1. Basic Elements of 3D Protein Structure


A detailed description of aspects of 3D protein structure is beyond the scope of this lecture. Excellent material about it can be found in:

1.1 The Peptide Unit

Amino acids in natural proteins are left-handed. They can be easily recognized: when the H atom is pointing towards the viewer the word 'CORN' can be read in a clockwise fashion.

The peptide bond is always planar, almost always trans (cis prolines occur once in a while). In all residues except for Gly the side chain severely limits the torsion angles about the CA atom. A good way to visualize the 'allowed torsion angles is the Ramachandran plot, discussed in section 5.4. Each of the torsion angles has a greek name:

1.2 Helices, Strands and Turns


© Copyright 1997 Christophe Verlinde

contact: verlinde@gouda.bmsc.washington.edu; tel: (206) 543 8865; fax: (206) 685 7002