Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance

Abstract

Interactions between the aromatic amino acid residues have a significant influence on the protein structures and protein-DNA complexes. These interactions individually provide little stability to the structure; however, together they contribute significantly to the conformational stability of the protein structure. In this study, we focus on the four aromatic amino acid residues and their interactions with one another and their individual interactions with the four nucleotide bases. These are analyzed in order to determine the extent to which their orientation and the number of interactions contribute to the protein and protein-DNA complex structures.

Figure 1

Schematic representation of the three types of orientations found in the aromatic-aromatic interactions.

Figure 2

The number of interactions between the aromatic amino acids (based on angle).

Figure 3

The number of specific and non-specific interactions (based on angle).