# What is the meaning of this data from a protein data bank (PDB) file? [closed]

The following rows are part of a large dataset:

... ...
16PK A  7 LYS C CCCCH  6.442  6.338  7.027  8.789 10.009 12.566
16PK A  8 SER C CCCHH  6.338  7.027  5.338 10.009  8.122 11.217
16PK A  9 ILE H CCHHH  7.027  5.338  5.335  8.122  5.537  6.408
16PK A 10 ASN H CHHHC  5.338  5.335  5.659  5.537  5.241  7.043
16PK A 11 GLU H HHHCC  5.335  5.659  6.954  5.241  8.470  8.474
16PK A 12 CYS C HHCCC  5.659  6.954  5.954  8.470  9.266  9.334
16PK A 13 ASP C HCCCC  6.954  5.954  6.117  9.266  9.243 12.200
... ...


I know that the right-hand side real numbers are the distances between the C-alpha atoms in a beta-strand.

The data is from the PDB file of 16PK protein. However, it is formatted like this after download.

What do other column values mean?

What information does this data-set convey altogether?

• What the very first header row says ? It should be just 7 lines away. Jul 13 '21 at 9:50
• Why don't you just download the .pdb and get the data you want directly from that? It will probably be quicker that way as these text files are easily edited. I just downloaded it and it seems quite normal. Jul 13 '21 at 11:27
• This is an interesting puzzle but it would be more useful if you provided information about the origin of the data (what program generated it?). Jul 13 '21 at 15:01

## 1 Answer

Column 1 is the PDB ID, column 2 the chain ID, column 3 the residue number, column 4 the residue type, column 5 the secondary structure designation by the authors, column 6 the secondary structure of a 5-residue window centered on the residue in question.

The remaining columns do appear to be distances. For example, columns 7, 8, and 9 are distances between C-alpha atoms N and N+2, and appear in three rows in different spots.

There are also distances from N to N+3 and N+4, as shown in the sketch provided by user366312 in the comment:

I could not, however, figure out how to obtain these data and what purpose they serve.

• What does it mean by C-alpha atoms N and N+2 ? Aug 22 '21 at 3:29
• Two residues apart ... @user366312 Aug 22 '21 at 11:51