Short Answer:

$sth->execute()
[download]

Long Answer:

Wanna bet most of those variables don't contain SQL literals?

my $sql = "
      insert into BiscHet 
      ( 
      pdbAndChainID1, 
      asaSingle1, 
      asaComplex1, 
      organismPdb1, 
      taxidPdb1, 
      scopClass1, 
      scopFold1, 
      scopSuperfamily1, 
      scopFamily1,
      intactID1,
      evalue1,
      length1,
      identity1,
      organismIntact1,
      taxidIntact1,
      pdbAndChainID2, 
      asaSingle2, 
      asaComplex2, 
      organismPdb2, 
      taxidPdb2, 
      scopClass2, 
      scopFold2,
      scopSuperfamily2,
      scopFamily2,
      intactID2,
      evalue2,
      length2,
      identity2,
      organismIntact2,
      taxidIntact2,
      sequenceAtom2, 
      sequenceSeqRes2, 
      jmolSelect,
      interface
      ) 
       VALUES 
      (".join(',', ('?')x34 ).")
      "
   my $sth = $dbh->prepare($sql) or die $dbh->errstr;
   $sth->execute(
      $id1, 
      $asaSingleC1,           
      $asaComplexC1,          
      $organismC1,           
      $taxidC1,              
      $scopClassC1,           
      $scopFoldC1,           
      $scopSuperfamilyC1,    
      $scopFamilyC1,        
      $uniprotID1,           
      $evalue1,              
      $length1,              
      $identity1,            
      $organismIntAct1,    
      $taxidIntAct1,         
      $id2, 
      $asaSingleC2,       
      $asaComplexC2, 
      $organismC2,       
      $taxidC2,          
      $scopClassC2,       
      $scopFoldC2,       
      $scopSuperfamilyC2,
      $scopFamilyC2,
      $uniprotID2,     
      $evalue2,          
      $length2,          
      $identity2,        
      $organismIntAct2,
      $taxidIntAct2,     
      'ATCGT',
      'GATAT',
      'NA',
      'interface'
   ) or die $dbh->errstr;
   $sth->finish();
[download]

Finally, the presence of fields X1 and X2 is usually a sign of a bad database design, and here is no exception.