$ cat col.awk

# Set up input and output separators
BEGIN { FS=","  ;       OFS="," }

# First line in a file?  Figure out what our columns are.
FNR == 1 {
        if(NR==1) # Very first line in very first file
        {
                COLMAX=NF
                # Mark down the contents of all the columns
                for(N=1; N<=NF; N++)
                {
                        ORDER[N]=$N
                        ORDER[$N]=N
                        REORDER[N]=N
                }
                print # Print columns
                next # Go to next line
        }

        # First line in the second/third/fourth file?  Find out how we need to reorder.

        # Delete old columns
        for(X in REORDER)       delete REORDER[X];

        # Match field M against column N.
        for(N=1; N<=COLMAX; N++)
        {
                for(M=1; M<=NF; M++)
                if($M == ORDER[N])
                {
                        REORDER[N]=M;
                        break;
                }

                if(!REORDER[N])
                {
                        print "Couldn't find " ORDER[M] " in " FILENAME >"/dev/stderr";
                        REORDER[N]=NF+10;
                }
        }

        # Only print the first line of columns
        if(NR != 1)     next;
}

# Reorder all input
{
        split($0, ZZT, FS);

        PFIX=""
        STR=""
        for(N=1; N<=COLMAX; N++)
        {
                STR=STR PFIX ZZT[REORDER[N]];
                PFIX=","
        }

        $0=STR
}

1 # Print all other lines

$ awk -f col.awk columnfile data

interacao,AspAsp,AspCys,CysAsp,CysCys,classe
beta_alfa,DA,DD,CA,CD,ppi

$