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

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

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

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.

ISSN: 1471-2105