If you want to do something with the amino acid triplets after splitting, you can try something like this to put them into an array:

#!/usr/bin/env perl
use strict;
use warnings;
use Data::Printer;

my $prot="HKTTLDSSRTTTTAABNNRFGHGHGYYH";
my @triplets = $prot =~ /.{1,3}/g;
p @triplets;
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The resulting array looks like this:

[
    [0] "HKT",
    [1] "TLD",
    [2] "SSR",
    [3] "TTT",
    [4] "TAA",
    [5] "BNN",
    [6] "RFG",
    [7] "HGH",
    [8] "GYY",
    [9] "H"
]
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