About undocumented conventions(?) in PDB files
First, your PDB data seems to have some formatting issues, in that the columns are in the wrong places.  I'm not sure if it's actually messed up, or if it simply got messed up when you posted it.

"In every amino acid there are two O atoms":  True for a single amino acid; not true for an amino acid residue.  I presume you're referring to the two oxygens on the carboxyl group.  However, one of these is lost when the amino acid forms an amide linkage with the next amino acid.

"What's this entry's nr.31 supposed to describe? ":  I opened the PDB in PyMol (after I corrected the format), and it seems to be the amide hydrogen

Regarding the branch designator -- I've never heard of such a thing in a PDB file, and I don't see any mention of it in the format description.  Could you clarify?

ETA:  I've tried to post the correctly formatted PDB data, but it seems to be messing up the formatting.  I'll try to figure out how to do that.
Here's an image of the residue