AminoAcids: Amino Acid Properties

In HDMD: Statistical Analysis Tools for High Dimension Molecular Data (HDMD)

Description

Amino Acids have several distinct and overlapping physiochemical characteristics. The single letter abbreviation for each amino acid is sorted alphabetically in the character vector AminoAcids. AAbyGroup, small, polar, and hydrophobic correspond to this order and describe various amino acid attributes.

Atchley et al 1999 categorized the 20 amino acids according to physiochemical attributes to form 8 functional groups. The group names are alphabetized in AAGroups, while AAbyGroup orders these names to pair with AminoAcids. small, polar, and hydrophobic contain the vector position of amino acids that characterize that attribute.

AA Groups: acidic = DE aliphatic = AGILMV aminic = NQ aromatic = FWY basic = HKR cysteine = C hydroxylated = ST proline = P

AminoAcids = c("A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "S", "T", "V", "W", "Y") AAbyGroup = c("aliphatic", "cysteine", "acidic", "acidic", "aromatic", "aliphatic", "basic", "aliphatic", "basic", "aliphatic", "aliphatic", "aminic", "proline", "aminic", "basic", "hydroxylated", "hydroxylated", "aliphatic", "aromatic", "aromatic") AAGroups = c("acidic","aliphatic", "aminic", "aromatic", "basic","cysteine","hydroxylated", "proline") small = c(1,2,3,6,12,13,16,17,18) polar = c(2,3,4,7,9,12,14,15,16,17,19,20) hydrophobic = c(1, 2,5,6,7,8,9,10,11,17,18,19,20)

Author(s)

Lisa McFerrin

References

Atchley, W.R., Terhalle, W. and Dress, A. (1999) Positional dependence, cliques and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48, 501-516

Examples

data(AA54)
AA54_PCA = princomp(AA54, covmat = cov.wt(AA54))

Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
Factor54$loadings[order(Factor54$loadings[,1]),]  

require(scatterplot3d)
  Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss", zlab="ms")
  Factor3d$plane3d(c(0,0,0), col="grey")
  Factor3d$points3d(c(0,0), c(0,0), c(-3,2), lty="solid", type="l" )
  Factor3d$points3d(c(0,0), c(-1.5,2), c(0,0), lty="solid", type="l" )
  Factor3d$points3d(c(-1.5,2), c(0,0), c(0,0), lty="solid", type="l" )
  Factor3d$points3d(Factor54$scores[hydrophobic,1:3], col="blue", cex = 2.7, lwd=1.5)
  Factor3d$points3d(Factor54$scores[polar,1:3], col="green", cex = 3.3, lwd=1.5)
  Factor3d$points3d(Factor54$scores[small,1:3], col="orange", cex = 3.9, lwd=1.5)
  legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

HDMD documentation built on May 1, 2019, 8:48 p.m.