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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. |
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| Interaction type |
Defined distance |
Proton donors |
Proton acceptors |
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| 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 |
Mihel et al. BMC Structural Biology 2008 8:21 doi:10.1186/1472-6807-8-21 |
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