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Color illustration
Per Sjoberg, Jane S. Murray, Tore Brinck, Patricia Evans, and Peter Politzer
The use of the electrostatic potential at the molecular surface in recognition interactions: Dibenzo-pldioxins and related systems
Color Plate 1. Calculated electrostatic potential on the molecular surface of dibenzo-p-dioxin (I). Yellow is for V(r) > 0 kcahmol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < - 10 kcahmol (1 kcal = 4.184 kJ)
Color Plate 2. Calculated electrostatic potential on the molecular surface of 2,3,7,8-tetrachlorodibenzo-p-dioxin (II). Yellow is for V(r) > 0 kcalimol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < - 10 kcal/mol
Color Plate 3. Calculated electrostatic potential on the molecular surface of 2,3,6,7-tetrachlorobiphenylene (III). Yellow is for V(r) > 0 kcahmol, purple for - 10 < V(r) < 0 kcahmol, and gray for V(r) < - 10 kcal/mol
Color Plate 4. Calculated electrostatic potential on the molecular surface of 2,3,6,7-tetrachloroanthraquinone (IV). Yellow is for V(r) > 0 kcahmol, purple for -10 < V(r) < 0 kcahmol, and gray for V(r) < - 10 kcal/mol
J. Mol. Graphics,
1990, Vol. 8, June
89
Color Plate 5. Calculated electrostatic potential on the molecular surface of 5,6-benzoflavone (V). Yellow is for V(r) > 0 kcal/mol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < -10 kcal/mol
Color Plate 6. Calculated electrostatic potential on the molecular surface of 7,Sbenzoflavone (VI). Yellow is for V(r) > 0 kcal/mol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < -10 kcal/mol
Color Plate 7. Calculated electrostatic potential on the molecular surface of methyl chloride, H$-Cl (VII). Yellow is for V(r) > 20 kcal/mol, purple for 0 < V(r) < 20 kcal/ mol, and gray for V(r) < 0 kcal/mol
(4
03
Color Plate 8. Calculated electrostatic potential on the molecular surface of tert-butyl chloride, (H3C)3C-Cl (VIII). Views shown are (a) perpendicular to C-Cl bond, and (b) along C-Cl bond, facing methyl groups. Yellow is for V(r) > 20 kcal/ mol, purple for 0 < V(r) < 20 kcal/mol, and gray for V(r) < 0 kcahmol
90
J. Mol. Graphics,
1990, Vol. 8, June
Alain Roussel, Juan-C. Fontecilla-Camps,
and Christian Camhillau
CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO
Color Plate 1. Crystal packing of form 1 trypsin-Markwardtype inhibitor crystals. Inhibitor is displayed in the active site with white spline surface
Color Plate 2. Crystal packing of form 2 trypsin-benzamidin crystals. Benzamidin is presented with a white spline surface in the active site
Color Plate 3. Color-coded representation of the form 1 crystal packing in the trypsin-benzamidin complex
Color Plate 4. Color-coded representation of the form 2 crystal packing in the trypsin-benzamidin complex
Color Plate 5. Crystal packing representation ochrus lectin C2 crystal form
of a Lathyrus
J. Mol. Graphics,
1990, Vol. 8, June
91
A. Thomas, M. C. Vaney, M. Le Bars, J. P. Mornon, and I. Morize
Symmetry and crystallography:
New facilities in the graphic software MANOSK
Color Plate 1. Representation of the four symmetry-equivalent structures of Erythromycin A,14 space-group P2,2,2,, with their van der Waals signature
Color Plate 2. Crystal packing space-group Pnma
of 27 cells of Goethite,”
T. L. Nero, M. G. Wong, S. W. Oliver, M. N. Iskander, and P.R. Andrews
Aspartate aminotransferase:
Investigation
Color Plate 1. Superimposition of the a-carbon backbone of cytosolic pig-heart AAT (green) and cytosolic chickenheart AAT (orange) in stereo
92
J. Mol. Graphics,
1990, Vol. 8, June
of the active sites
Color Plate 2. Stereo view of cytosolic pig-heart AAT subunit 1 active site. Orange residues are Arg-292* (top) and Arg-386 (bottom). Blue residues (left to right) are Trp- 140, PLP, and Lys-258. Hydrogen bonds are shown as white dashed lines
Color Plate 3. Active site of subunit 1 with the ligand Laspartate (yellow) docked into the initial binding position. Orange residues are Arg-292* (top) and Arg-386 (bottom). Blue residues (left to right) are Trp-140, PLP, and Lys-258. Hydrogen bonds are shown as white dashed lines
(a)
Color Plate 4. Su~~mposition of the AAT dimer’s two active sites (via residues 257 and 258). Active site residues in subunit 1 (green) and subunit 2 (orange)
(W
Color Plate 5. (a) Hotspots for a carboxylate probe (yellow contours at a level of -4 kcal/mol) and an ammonium probe (blue contours at a level of -5 kcalimol) displayed together with the active site residues for subunit 1 (orange) and the docked ligand, L-aspartate (light green). Energy of the interaction is that calculated by the program SHOW (-38 kcallmol). (B) 90” rotation from the view shown in (a)
(a)
04
Color Plate 6. (a) Difference map for a carboxylate probe (yellow contours) and an ammonium probe (blue contours) in the active site of subunit 1 (orange) containing the docked L-aspartate ligand (light green). The energy of the interaction is that calculated by the program SHOW (- 38 kcal/mol). (b) 90” rotation from the view in (a)
