Table 1 Definition of ionic and polar interactions utilized in PIADA. Protein interaction partners used in the PIADA algorithm for the definition of ionic and polar interactions. The hydrogen bonds are included in the latter, but due to the lack of information about directionality they are not explicitly specified.

Ionic

< 6Å

Lys N(NH3+)

Arg N(NH2+)

terminal N(NH3+)

Asp O(COO-)

Glu O(COO-), terminal O (COO-)

Polar Group I

< 4.7Å

Asn N(H2)

Cys S(H)

Gln N(H2)

His N(H)

Ser O(H)

Thr O(H)

Trp N(H)

Tyr O(H)

N backbone

Asp O(COO-)

Glu O(COO-)

Polar Group II

< 4.7Å

Lys N(NH3+)

Arg N(NH2+)

Asn O (C=O)

Cys S(H)

Gln O(C=O)

His N

Ser O(H)

Thr O(H)

Tyr O(H)

O backbone

Polar Group III

< 4.7Å

Asn N(H2)

Cys S(H)

Gln N(H2)

His N(H)

Ser O(H)

Thr O(H)

Trp N(H)

Tyr O(H)

N backbone

Asn O(C=O)

Cys S(H)

Gln O(C=O)

His N

Ser O(H)

Thr O(H)

Tyr O(H)

O backbone