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>##


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

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

##</code><code>##

#!/usr/bin/perl

use strict;

my (%hash, %hash_key);
my $x = 0;
while (<DATA>){
my @array = split(' ', $_);
$x++;
$hash{"$array[1]-$array[4]"} = $_;
$hash_key{$x} = "$array[1]-$array[4]";
}

foreach my $i (sort {$a <=> $b} keys %hash_key){
  (exists $hash{$hash_key{$i}}) ? (print "$hash{$hash_key{$i}}") : (print "deleted\n");
  delete($hash{$hash_key{$i}}) if (exists $hash{$hash_key{$i}});
}

__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>##


#!/usr/bin/perl

use strict;

my (%hash, %hash_key); # hashes
my $x = 0;    # counters
while (<DATA>){        #starts reading the data line by line
my @array = split(' ', $_);  # split the data using spaces
$x++;                        # global counter
$hash{$array[1]}->{$array[4]} = $_;   # primary database
$hash_key{$x}= [$array[1],$array[4]]; # key database
}


foreach my $i (sort {$a <=> $b} keys %hash_key){

  (exists $hash{$hash_key{$i}->[0]}->{$hash_key{$i}->[1]}) ? (print "$hash{$hash_key{$i}->[0]}->{$hash_key{$i}->[1]}") : (print "deleted\n"); # if the record in the database (hash) exists print it out otherwise print 'deleted'
  next if ($hash_key{$i}->[0] eq ''); # you need the empty lines so if you reached an empty line, skip the deleting part 
  delete($hash{$hash_key{$i}->[0]}->{$hash_key{$i}->[1]}) if (exists $hash{$hash_key{$i}->[0]}->{$hash_key{$i}->[1]} || $hash{$hash_key{$i}->[1]}->{$hash_key{$i}->[0]}); # if you printed the entry from the database delete it , you don't need duplicates. this goes if your record has 80 90 situation or 90 80 situation
}

__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>##

($a ==1) ? (print "yes") : (print "no");