Are you unclear on the difference between a bolt and a screw (e.g., cap screw)? Here is a common distinction:
Screw - Wikipedia, the free encyclopedia
Even though a clear distinction can be made, the terms are often used interchangeably. I apologize for assuming your question had to do with how to actually draft the threaded hold (like for a cap screw). If your question is about clearances, there are appropriate standards for the various clearances involved and standard fastener sizes. Machinery's Handbook (as mentioned in the reference) is a common resource.
John