You could start with List::MoreUtils. Use the uniq method. For example,

#!/usr/bin/perl

use strict;
use warnings;
use List::MoreUtils qw(uniq);

my @lines = uniq(<DATA>);
print @lines, "\n";

__DATA__
A  83    GLU       A  90    GLU^?     
A 163    ARG       A  83    ARG^?     
A 222    ARG       A   5    ARG^?

A 229    ALA       A 115    ALA~?     
A 257    ALA       A 118    ALA~?     
A 328    ASP       A  95    ASP~?

A  83    GLU       A  90    GLU^?     
A 163    ARG       A  83    ARG^?     
A 222    ARG       A   5    ARG^?

A  83    GLU       B  90    GLU^?     
A 163    ARG       B  83    ARG^?     
A 222    ARG       B  5     ARG^?
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