Introduction - This script shows three protein helical structures:
the alpha-helix, a 3.10 helix, and a pi-helix. Each structure is composed
of a polyalanine peptide, where the phi/psi angles have been chosen
to give the desired helix. For each structure, please note two important
features: The degree of packing in the interior of the helix and the
orientation of the hydrogen bonding found in these structures.
These images show the most common form of a helical structure, the
alpha-helix. There are several ways to represent this structure graphically.
The first representation is called a stick or wireframe diagram, similar
to what is seen in organic chemistry.
This view is an expansion of the wireframe where the individual atoms
are shown as little spheres.
This view is a cartoon or ribbon diagram. In this and the previous
two models give the false impression that the interior of the helix
is hollow, which it is not.
This view is a space-filling or CPK representation of the alpha helix.
Note how the "hollow" core is in fact very filled.
A second important aspect of the helix is the nature of the hydrogen
bonding that helps stabilize the structure. Notice that the hydrogen
bonds run almost parallel with the axis of the helix. There are 3.6
residues per turn of an alpha helix and there are 13 atoms in the
ring formed by closing the hydrogen bond, including the proton (not
shown in this figure). Thus an alpha helix is referred to as a 3.6(13)
helix. Residue numbers
are RED and HBOND
Ring Atom numbers are YELLOW.
This image shows a less commonly encountered 3(10) helix. Note, there
are three residues per turn and 10 atoms forming the ring closing
the hydrogen bond. Note, when compared to the alpha helix, this helix
has an almost perfectly triangular core. Also notice the greater angle
of the hydrogen bonds, compared to those seen in the alpha-helix.
This view show the 3(10) helix in a CPK or spacefilling representation.
Notice that the core is completely filled.
The yellow trace in this image highlights the 10 atoms comprising
the ring closed by the hydrogen bonding. The 10th atom, the proton,
is not shown.
These images show a third helical structure, the pi-helix. There
are 4.4 residues per turn of a pi-helix and 16 residues forming the
ring created by the hydrogen bonding. Thus, this is a 4.4(16) helix.
Notice that the core of this the pi-helix is almost perfectly square.
This image shows a spacefilling representation of the pi-helix. Note
that there is a small gap in the interior of the helix barrel.
This image shows a trace of the 16 atoms comprising the ring formed
by hydrogen bonding and the 4.4 residues per turn of the the helix.