If you're only interested in processing the ATOM records, then this may be good enough:

#! perl -slw
use strict;
use List::Util qw[ sum ];

my %stats;

while( <DATA> ) {
    next unless m[^ATOM];
    my @fields = unpack 'a6 a5 a3 a3 a4 x2 a3 x4 a8 a8 a7 a7 a6 a12', 
+$_;
#    print join'|', @fields;
    push @{ $stats{ $fields[ 4 ] } }, $fields[ 10 ];
}

printf "%3s : %.3f%%\n", $_,
    sum( @{ $stats{ $_ } } ) / @{ $stats{ $_ } }
    for sort keys %stats;

=output
C:\test>junk2
GLN : 35.962%
LEU : 25.250%
LYS : 64.087%
=cut

__DATA__
1234567890123456789012345678901234567890123456789012345678901234567890
+1234567890
ATOM      1  N   LYS A   2     -10.231   0.078  18.128  1.00 28.52    
+       N
ATOM      2  CA  LYS A   2      -9.472  -0.327  19.297  1.00 28.52    
+       C
ATOM      3  C   LYS A   2     -10.308  -0.875  20.459  1.00 28.52    
+       C
ATOM      4  O   LYS A   2     -10.180  -2.054  20.801  1.00 28.52    
+       O
ATOM      5  CB  LYS A   2      -8.592   0.833  19.765  1.00 92.54    
+       C
ATOM      6  CG  LYS A   2      -7.346   0.373  20.498  1.00 92.54    
+       C
ATOM      7  CD  LYS A   2      -6.207   1.375  20.382  1.00 92.54    
+       C
ATOM      8  CE  LYS A   2      -4.929   0.810  21.002  1.00 92.54    
+       C
ATOM      9  NZ  LYS A   2      -3.756   1.724  20.882  1.00 92.54    
+       N
ATOM     10  N   GLN A   3     -11.162  -0.038  21.053  1.00 28.24    
+       N
ATOM     11  CA  GLN A   3     -11.998  -0.465  22.181  1.00 28.24    
+       C
ATOM     12  C   GLN A   3     -12.749  -1.750  21.849  1.00 28.24    
+       C
ATOM     13  O   GLN A   3     -12.882  -2.639  22.694  1.00 28.24    
+       O
ATOM     14  CB  GLN A   3     -13.019   0.618  22.556  1.00 42.14    
+       C
ATOM     15  CG  GLN A   3     -12.450   2.018  22.718  1.00 42.14    
+       C
ATOM     16  CD  GLN A   3     -12.541   2.849  21.437  1.00 42.14    
+       C
ATOM     17  OE1 GLN A   3     -12.042   2.453  20.377  1.00 42.14    
+       O
ATOM     18  NE2 GLN A   3     -13.180   4.012  21.536  1.00 42.14    
+       N
ATOM      1  N   LEU A  62      32.071  22.080  63.175  1.00 25.25    
+       N
ATOM      2  CA  LEU A  62      32.171  21.102  62.056  1.00 25.25    
+       C
ATOM      3  C   LEU A  62      31.367  19.843  62.260  1.00 25.25    
+       C
ATOM      4  O   LEU A  62      31.676  18.842  61.650  1.00 25.25    
+       O
ATOM      5  CB  LEU A  62      33.640  20.698  61.795  1.00 25.25    
+       C
ATOM      6  CG  LEU A  62      34.589  21.606  60.965  1.00 25.25    
+       C
ATOM      7  CD1 LEU A  62      35.877  20.829  60.616  1.00 25.25    
+       C
ATOM      8  CD2 LEU A  62      33.903  22.137  59.675  1.00 25.25    
+       C
ATOM      9  N   LEU A  63      30.358  19.879  63.124  1.00 25.25    
+       N
ATOM     10  CA  LEU A  63      29.497  18.715  63.396  1.00 25.25    
+       C
ATOM     11  C   LEU A  63      28.036  19.160  63.458  1.00 25.25    
+       C
ATOM     12  O   LEU A  63      27.574  19.700  64.489  1.00 25.25    
+       O
ATOM     13  CB  LEU A  63      29.869  17.995  64.717  1.00 25.25    
+       C
ATOM     14  CG  LEU A  63      29.125  16.690  65.118  1.00 25.25    
+       C
ATOM     15  CD1 LEU A  63      29.725  15.515  64.383  1.00 25.25    
+       C
ATOM     16  CD2 LEU A  63      29.208  16.398  66.606  1.00 25.25    
+       C
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