How to calculate degree of freedom of molecules like h2o,n2,,he

This leaves three vibrational degrees of freedom: two internuclear distances between the oxygen and the hydrogens, and the bond angle at the oxygen. It should be clear that these are sufficient to specify a shape for the molecule and that they are independent. 

It's also worth mentioning, by the way, that those degrees of freedom are not the most useful way to describe the vibrations, because it's essentially impossible for one internuclear distance to vibrate without affecting the other bond. Instead, you normally rewrite the dynamics in terms of three which are able to vibrate on their own without affecting the others: thus, the coordinates of interest are in essence 

• the sum of the O-H internuclear distances, corresponding to a symmetric stretch;
• the difference of the O-H internuclear distances, corresponding to an antisymmetric stretch; an
• the bond angle at the oxygen, corresponding to a bending mode of the molecule.