - + +
96A ASP 3.9 1.8 - - - +
98A PHE* 1.3 78.6 - - - +
100A SER* 1.3 60.1 + - - +
101A CYS 3.3 0.9 + - - -
102A PHE* 3.4 11.2 + - - -
104A TRP* 3.0 35.9 + - + -
156A CYS* 3.6 41.1 - - - +
159A THR* 4.0 18.6 - - + -
160A LEU* 3.8 32.3 - - + -
3201A O16 3.5 47.6 - - + -
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Residues in contact with SER 100 (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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14A ARG* 2.7 30.1 + - - +
96A ASP* 2.8 30.3 + - - -
97A ASP* 3.6 7.4 - - - -
99A MET* 1.3 74.9 - - - +
101A CYS* 1.3 63.6 + - - +
102A PHE 3.2 7.0 + - - +
104A TRP* 4.9 2.0 - - - +
3200A GSH 5.6 0.5 + - - -
697D ASP* 5.7 0.5 + - - -
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Residues in contact with CYS 101 (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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97A ASP* 3.3 22.5 + - - -
98A PHE* 2.8 18.4 + - + +
100A SER* 1.3 77.9 - - - +
102A PHE* 1.3 63.2 + - - +
103A PRO* 3.5 6.4 - - - +
115A MET* 6.0 0.3 - - - +
119A LEU* 3.7 27.9 - - + +
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Residues in contact with PHE 102 (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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98A PHE* 3.3 54.7 - + - -
99A MET* 3.5 9.6 - - - -
100A SER 3.2 6.7 - - - +
101A CYS* 1.3 77.7 - - - +
103A PRO* 1.3 63.1 - - + +
104A TRP* 2.8 50.4 + + + -
116A PHE* 3.7 28.3 - + + -
119A LEU* 3.8 18.4 - - + -
120A LEU* 3.0 36.8 - - + -
160A LEU* 3.8 17.5 - - + -
163A PHE* 6.0 2.5 - + - -
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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
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Atomic class I II III IV V VI VII VIII
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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