I used your code and add the function split

#!/usr/local/bin/perl
use strict;
use warnings;
use LWP::Simple;
use HTML::TreeBuilder::XPath;
use Data::Dumper;

my $url="http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/Ge
+tPage.pl?pdbcode=1r9t&template=main.html";
my $p = HTML::TreeBuilder::XPath->new_from_content(get($url));
my @chain_tags = $p->findnodes("//td//a[contains(\@href,'chain=')]");
my @chains = map { $_->attr('href') =~ /chain=(\w)/ } @chain_tags;
my @chain = map {split ' '} @chains;
foreach my $chain (@chain){print "$chain\n";}
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the output was:

pisolo@pisolo:~/Scrivania/test$ perl test7.pl 
A
A
B
C
E
F
H
I
J
K
L
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so I think I can iterate my analysis for every chain....using as array with foreach....Thanks.... :-)