J. Mol. Graphics, 1990, Vol. 8, June
93
The use of the electrostatic potential at the molecular surface in recognition interactions: Dibenzo-pldioxins and related systems
Color Plate 1. Calculated electrostatic potential on the molecular surface of dibenzo-p-dioxin (I). Yellow is for V(r) > 0 kcahmol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < - 10 kcahmol (1 kcal = 4.184 kJ)
Color Plate 2. Calculated electrostatic potential on the molecular surface of 2,3,7,8-tetrachlorodibenzo-p-dioxin (II). Yellow is for V(r) > 0 kcalimol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < - 10 kcal/mol
Color Plate 3. Calculated electrostatic potential on the molecular surface of 2,3,6,7-tetrachlorobiphenylene (III). Yellow is for V(r) > 0 kcahmol, purple for - 10 < V(r) < 0 kcahmol, and gray for V(r) < - 10 kcal/mol
Color Plate 4. Calculated electrostatic potential on the molecular surface of 2,3,6,7-tetrachloroanthraquinone (IV). Yellow is for V(r) > 0 kcahmol, purple for -10 < V(r) < 0 kcahmol, and gray for V(r) < - 10 kcal/mol
J. Mol. Graphics,
1990, Vol. 8, June
89
Color Plate 5. Calculated electrostatic potential on the molecular surface of 5,6-benzoflavone (V). Yellow is for V(r) > 0 kcal/mol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < -10 kcal/mol
Color Plate 6. Calculated electrostatic potential on the molecular surface of 7,Sbenzoflavone (VI). Yellow is for V(r) > 0 kcal/mol, purple for - 10 < V(r) < 0 kcal/mol, and gray for V(r) < -10 kcal/mol
Color Plate 7. Calculated electrostatic potential on the molecular surface of methyl chloride, H$-Cl (VII). Yellow is for V(r) > 20 kcal/mol, purple for 0 < V(r) < 20 kcal/ mol, and gray for V(r) < 0 kcal/mol
(4
03
Color Plate 8. Calculated electrostatic potential on the molecular surface of tert-butyl chloride, (H3C)3C-Cl (VIII). Views shown are (a) perpendicular to C-Cl bond, and (b) along C-Cl bond, facing methyl groups. Yellow is for V(r) > 20 kcal/ mol, purple for 0 < V(r) < 20 kcal/mol, and gray for V(r) < 0 kcahmol
90
J. Mol. Graphics,
1990, Vol. 8, June
Alain Roussel, Juan-C. Fontecilla-Camps,
and Christian Camhillau
CRYStallize: A crystallographic symmetry display and handling subpackage in TOM/FRODO
Color Plate 1. Crystal packing of form 1 trypsin-Markwardtype inhibitor crystals. Inhibitor is displayed in the active site with white spline surface
Color Plate 2. Crystal packing of form 2 trypsin-benzamidin crystals. Benzamidin is presented with a white spline surface in the active site
Color Plate 3. Color-coded representation of the form 1 crystal packing in the trypsin-benzamidin complex
Color Plate 4. Color-coded representation of the form 2 crystal packing in the trypsin-benzamidin complex
Color Plate 5. Crystal packing representation ochrus lectin C2 crystal form
of a Lathyrus
J. Mol. Graphics,
1990, Vol. 8, June
91
A. Thomas, M. C. Vaney, M. Le Bars, J. P. Mornon, and I. Morize
Symmetry and crystallography:
New facilities in the graphic software MANOSK
Color Plate 1. Representation of the four symmetry-equivalent structures of Erythromycin A,14 space-group P2,2,2,, with their van der Waals signature
Color Plate 2. Crystal packing space-group Pnma
of 27 cells of Goethite,”
T. L. Nero, M. G. Wong, S. W. Oliver, M. N. Iskander, and P.R. Andrews
Aspartate aminotransferase:
Investigation
Color Plate 1. Superimposition of the a-carbon backbone of cytosolic pig-heart AAT (green) and cytosolic chickenheart AAT (orange) in stereo
92
J. Mol. Graphics,
1990, Vol. 8, June
of the active sites
Color Plate 2. Stereo view of cytosolic pig-heart AAT subunit 1 active site. Orange residues are Arg-292* (top) and Arg-386 (bottom). Blue residues (left to right) are Trp- 140, PLP, and Lys-258. Hydrogen bonds are shown as white dashed lines
Color Plate 3. Active site of subunit 1 with the ligand Laspartate (yellow) docked into the initial binding position. Orange residues are Arg-292* (top) and Arg-386 (bottom). Blue residues (left to right) are Trp-140, PLP, and Lys-258. Hydrogen bonds are shown as white dashed lines
(a)
Color Plate 4. Su~~mposition of the AAT dimer’s two active sites (via residues 257 and 258). Active site residues in subunit 1 (green) and subunit 2 (orange)
(W
Color Plate 5. (a) Hotspots for a carboxylate probe (yellow contours at a level of -4 kcal/mol) and an ammonium probe (blue contours at a level of -5 kcalimol) displayed together with the active site residues for subunit 1 (orange) and the docked ligand, L-aspartate (light green). Energy of the interaction is that calculated by the program SHOW (-38 kcallmol). (B) 90” rotation from the view shown in (a)
(a)
04
Color Plate 6. (a) Difference map for a carboxylate probe (yellow contours) and an ammonium probe (blue contours) in the active site of subunit 1 (orange) containing the docked L-aspartate ligand (light green). The energy of the interaction is that calculated by the program SHOW (- 38 kcal/mol). (b) 90” rotation from the view in (a)
J. Mol. Graphics, 1990, Vol. 8, June
93