confused with distances Perl

Hello all,
I have a school assignment in Biology but I seem to be unable to begin...
What I was given is something like the following :

HELIX1: x y z
A 1 -1.115 8.537 7.075
B 2 -2.745 5.280 7.165
C 3 -0.777 3.267 7.329
D 4 1.610 5.225 10.885
E 5 0.296 5.263 10.912

HELIX2:
K 1 -0.696 13.041 22.357
L 2 1.152 11.081 23.082
M 3 2.200 17.590 18.424

What I must do is :
take each atom from each helix (for example atoms A, B, C, D, E from helix1 , atoms K,L,M from helix2)
and calculate the distance from all other atoms of the remaining helices.
An example :
1) Take atom A from helix1
2) Calculate distance with atom K from helix2
3) Calculate distance with atom L from helix2
4) Calculate distance with atom M from helix2

In order to calculate the distance ,for example, between A(helix1) and K(helix2), I use the formula:
distance = (Xa-Xk)^2 + (Ya-Yk)^2 + (Za-Zk)^2

So, what I need to store is :
x,y,z for each atom
then, using the formula above ,I will calculate the distance...
I don't know if I need a hash of arrays, an array of hashes or something more or less complicated...
Any help?