Amino Acids

Amino acid information is from Zubay [84] and the graphics are produced using Rasmol [62]. In general, the amino acid backbone is the sequence of four amino acids at the bottom of the image. $\mathbf{N}$ (blue ball), $\mathbf{C_{\alpha}}$ (gray ball), $\mathbf{C'}$ (gray ball) and $\mathbf{O}$ (red ball) make up the backbone of the amino acid. Three of the amino acids shown have special characteristic. Proline is the only amino acid where the residue forms bonds with backbone atoms other than $\mathbf{C_{\alpha}}$ . It forms a loop with the backbone $\mathbf{N}$ . Glycine has only a $\mathbf{H}$ for a residue, so no atom is shown in this rendering. None of the $\mathbf{H}$ atoms are shown of which there are many for each amino acid. And finally, Glutamic acid has not one, but two $\mathbf{O}$ atoms attached to its backbone $\mathbf{C'}$ . All amino acids at the $\mathbf{C}$ -terminus of the protein (the last amino acid of the sequence) have a pair of $\mathbf{O}$ rather than the single $\mathbf{O}$ usually seen. This substitutes for the fact that no peptide bond is formed. The amino acid's full name, three-letter abbreviation, and one-letter abbreviation is given for each amino acid.

**Figure A.1:** Sidechain representations for Ala, Arg, Asn and Asp.
$\begin{displaymath} \begin{array}{c c} \multicolumn{1}{l}{\mbox{\bf Alanine, Ala... ...udegraphics[height=2.5in]{GRAPHICS/ASP_tri.ps} \\ \end{array}\end{displaymath}$

**Figure A.2:** Sidechain representations for Cys, Gln, Glu, and Gly.
$\begin{displaymath} \begin{array}{c c} \multicolumn{1}{l}{\mbox{\bf Cysteine, Cy... ...egraphics[height=2.5in]{GRAPHICS/GLY_tri.ps} \\ \end{array} \end{displaymath}$

**Figure A.3:** Sidechain representations for His, Ile, Leu, and Lys.
$\begin{displaymath} \begin{array}{c c} \multicolumn{1}{l}{\mbox{\bf Histidine, H... ...phics[height=2.5in]{GRAPHICS/LYS_tri.ps} \\ \par\end{array} \end{displaymath}$

**Figure A.4:** Sidechain representations for Met, Phe, Pro, and Ser.
$\begin{displaymath} \begin{array}{c c} \multicolumn{1}{l}{\mbox{\bf Methionine, ... ...egraphics[height=2.5in]{GRAPHICS/SER_tri.ps} \\ \end{array} \end{displaymath}$

**Figure A.5:** Sidechain representations for Thr, Trp, Tyr, and Val.
$\begin{displaymath} \begin{array}{c c} \multicolumn{1}{l}{\mbox{\bf Threonine, ... ...udegraphics[height=2.5in]{GRAPHICS/VAL_tri.ps} \\ \end{array}\end{displaymath}$