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Is there a way to figure out what percentage of entries in PDB have SS bonds? In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?

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The easiest way is to check annotations in mmCIF or PDB files.

Looking at my page with statistics of mmCIF tags, last updated in March:

_struct_conn_type.id        59137×metalc 42706×covale 36195×disulf 10725×hydrog
_struct_conn.conn_type_id   5350402×hydrog 1733277×metalc 559092×covale 226472×disulf

Which means 226472 disulfide bonds in 36195 PDB entries at the time when the PDB had 161470 entries.

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  • $\begingroup$ Great, thanks! Exactly what I needed. What about ionic interaction (salt bridges), do you have the numbers? $\endgroup$ – Jake B. Oct 6 '20 at 18:03
  • $\begingroup$ No, I'm afraid I can't help with salt bridges. $\endgroup$ – marcin Oct 6 '20 at 20:29

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