How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?
Protein autocorrelation is similar to usual autocorrelation of time series (that is, function $r(k)$ measuring correlation between values lagged by $k$), except that instead of time dimension we slide along the backbone of amino acid chain. The "dependent variable" can be any quantifiable property of the amino acids - then the autocorrelation measures similarity in that particular property.

See e.g. Fernandez et al., 2008, for more extensive background:
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