Real World Studies VI: Amino Acids.
Not being a chemist, I soon gave up on using bonding energy as the means of measuring interaction between atoms in each molecule, and opted for just a count of number of bonds for an initial try. Still, there seemed to be several possible ways of counting, so I looked at several. In my first try, I only looked at the better known amino acids that contained only those four atoms. The list: alanine, glycine, valine, leucine, isoleucine, serine, proline, threonine, phenylalanine, lysine, arginine, tryptophan, tyrosine, histidine, aspartic acid, glutamic acid, glutamine, and asparagine, eighteen in all.
For alanine, C3H7NO2, one of the resulting models for the matrix of interacting bonds is coded as follows (order of rows and columns: CNOH):
10 1 3 4
This is then double-standardized as in the other examples given here, to determine whether a symmetric matrix of z scores is produced.
For the seven different ways of counting, the following results were obtained:
Thus, two of the models produced results that passed the test eight out of nine times. These are pretty impressive confirmations, considering the coarseness of the form of measurement.
Encouraged, I used the three best counting methods to look at all the remaining amino acids listed in the Handbook of Chemistry and Physics that were made up only of C, O, H, and N. This added thirty-two more amino acids to the list. The results this time were not quite so good:
Still, on the whole these are interesting results. It remains for a real chemist to investigate the matter from a more exhaustive point of view.
Copyright 2006-2014 by Charles H. Smith.
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