  We seek to understand the interplay between amino acid sequence and local
structure in proteins. Are some amino acids unique in their ability to fit
harmoniously into certain local structures? What is the role of sequence in
sculpting the putative native state folds from myriad possible conformations?
In order to address these questions, we represent the local structure of each
C-alpha atom of a protein by just two angles, theta and mu, and we analyze a
set of more than 4000 protein structures from the PDB. We use a hierarchical
clustering scheme to divide the 20 amino acids into six distinct groups based
on their similarity to each other in fitting local structural space. We present
the results of a detailed analysis of patterns of amino acid specificity in
adopting local structural conformations and show that the sequence-structure
correlation is not very strong compared to a random assignment of sequence to
structure. Yet, our analysis may be useful to determine an effective scoring
rubric for quantifying the match of an amino acid to its putative local
structure.
