It looks like you want something like:

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

my $resfile = shift;
my $csafile = shift;

open my $RESFILE, '<', $resfile or die "unable to open $resfile: $!\n"
+;

my %hashlookup;
while ( <$RESFILE> ) {
    my ( undef, $num, $str ) = split;
    $hashlookup{ substr( $str, 0, 5 ) . " $num" } = 1;
    }
close $RESFILE;

open my $CSAFILE, '<', $csafile or die "unable to open $csafile: $!\n"
+;

while ( <$CSAFILE> ) {
    chomp;
    my ( $pdb, $chain, $csanum ) = ( split /,/ )[ 0, 3, 4 ];
    my $key = "$pdb$chain $csanum";
    print "$key\n" if $hashlookup{ $key };
    }
close $CSAFILE;
[download]