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Section 3 - Protein Geometry

To best appreciate the contents of this chapter you need to INTERACTIVELY EXAMINE a number of structures. If you haven't done so already, we STRONGLY URGE you to install the FREE molecular viewer software packages, RasMol and Mage, and configure them to be automatically invoked by chemical/MIME. See our Technology Page to find out how.
In this section we examine how the molecular geometry of a polypeptide chain relates to the way it folds into a three-dimensional conformation. The different types of secondary structures are introduced, but this subject will be covered in more detail in a later section of the course.

Note that main-chain and side-chain geometry are inter-related; particular conformations of certain types of side chains exclude some main chain conformations of nearby residues, and vice versa. See MacGregor, M.J., Islam, S.A. and Sternberg, M.J.E. (1987) J. Mol. Biol. 198, 295-310

Also read the Introduction To Molecular Surfaces


If you do not have yet have Mage, refer to the information under the Technology Index, which includes links telling you how to (1) get and install Mage and (2) configure your WWW browser so that it automatically invokes Mage when you click on an appropriate link (i.e. the URL of a kinemage file; MIME type chemical/x-kinemage). Then examine this kinemage from the companion set to Branden and Tooze. This page indexing the B&T kinemages has been set up by Gail Schuman of Brookhaven Structural Biology.

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Last updated 4th Nov'96