Validating OLIVES for Solution Proteins UBA domain/Ubiquitin Complex Our first test system is the Ubiquitin-associated domain (UBA) from Cbl-b Ubiquitin ligase in complex with Ubiquitin 32 (Figure ). The UBA domain consists of three short helices packed around a hydrophobic core. The UBA domain has 44 residues in native contacts out of which 21 are hydrogen bonding (SI Table , SI Figure ). Ubiquitin, widespread in the cell and a canonical test system in biochemistry, consists of two helical segments and an antiparallel β-sheet with 5 strands which together form a barrel-shaped protein fold. The sheet and the longer helix have hydrophobic residues lining the inside of the barrel. The solvent-exposed side consists of polar residues apart from a hydrophobic site on the β-sheet which can bind the UBA domain. Ubiquitin has 76 residues in native contacts out of which 43 are potentially hydrogen bonding (SI Figure ). The interface between Ubiquitin and the UBA domain is mainly hydrophobic where the first helix of the UBA domain has a small hydrophobic patch complementary to Ubiquitin. There are 21 residues in the interfacial native contacts out of which 13 are hydrophobic (SI Figure ). However, the interface is also stabilized by a few hydrogen bonds. Inspecting the atomistic structure complex ASP933(5) from the UBA domain (the index in parenthesis denotes the corresponding residue index in Figure ,B where the indexing is shifted to start from 1) binds to the backbone amides of ALA46 and GLY47 on Ubiquitin, and the amide carbonyl on GLY47 interacts with LYS950( ) on the UBA domain. OLIVES correctly identifies the hydrogen bond between GLY47 and LYS950( ), but it pairs ASP933(5) with the backbone of PHE45 instead of ALA46. The OLIVES algorithm also forms a few additional bonds not observed in the atomistic structure due to close proximity between hydrogen bond donors and acceptors, that do not have favorable hydrogen bond directionality in the atomistic structure. Specifically, OLIVES identifies a hydrogen bond between HIS68 and the backbone of ASP933(5), and a π-hydrogen bond between PHE18 and the backbone of GLN49. We find this behavior acceptable since the goal of OLIVES is to stabilize coarse-grained structures via native contacts, however, one should have this in mind if inspecting the OLIVES networks closely, and as such, the OLIVES network should be regarded as a coarse-grained representation of a more detailed atomistic hydrogen bond network. The OLIVES network for the UBA domain/Ubiquitin complex is illustrated in Figure .