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Method for analyzing relative frequency of occurrence
Throughout this study, we will be comparing how often a particular entity (be it a certain
amino acid, a certain pair of amino acids, a certain class of amino acids, a certain
secondary structural element etc.) occurs in hinges versus everywhere in the Hinge Atlas
or another of the datasets described above. The statistical analysis will be the same
regardless of the particulars, so we will here present the general approach and later only
mention adjustments particular to the specific question addressed.
First we defined the following variables:
D = total number of residues in the dataset
H = total number of residues in hinges in the dataset
C = classification scheme used to create groups of residue positions. For example, C
could be secondary structure, degree of conservation, etc.
c = a particular grouping of residues, where
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c " C . For instance, if C = secondary
structure, then c = helix is the class of all residues in helices, c = strand is the class of all
residues in strands, etc. Another example might be C = evolutionary conservation, with c
= cons1 = top 20% most conserved residues, c = cons2 = second 20% most conserved,
etc.
a c= set of all residues of class c in the dataset.
d c = number of times residues of class c occurred anywhere in the dataset.
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