Once the molecule file is fully loaded, the image at right will become live. At that time the "activate 3-D" icon will disappear.

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α-Helix and β-Sheet Structures.

This page shows some interactive JSmol views of the common protein secondary structures, α-helix and β-sheet.

The first view, [helix1], shows a section of an α-helix. The figure is a bit complex - there are too many atoms to see the underlying structure easily.
To see only the protein backbone:
right-click in the graphics box, then choose "Select", then "Protein", then "Side Chains".
Now right-click again, choose, "Style", then "Atoms", then "Off".
Finally, right-click again, choose, "Style", then "Bonds", then "Off".

The button [helix2[ causes the hydrogen bonds to be added (red) and the backbone of the protein to be emphasised using a 'cartoon" representation (green). Note how the H-bonds control the helical structure and that the residues are arranged about the helical core.

The button [helix3] shows a standard shorthand representation - only the backbone of the helix is shown.

Three adjoining sections of β-sheet are shown in [sheet1]. Hydrogen bonds are included (red). Again, a little hard to see when all the atoms are present.

In the [sheet2] the backbone sections of the protein chains are emphasised using a cartoon. Note that the central protein chain runs in the opposite sense to the other two. Also note that adjacent residues on each chain lie on opposite sides of the sheet.

In [sheet3] the amino acid residues are hidden and the sheet structure is emphasised.

Finally, a small protein is shown in cartoon form [protein]. The helical sections are coloured pink and sheet regions are coloured yellow, white (wire) represents unstructured sections (ie neither helix or sheet). This shows the structure much more clearly than when all the atoms are shown individually.
To check this for yourself, right-click in the graphics box, choose "Style", then "Scheme", then "Ball & Stick".
To measure distances, doubleclick on an atom, drag to the bonded atom and doubleclick again.

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