Estimating hydropathy of proteins containing Selenocysteine or Pyrrolysine?

Question

[unksci]

I would like to estimate the hydropathy of proteins, of which some contain Selenocysteine or Pyroolysine .

These amino acids seem excluded from standard implementations of algorithms such as gravy. Similarly I could not find information regarding the hydropathy of those amino acids within proteins, which would enable me a custom estimation of the hydropathy of these proteins.

Is there an accepted adaptation for estimating hydropathy of proteins containing Selenocysteine or Pyrrolysine?

Answer 1

[natasha.sernova]

See this paper:

http://lori.academicdirect.org/works/?f=208

MODELLING ANALYSIS OF AMINO ACIDS HYDROPHOBICITY

This examplr of organism with these aminoacids:

High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic

deltaproteobacterium of gutless worm Olavius algarvensis

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976440/