3. Acid or base hydrolysis of proteins yields amino acids of this general form. The central carbon atom is called the Calpha-atom and is a chiral centre. All amino acids found in proteins encoded by the genome have the L-configuration at this chiral centre. This configuration can be remembered as the CORN law. Imagine looking along the H-Calpha bond with H atom closest to you.
4. Side Chains or R-groups. There are 20 side chains in found in proteins encoded by the genetic machinery of the cell. Some are acidic, some basic, neutral, hydrophobic, etc (see Primary Structure of Proteins). The side chains confer important properties on a protein such as the ability to bind ligands and catalyse biochemical reactions. They also direct the folding of the nascent polypeptide and stabilise its final conformation. Certain colours are used conventionally to represent the different atom types found in proteins. In this section red is used for oxygen, blue for nitrogen, white for carbon and yellow for sulphur. Hydrogen atoms cannot be located in most protein structures since they scatter X-rays too weakly. The figure below indicates atoms types by colouring each half of the chemical bonds according to the atoms involved.
5.
6. In molecular graphics, atoms can be represented in different ways. For expedience molecules are often displayed only as lines or vectors between the atoms bonded together covalently. An elegant representation is the ball-and-stick type in which atoms are drawn as coloured spheres and their bonds as rod-like connections. Another useful display is the space-filling representation in which a surface is drawn around the atoms to indicate their van der Waals radi. This surface can be drawn as a series of dots or as a solid entity.
7. Atoms are named using letters in the Greek alphabet; a selection relating to the atom names and torsion angles used with amino acids is given below.
8. The polypeptide chain. Amino acids in proteins (or polypeptides) are joined together by peptide bonds. The sequence of R-groups along the chain is called the primary structure. Secondary structure refers to the local folding of the polypeptide chain. Tertiary structure is the arrangement of secondary structure elements in 3 dimensions and quaternary structure describes the arrangement of a protein's subunits.
9. the geometry and dimensions of the peptide bonds in the crystal structures of molecules containing one or a few peptide bonds Bond angles in degrees are also shown for the peptide N and C atoms
10. Note that the C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds. This is because the peptide bond has some double bond character (40%) due to resonance which occurs with amides. The two canonical structures are: As a consequence of this resonance all peptide bonds in protein structures are found to be almost planar, ie atoms Calpha(i), C(i), O(i), N(i+1) H(i+1) and Calpha(i+1) are approximately co-planar. This rigidity of the peptide bond reduces the degrees of freedom of the polypeptide during folding.
11. The peptide bond nearly always has the trans configuration since it is more favourable than cis, which is sometimes found to occur with proline residues.
12. As can be seen above, steric hindrance between the functional groups attached to the Calpha atoms will be greater in the cis configuration. However for proline residues, the cyclic nature of the side chain means that bothcis and trans configurations have more equivalent energies. Thus proline is found in the cis configuration more frequently than other amino acids. The omega torsion angle of proline will be close to zero degrees for the cisconfiguration, or most often, 180 degrees for the trans configuration.
