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Table 7 Validation of the topological measures (snet, dnet) used to compare fold specific subgraphs

From: Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs

PDB ID Sequence identity (%) Number of residues aligned Rmsd (Å) Similarity (snet) Distance (dnet)
2POE_A 39 152 1.2 0.806 0.390
3BO7_B 37 152 1.5 0.742 0.489
2NUL_A 37 147 1.8 0.774 0.385
2OSE_A 30 153 2.1 0.548 0.614
1ZX8_A 15 108 2.5 0.516 0.679
3KOP_F 11 126 2.8 0.484 0.712
2P0O_A 10 96 2.9 0.452 0.725
  1. 7 crystal structures (from the cyclophilin-like fold) with varying sequence identities (less than 40% w.r.t. 2HAQ) were superposed onto 2HAQ and the corresponding subgraphs of {Lcyp} constructed, prior to the estimation of snet, dnet. Both the topological measures show very high correlations with sequence identities as well as root mean square deviation upon structural alignment with 2HAQ.