Figures for Notes on Helices

This page contains all the figures used in the notes on helices. You may want to keep this page open, or print this page when going through the notes. Please note that the helix pdb presentations (Figures 1.11 and 1.12) are kept on a different page to avoid long download times.


Figure 1.1 Description of the parameters of 'ideal' helices

(Modified from Mathews and Van Holde (1996) Biochemistry 2nd Edition. Benjamin Cummings Publishing)

Helix Parameters



Figure 1.2 Right and Left Hand Helix

If the helix spirals in the same direction that the four fingers of the right hand are pointing then it is a right handed helix. Similarly if the helix spirals in the same direction that the four fingers of the left hand are pointing then it is a left handed helix.

(Modified from Lehninger et al (1993) Principles of Biochemistry 2nd Edition Worth Publishers)




Figure 1.3 Naming helices

The number in the name is the number of residues per turn of the helix. The subscript indicates the number of atoms in the ring formed by the hydrogen bond.

Note: in Web pages its not always possible to show a subscript, so instead the subscript is separated by a period eg. 3.10

(Modified from Mathews and Van Holde (1996) Biochemistry 2nd Edition. Benjamin Cummings Publishing)




Figure 1.4 Three regular polypeptide helices

A cartoon of a icosapeptide in a right-handed alpha-helical conformation is shown in the middle. Idealized model 3.10-helical (-74.0, -4.0), alpha-helical (phi = -57.8, psi = -47.0), and pi-helical (-57.1, -69.7) conformations of a polyalanine icosapeptide are displayed (without hydrogens) using CPK representations. Views are perpendicular to the helical axis with the N-terminal at the bottom (lower) and following a 90 rotation (top). Standard CPK color is used with the exception that the alanine side chain (CB) carbon is a lighter shade of grey for distinction from backbone carbons. All structures are reproduced at the same scale using the program RasMol (Modified from Kurt D. Berndt Principles of Protein Structure 1996).

Three helices


Figure 1.5 Cylindrical Plots of the three typical helices

The plots shown at the bottom of each of the ball and stick models are derived as if a translucent 'cylinder' covered the helix and you were able to trace the path of the alpha carbon atoms (the black dots on the trace) of the polypeptide backbone. If you could then slice down the length of the cylindrical plot and rolled it out, then it would form a rectangle as shown below (this is also called a 'surface net').

(Modified from Schultz and Schirmer (1979) Principles of Protein Structure)



Figure 1.6 Helical Wheel representation of an alpha helix

The view is looking up through the axis of a alpha helix (from N terminal end to C terminal end). Each apex (or 'corner' if you like) of the polygon represents the alpha carbon of the polypeptide chain within the helix and of course attached to each alpha carbon is the side chain. Each residue has a turn of about 100 degrees within an alpha helix. The helix starts at the proline residue (residue 119) and spirals up clockwise until it reaches the end of the helix at the leucine residue (residue 136). (Of course, this diagram could also be viewed as though you were looking down through the axis of a alpha helix where the helix spirals anti clockwise down the axis from Leucine to Proline.)

This helical wheel was created using the Helical Wheel Program (in GCG software) to analyse a helix (residues 119 to 136) in human haemoglobin.

Helical Wheel


Figure 1.7 Ramachandran Plot - the position of the alpha helix

Allowed conformation of alpha helix (with phi about -60 and psi about -50). Allowed conformations are indicated by the hatched areas.

(Modified from Mathews and Van Holde (1996) Biochemistry 2nd Edition. Benjamin Cummings Publishing)

Rama Plot


Figure 1.8 Distribution of side chains on a alpha helix

Each side chain in this helix radiates out from the helix. The residues making up this model helix are all alanines and the hydrogen for each alanine side chain is coloured blue.

Alanine Sidechains


Figure 1.9 Peptide and Helix dipole

Peptide plane

Figure 1.10 Helix 'cut out'

To practice 'putting a helix together' print this drawing (you may also have to enlarge it to make it easier to work with) and cut out around the outline. Then twist the drawing into a helix using your knowledge of helix structure and join the appropriate residues with tape.

Reproduced from: Stephenson, William (1988) Concepts in Biochemistry 3rd Edition. John Wiley & Sons

Helix cut out


Figure 1.11 A polyalanine helix


Figure 1.12 Helix from haemoglobin


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