Python Programming for Biology: Bioinformatics and Beyond

Primary structure: this is the sequence of amino acids in the polypeptide chain and

traditionally also includes any disulphide links and post-translational modifications.

Essentially, this describes the covalent bond connectivity of the residues. It should be

noted  that  although  amino  acids  have  two  mirror-image  (chiral)  forms,  unless

explicitly stated, it will always be the usual, biologically abundant left-handed form

that is present.

Secondary structure:  this  is  a  regular  arrangement  of  hydrogen  bonding  along  the

protein  backbone  giving  characteristic  twist  angles  (dihedral/torsion)  to  the

polypeptide chain. The common secondary-structure categories are alpha-helix, beta-

sheet,  turn  and  random  coil  (no  regular  structure).  Secondary  structure  is  often

displayed in terms of the Ramachandran angles: the twist of the backbone either side

of the alpha carbon atoms (the atom where the amino acid side chain branches). The

twist  about  the  peptide  bond  is  not  so  descriptive  here  because  it  is  almost  always

very flat.