Question

Dihedral Angles Chi Plots.

Usually Dihedral angle Chi Plots are explored for side chain conformations. Max possible side chain angle values are up to Chi 5. My question is that why UCLA-Procheck generates only Chi1-Chi-2 plots. Why not Chi2-Chi3 and so on. Is that is not significant to calculate or due to huge possible combinations defining sterically favorable regions is tough. Is there any tool or online interface which interpret other Chi plots also?

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All Answers (4)

  • Tarak Karamakar · Jawaharlal Nehru Centre for Advanced Scientific Research
    Yes, u r right in the sense that the fluctuations in the side chain dihedral values are more. I am not sure about any software or interface, but I would rather suggest u to write a vmd tcl script to analyse these dihedral too.
  • Robbie Joosten · Netherlands Cancer Institute
    Keep in mind that Procheck was written in a time when the PDB was much smaller. Lack of data is a good reason for not exploring the higher order torsion angles. For the current PDB you could mine these torsion angles quite easily and make the plots yourself. Obviously, you really need to filter the data properly for instance on real-space electron density correlation. The problem is likely also no longer 2-dimensional, the distribution of chi2-chi3 must be dependent on chi1.That will either be a lot of plots or a very complex plot.
  • Robbie Joosten · Netherlands Cancer Institute
    By the way, chi-5 for ARG is not a freely rotable bond and for LYS there is typically not experimental evidence to put it in a non-staggered conformation.
  • Maria Teresa Buenavista · University of Reading
    g_chi of Gromacs can generate other chi plots you are interested in. specify using the option -maxchi

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