Please see How do I post a question effectively?. In particular, note how the whitespace in your posted input has become mangled. This is because you did not include <code> tags. It's hard to help you code/debug if we see something different than what you see. Markup in the Monastery or Writeup Formatting Tips may be helpful.

For some sample code for list comparisons, which is close enough to be informative for your use case, see How can I tell whether a certain element is contained in a list or array? and/or How do I compute the difference of two arrays? How do I compute the intersection of two arrays? in perlfaq4.

You may also want to use a pre-rolled parsing solution, such as Text::CSV.

Have you actually written an code we can look at? Even if it doesn't work, it's very helpful in understanding how you are thinking.

here is the code I have so far:

#!/usr/bin/perl
@cand (63, 66, 69, 72, 73, 74, 95, 96, 98, 134, 135, 137, 138, 139, 14
+0, 159, 162, 172, 173, 175, 177, 178, 197, 198, 201, 210, 225, 232, 2
+37, 240, 243, 246, 247);
open (<CONTACT0>, "Contactmap00_0.txt");
while (<CONTACT0>) {
foreach $c (@cand){
    foreach $_ {
    @line = split (//, $_);
    if $c = $line[2] {
        if $line[4] >= 133 {
            if $line[4] <= 298 {
                if $line[6] != ['Asterisk' 'Colon']{
                    print $_ "\n"; }
                else print "Mismatch at level Type \n";}
            else print "Too large for range\n";}
        else print "To small for range \n";}
    else print "Not a match to candidates\n";}
    }
  }
[download]

My data looks like this

ILE    105    GLY    404    9.31639356    Blank    Asterisk
ILE    105    VAL    430    7.716578207    Blank    Colon
GLY    106    SER    429    9.615782075    Asterisk    Asterisk
GLY    106    VAL    430    6.799878306    Asterisk    Colon
GLY    106    LEU    433    8.984377971    Asterisk    Colon
GLY    106    SER    434    9.609582172    Asterisk    Asterisk
GLY    107    SER    428    8.263658329    Asterisk    Asterisk
GLY    107    SER    429    6.30787898    Asterisk    Asterisk
GLY    107    VAL    430    4.124362412    Asterisk    Colon
GLY    107    LEU    431    7.670615378    Asterisk    Asterisk
GLY    107    ALA    432    8.308317297    Asterisk    Period
GLY    107    LEU    433    5.934571065    Asterisk    Colon
GLY    107    SER    434    7.71234967    Asterisk    Asterisk
LYS    108    ASN    427    8.67223833    Blank    Asterisk
LYS    108    SER    428    5.458321198    Blank    Asterisk
[download]