There are R-groups that predominantly contain carbon and hydrogen and are very nonpolar or hydrophobic. The different R-groups have different characteristics based on the nature of atoms incorporated into the functional groups.

There are a total of 20 alpha amino acids that are commonly incorporated into protein structures (Figure 2.x). The basic structure of an amino acid is shown below:įigure 2.1 General Structure of an Alpha Amino Acid They differ from one another only at the R-group position. Within living organisms there are 20 amino acids used as protein building blocks. In the diagram below, this group is designated as an R-group. In addition to the amine and the carboxylic acid, the alpha carbon is also attached to a hydrogen and one additional group that can vary in size and length. The alpha designation is used to indicate that these two functional groups are separated from one another by one carbon group. As their name implies they contain a carboxylic acid functional group and an amine functional group. The major building block of proteins are called alpha (α) amino acids. They are all, however, polymers of alpha amino acids, arranged in a linear sequence and connected together by covalent bonds. Their structures, like their functions, vary greatly. Each cell in a living system may contain thousands of different proteins, each with a unique function. Proteins may be structural, regulatory, contractile, or protective they may serve in transport, storage, or membranes or they may be toxins or enzymes. Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. In a conventional representation the longest strand, beta-C, running from G58 to L69 would be broken somewhere around K65 to R67 to give a small beta-D strand that would then lie anti-parallel to the final small beta strand G73 to Y75.Chapter 2: Protein Structure 2.1 Amino Acid Structure and Properties 2.2 Peptide Bond Formation and Primary Protein Structure 2.3 Secondary Protein Structure 2.4 Supersecondary Structure and Protein MotifsĢ.5 Tertiary and Quaternary Protein Structure 2.6 Protein Folding, Denaturation and Hydrolysis 2.7 References This is because the beta-D strand has been 'welded' seamlessly onto the end of the beta-C strand making one long beta-C strand. We see only four beta strands but descriptions often refer to five. In this representation of this LCK-SH2 domain, there is a marked difference from that found in many papers and some text books describing SH2 domains. Take careful note of the secondary structure. For your convenience the N-terminal has been coloured blue. Make sure that you can identify the strands, helices and loops in the secondary structure. The top of the pocket is marked by a loop between beta 1 and beta 2. You can see clearly that this group fits into one pocket on the side of the central beta sheet. The pTyr residue in the ligand can be revealed with this button, the amino acid side chain is spacefilled and coloured grey whilst the phosphate group is 'cpk' coloured. The phosphotyrosine residue All high affinity peptide ligands for SH2 domains contain phosphotyrosine residues.

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