Protein structure

Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. The shape into a which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids. Below about 40 residues the term peptide is frequently used. A certain number of residues is necessary to perform a particular biochemical function, and around 40-50 residues appears to be the lower limit for a functional domain size. Protein sizes range from this lower limit to several thousand residues in multi-functional proteins. However, the current estimate for the average protein length is around 300 residues. Very large aggregates can be formed from protein subunits, for example many thousand actin molecules assemble into a an actin filament. Large protein complexes with RNA are found in the ribosome particles, which are in fact 'ribozymes'.

Side chain conformation

The atoms along the side chain are named with Greek letters in Greek alphabetical order: alpha, beta, gamma, delta, epsilon... and so on. The angles between these are named chi1, chi2, chi3... E.g. the first and second carbon atom in the side chain of lysine is named alpha and beta and the angle between them is named chi1. Side chains can be in different conformations called gauche(-), trans and gauche(+). Side chains generally tend to try to come into a staggered conformation around chi2.

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