Results and Discussion
All chalcogen and hydrogen bonds were identified according to the
procedures described in the Methods (see below). Interatomic contacts
that might be considered, according to the stereochemical criteria used
in this study, both hydrogen and chalcogen bonds were discarded (about
20% of the chalcogen bonds may be confused with hydrogen bonds and
about 1% of the hydrogen bonds may be confused with chalcogen bonds).
Details about hydrogen and chalcogen bonds are given in Supplementary
Material (Tables S1-S4 ) and are only briefly presented here.
As it can be expected, given the high frequency of occurrence – one per
residue – the most common nucleophile that forms chalcogen bonds is the
main-chain oxygen atom. Surprisingly, sulfur atoms act rather frequently
as nucleophiles, too, despite their low frequency of occurrence in
proteins [16]. As it was already observed, cysteines tend to be more
frequently hydrogen donors that hydrogen acceptors in hydrogen bonds,
roughly with a ratio 2:1 [4]. When the cysteine thiol group acts as
a hydrogen donor, the hydrogen acceptor is often a main-chain oxygen
atom and when it acts as a hydrogen acceptor, the hydrogen donor is
frequently a main-chain or a water oxygen.