The three-dimensional structure of proteins plays and important role in their function. The shape of a protein is typically described using four levels of structural complexity: the primary, secondary, tertiary, and quaternary structural levels.

The primary structure of a protein is its amino acid sequence. Each protein has a unique amino acid sequence, and the unique order in which the amino acids are linked together determined the higher levels of structural organization.

Protein Secondary Structure: In most cases the polypeptide chain of a protein does not exist as an extended chain of amino acids. Instead amino acids adjacent to one another interact to form segments with defined structure. These local structural elements comprise the secondary structure of a protein.
The most common secondary structure elements are the α-helix and the β-pleated sheet. The α-helix and the β-pleated sheet are secondary structure elements since the Φ and Ψ angles within each element remains the same (or almost the same).
Some segments do not have similar Φ and Ψ angles for all amino acids in the segment. Such segments are sometimes referred to as random coil regions. Random coil does not (necessarily) mean that the amino acids within this region take on random conformations from protein to protein (i.e. that the segment is highly flexible). Rather, random coil implies dissimilar Φ and Ψ angles within the segment.

into the JMol window (left). The molecule is shown using the 'cartoon' rendering scheme and is colored to show the various secondary structure elements. Rotate the molecule around and observe the distribution of secondary structures in the α-subunit of human hemoglobin.

residues 53-71. It can be seen that these 19 residues interact with each other to form an α-helical secondary structure element. Similarly each of the other secondary structure elements present in the protein is composed of residues that are adjacent to each other in sequence.


The α-subunit of human hemoglobin is a predominantly helical protein.

on the other hand is an example of a protein with both helical and sheet secondary structures. The molecule is colored to show the various secondary structure elements. Rotate the molecule around and familiarize your self with the protein and its structure.