Let`s try to get this in perspective.

First , I named the facts :

1 - he has your Phone number
2 - you gave it to him
3 - this could mean , that the r4elation , is at another level
4 - you 2 were talking , earlier that evening (you didn`t say , what the conversation was about - but I understand that it is private)
5 - was there something in that conversation , which made him , call you at 03.00AM
6 - the relation is at a stage , where he feels , that it is oke , to call you ,
at 03.00AM in the morning
7 - he was either checking on you , or he was really missing you ??

You are the only person , who can answer this!

Do you feel , that the relation , is developing , in a positive and a healthy way ?

If you believe , that , there is some Chemistry , between you two , then you must not be surprised , when he calls you , at such time.

I mean , why would you give him , your Phone number ??
You can let it switch to your voice mail , when you don`t want to be disturbed in the night.

I feel many questions here

But , I do agree , that a good and a solid relation , must be built on trust and honesty and respect.
So , what is missing here ?

Eric