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ATOM     30  N   HIS A  66       7.514  15.296  11.222  1.00 12.98    
+  A    N  
ATOM     31  CA  HIS A  66       7.318  14.688  12.568  1.00 12.48    
+  A    C  
...
ATOM    627  CE  LYS B 101      -9.211  -7.515 -25.929  1.00  6.68    
+  B    C  
ATOM    628  NZ  LYS B 101      -8.981  -8.833 -25.272  1.00  7.38    
+  B    N  
ATOM    629  OXT LYS B 101     -13.313  -2.643 -25.782  1.00  4.28    
+  B    O

    while($_=~/ATOM\s+\d+\s+.*?\s+.*?\s+(\w{1})\s+(\d+)\s+[\d\.\-]+\s+
+[\d\.\-]+\s+([\d\.\-]+)\s+.*/mg)
    {
...
        $position=$2;
        $Zcoordinate=$3;
}