Exploring the Peptide Bond
In this chapter, we will learn to examine the arrangements of the atoms that make up the backbone of a protein and how the arrangements derive from the properties of the peptide bond. Using the modest but biochemically famous protein RNase A, you will discover how to measure the bond lengths and angles in the main chain and how to decide whether a proline residue is in the cis or trans configuration. Finally, two internet algorithms are introduced that allow you to generate a Ramachandran plot from any protein structure in the PDB.
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