Amino Acid Chemistry Data
Nathan Brouwer
10/16/2020
Build the dataframe
This code makes all of the columns and makes a dataframe
aa <-c('A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y')
MW.da <-c(89,121,133,146,165,75,155,131,146,131,149,132,115,147,174,105,119,117,204,181)
volume <-c(67,86,91,109,135,48,118,124,135,124,124,96,90,
114,148,73,93,105,163,141)
bulkiness <-c(11.5,13.46,11.68,13.57,19.8,3.4,13.69,21.4,
15.71,21.4,16.25,12.28,17.43,
14.45,14.28,9.47,15.77,21.57,21.67,18.03)
polarity <-c(0,1.48,49.7,49.9,0.35,0,51.6,0.13,49.5,0.13,
1.43,3.38,1.58,3.53,52,1.67,1.66,0.13,2.1,1.61)
isoelectric.pt <-c(6,5.07,2.77,3.22,5.48,5.97,7.59,6.02,9.74,5.98,
5.74,5.41,6.3,5.65,10.76,5.68,6.16,5.96,5.89,5.66)
hydrophobe.34 <-c(1.8,2.5,-3.5,-3.5,2.8,-0.4,-3.2,4.5,-3.9,3.8,1.9,
-3.5,-1.6,-3.5,-4.5,-0.8,-0.7,4.2,-0.9,-1.3)
hydrophobe.35 <-c(1.6,2,-9.2,-8.2,3.7,1,-3,3.1,-8.8,2.8,3.4,-4.8,
-0.2,-4.1,-12.3,0.6,1.2,2.6,1.9,-0.7)
saaH2O <-c(113,140,151,183,218,85,194,182,211,180,204,158,
143,189,241,122,146,160,259,229)
faal.fold <-c(0.74,0.91,0.62,0.62,0.88,0.72,0.78,0.88,0.52,
0.85,0.85,0.63,0.64,0.62,0.64,0.66,0.7,0.86,0.85,0.76)
polar.req <-c(7,4.8,13,12.5,5,7.9,8.4,4.9,10.1,4.9,5.3,10,
6.6,8.6,9.1,7.5,6.6,5.6,5.2,5.4)
freq <-c(7.8,1.1,5.19,6.72,4.39,6.77,2.03,6.95,6.32,
10.15,2.28,4.37,4.26,3.45,5.23,6.46,5.12,7.01,1.09,3.3)
charge<-c('un','un','neg','neg','un','un','pos','un','pos',
'un','un','un','un','un','pos','un','un','un','un','un')
hydropathy<-c('hydrophobic','hydrophobic','hydrophilic','
hydrophilic','hydrophobic','neutral','neutral','hydrophobic','hydrophilic','hydrophobic','hydrophobic','hydrophilic','neutral',
'hydrophilic','hydrophilic','neutral','neutral',
'hydrophobic','hydrophobic','neutral')
volume.cat<-c('verysmall','small','small','medium',
'verylarge','verysmall','medium','large','large',
'large','large','small','small','medium','large','verysmall','small','medium','verylarge','verylarge')
polarity.cat<-c('nonpolar','nonpolar','polar','polar',
'nonpolar','nonpolar','polar','nonpolar',
'polar','nonpolar','nonpolar','polar','nonpolar','polar',
'polar','polar','polar','nonpolar','nonpolar','polar')
chemical<-c('aliphatic','sulfur','acidic','acidic','aromatic',
'aliphatic','basic','aliphatic','basic','aliphatic','sulfur',
'amide','aliphatic','amide','basic','hydroxyl','hydroxyl',
'aliphatic','aromatic','aromatic')
aa_dat <- data.frame(aa,MW.da,volume,bulkiness,
polarity,isoelectric.pt,hydrophobe.34,hydrophobe.35,
saaH2O,faal.fold, polar.req,freq,charge,hydropathy,volume.cat,polarity.cat,chemical)
aa_dat## aa MW.da volume bulkiness polarity isoelectric.pt hydrophobe.34
## 1 A 89 67 11.50 0.00 6.00 1.8
## 2 C 121 86 13.46 1.48 5.07 2.5
## 3 D 133 91 11.68 49.70 2.77 -3.5
## 4 E 146 109 13.57 49.90 3.22 -3.5
## 5 F 165 135 19.80 0.35 5.48 2.8
## 6 G 75 48 3.40 0.00 5.97 -0.4
## 7 H 155 118 13.69 51.60 7.59 -3.2
## 8 I 131 124 21.40 0.13 6.02 4.5
## 9 K 146 135 15.71 49.50 9.74 -3.9
## 10 L 131 124 21.40 0.13 5.98 3.8
## 11 M 149 124 16.25 1.43 5.74 1.9
## 12 N 132 96 12.28 3.38 5.41 -3.5
## 13 P 115 90 17.43 1.58 6.30 -1.6
## 14 Q 147 114 14.45 3.53 5.65 -3.5
## 15 R 174 148 14.28 52.00 10.76 -4.5
## 16 S 105 73 9.47 1.67 5.68 -0.8
## 17 T 119 93 15.77 1.66 6.16 -0.7
## 18 V 117 105 21.57 0.13 5.96 4.2
## 19 W 204 163 21.67 2.10 5.89 -0.9
## 20 Y 181 141 18.03 1.61 5.66 -1.3
## hydrophobe.35 saaH2O faal.fold polar.req freq charge
## 1 1.6 113 0.74 7.0 7.80 un
## 2 2.0 140 0.91 4.8 1.10 un
## 3 -9.2 151 0.62 13.0 5.19 neg
## 4 -8.2 183 0.62 12.5 6.72 neg
## 5 3.7 218 0.88 5.0 4.39 un
## 6 1.0 85 0.72 7.9 6.77 un
## 7 -3.0 194 0.78 8.4 2.03 pos
## 8 3.1 182 0.88 4.9 6.95 un
## 9 -8.8 211 0.52 10.1 6.32 pos
## 10 2.8 180 0.85 4.9 10.15 un
## 11 3.4 204 0.85 5.3 2.28 un
## 12 -4.8 158 0.63 10.0 4.37 un
## 13 -0.2 143 0.64 6.6 4.26 un
## 14 -4.1 189 0.62 8.6 3.45 un
## 15 -12.3 241 0.64 9.1 5.23 pos
## 16 0.6 122 0.66 7.5 6.46 un
## 17 1.2 146 0.70 6.6 5.12 un
## 18 2.6 160 0.86 5.6 7.01 un
## 19 1.9 259 0.85 5.2 1.09 un
## 20 -0.7 229 0.76 5.4 3.30 un
## hydropathy volume.cat polarity.cat chemical
## 1 hydrophobic verysmall nonpolar aliphatic
## 2 hydrophobic small nonpolar sulfur
## 3 hydrophilic small polar acidic
## 4 \n hydrophilic medium polar acidic
## 5 hydrophobic verylarge nonpolar aromatic
## 6 neutral verysmall nonpolar aliphatic
## 7 neutral medium polar basic
## 8 hydrophobic large nonpolar aliphatic
## 9 hydrophilic large polar basic
## 10 hydrophobic large nonpolar aliphatic
## 11 hydrophobic large nonpolar sulfur
## 12 hydrophilic small polar amide
## 13 neutral small nonpolar aliphatic
## 14 hydrophilic medium polar amide
## 15 hydrophilic large polar basic
## 16 neutral verysmall polar hydroxyl
## 17 neutral small polar hydroxyl
## 18 hydrophobic medium nonpolar aliphatic
## 19 hydrophobic verylarge nonpolar aromatic
## 20 neutral verylarge polar aromaticPlot the data
Load the data and make a plot that matches Figure 2.8 on page 26 of the Higgs and Atwood chapter 2 reading
In order to make this plot, you will have to
- Read Chapter
- Examine Figure 2.8 carefully
- Examine Table 1 of Higgs 2009, especially the notes at the bottom of the table under the data themselves
- Use the basic R code below and change the variables being plotted
- Label the axes as in Chapte 2.
- Render your plot to RPubs, screen grab it, and submit it.
- Contact me AND your UTA if/when you run into trouble.
- The UTAs and I all have office hours on Monday
The plot() function is set up to make a blank plot. text() then uses the same tilda notation as plot() to plot the labels.
plot(polar.req ~ freq, data = aa_dat,
xlab = "Frequency",
ylab = "Polar Requirement",
main = "Amino Acid Frequency vs. Polarity Requirement",
col = 0)
text(polar.req ~ freq,
labels = aa,
data = aa_dat,
col = 1:20)
See below the code for replicating Figure 2.8 from pg 26, Higgs & Atwood (2005)
- Higgs and Atwood show a figure that plots the volume of amino acids on the y axis and compares it to the isoelectric point (pI) of those amino acids, which is plotted on the x axis. The plot() function is all that is needed once a data frame with the data is created.
plot(isoelectric.pt, volume,
xlab = "pI",
ylab = "Volume",
main = "Volume vs. Isoelectric Point",
col = 1:20)