#!/usr/bin/perl
use strict;
use warnings;

# Records separated by blank line
$/ = "\r\n\r\n";

# Records we've seen before
my %records_seen;

while (my $line = <DATA>) {
   # Get list of key fields for record
   my @key_fields = (split /\s+/, $line)[
      -2, -8, -14, -5, -11, -17
   ];

   # Create composite key for record
   my $key = join("|",@key_fields);

   # Process the record if we haven't seen it before
   if (! exists $records_seen{$key}) {
      print $line;
   }

   # Remember that we've processed the record
   $records_seen{$key} = $line;
}
__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^?
##</code><code>##

Roboticus@Roboticus-PC /robo/Desktop
$ perl 856427.pl
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~?

Roboticus@Roboticus-PC /robo/Desktop
$

##</code><code>##

  my ($i_new, $j_new, $k_new, $l_new, $m_new, $n_new)
    = (split /\s+/,$line)[ -2, -8, -14, -5, -11, -17 ];