Lecture 3

Protein conformation

Aims

• To introduce concepts related to protein conformation.

Objectives

After this lecture you will be able to:

• describe the polypeptide backbone and the 20 common side chain types;
• describe protein secondary structure elements, and the main chain hydrogen bond patterns associated with these;
• discuss factors that affect protein stability;
• implement code to compute distances and angles.

Supplementary Material

Some of the lecture slides are available on-line (PDF).

The article Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains (Eur. J. Biochem., 1969, 17, 193-201) contains the Rules prepared by the IUPAC-IUB Commission on Biochemical Nomenclature. I encourage you to read through all six sections of this article, and the appendices.

The source code for the geometry routines mentioned in the lecture is available online (local access only).