Computational protocol: A new structural arrangement in proteins involving lysine NH3+ group and carbonyl

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Protocol publication

[…] A subset of high-quality protein x-ray structures has been extracted from Protein Data Bank on 06.09.2017 using the following criteria: resolution is 2.0 Å or better and R free is 0.25 or better. Further analysis was restricted to the first model from each PDB file. All atoms with alternate conformations have been ignored. The program HBPLUS has been used to identify hydrogen bonds and the program STRIDE has been used for secondary structure classification. We have also used other selection criteria: (i) resolution is 1.5 Å or better, R free is 0.20 or better and/or (ii) sequence identity between any two structures in the subset is 90% or lower. The results from these additional analyses are presented in Fig. . The propensity of linear interactions toward certain elements of secondary structure is calculated as explained in the caption of Fig. . […]

Pipeline specifications

Software tools HBPLUS, STRIDE
Application Protein sequence analysis
Chemicals Hydrogen