Amino Acid Properties

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
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> library(HDMD)
Loading required package: psych
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HDMD/AminoAcids.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AminoAcids
> ### Title: Amino Acid Properties
> ### Aliases: AminoAcids AAbyGroup AAGroups small polar hydrophobic
> 
> ### ** Examples
> 
> data(AA54)
Warning message:
In data(AA54) : data set 'AA54' not found
> AA54_PCA = princomp(AA54, covmat = cov.wt(AA54))
> 
> Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
Could not solve for inverse correlation.  Using general inverse ginv(r) 
Warning message:
In cor.smooth(R) : Matrix was not positive definite, smoothing was done
> Factor54$loadings[order(Factor54$loadings[,1]),]  
                                                     F1    F2    F3    F4    F5
Percentage of buried residues                     -1.03 -0.13 -0.19 -0.07 -0.03
Transfer free energy                              -1.02 -0.04 -0.14 -0.11  0.15
Average interactions per side chain atom          -0.94 -0.13 -0.17  0.06 -0.13
Average side chain orientation angle              -0.90 -0.16 -0.01 -0.11 -0.18
Solvation free energy                             -0.87  0.01  0.15  0.01  0.27
Hydropathy index                                  -0.86 -0.16  0.10  0.22  0.03
Information measure for pleated-sheet             -0.51 -0.11  0.44  0.06 -0.17
Normalized frequency of beta-sheet                -0.48  0.04  0.58  0.02 -0.11
Normalized frequency of beta-sheet unweighted     -0.43  0.13  0.61  0.12 -0.04
Normalized frequency of extended structure        -0.36  0.36  0.70  0.15 -0.05
Hydrophobicity factor                             -0.19  0.23  0.84 -0.01  0.10
Heat capacity                                     -0.17 -0.38  0.18 -0.65  0.00
Free energy in alpha-helical region               -0.17  0.85 -0.01 -0.09  0.10
Normalized frequency of left-handed alpha-helix   -0.10  0.34 -0.65 -0.07 -0.27
Normalized relative frequency of coil             -0.07  0.33 -0.59 -0.08 -0.13
Refractivity                                      -0.04 -0.06  0.51 -0.62 -0.09
Bulkiness                                          0.00 -0.07  1.00  0.06  0.24
Average non-bonded energy per residue              0.04  0.36  0.02 -0.50  0.30
Relative frequency in alpha-helix                  0.04 -1.00 -0.26 -0.22 -0.02
Normalized frequency of turn                       0.08  0.82 -0.08 -0.39  0.05
Net charge                                         0.09  0.06  0.01  0.13 -0.96
Amino acid composition                             0.10 -0.01 -0.28  0.85 -0.06
Number of codon(s)                                 0.10  0.16  0.06  0.85 -0.30
Helix-coil equilibrium constant                    0.11 -0.71  0.39 -0.12 -0.05
Alpha-helix indices                                0.12 -0.95 -0.17 -0.22 -0.01
Relative frequency of occurrence                   0.12 -0.10 -0.12  0.92 -0.01
Average relative probability of helix              0.13 -1.01 -0.16 -0.07  0.04
AA composition of total proteins                   0.16 -0.14 -0.08  0.95 -0.05
Free energy in beta-strand region                  0.19  0.44 -0.13  0.13  0.15
Chou-Fasman parameter of the coil conformation     0.20  0.77 -0.34 -0.05 -0.05
Information measure for loop                       0.20  0.77 -0.18 -0.33 -0.18
Side chain volume                                  0.21 -0.18  0.79 -0.30 -0.09
Optimized propensity to form reverse turn          0.21 -0.02 -0.45  0.32  0.19
Conformational parameter of beta-turn              0.24  0.68 -0.17 -0.43 -0.07
Isolelectric point                                 0.24 -0.04 -0.03  0.14 -0.96
Residue volume                                     0.26 -0.15  0.83 -0.30 -0.04
Normalized frequency coil                          0.29  0.87  0.03  0.12 -0.08
Average volume of buried residue                   0.30 -0.13  0.81 -0.34 -0.02
Relative mutability                                0.33 -0.17 -0.20  0.30  0.29
Molecular weight                                   0.39 -0.08  0.70 -0.50  0.05
Normalized frequency of beta-turn                  0.41  0.63 -0.35 -0.02  0.08
Positive charge                                    0.44 -0.25 -0.20 -0.10 -0.70
Negative charge                                    0.44 -0.23 -0.02 -0.04  0.70
Normalized relative frequency of bend              0.44  0.66 -0.23  0.08  0.11
Size                                               0.48 -0.08  0.85 -0.15 -0.11
Long range non-bonded energy per atom              0.71 -0.03 -0.39  0.19  0.09
Polar requirement                                  0.76 -0.14 -0.33 -0.02  0.24
Hydrophobicity value                               0.77 -0.16 -0.33  0.21 -0.03
Polarity                                           0.78 -0.06 -0.38  0.03  0.08
Number of hydrogen bond donors                     0.83  0.03  0.15  0.01 -0.36
Residue accessible surface area in folded protein  0.97  0.11  0.21  0.03 -0.24
Average accessible surface area                    1.02 -0.02  0.19  0.05 -0.16
Percentage of exposed residues                     1.04  0.03  0.22  0.09 -0.03
Average non-bonded energy per atom                 1.04  0.08  0.18  0.04  0.07
> 
> require(scatterplot3d)
Loading required package: 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)
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>