This data set provides the atomic masses of a selection of amino acids regularly occuring in proteins.

aa.table

Format

A data frame with the following components.

aa3

a character vector containing three-letter amino acid code.

aa1

a character vector containing one-letter amino acid code.

mass

a numeric vector containing the mass of the respective amino acids.

formula

a character vector containing the formula of the amino acid in which the mass calculat was based.

name

a character vector containing the full names of the respective amino acids.

See also

aa2mass, aa.index, atom.index, elements,

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

Examples

data(aa.table) aa.table
#> aa3 aa1 mass formula name #> ALA ALA A 71.078 C3 H5 N O1 Alanine #> ARG ARG R 157.194 C6 H13 N4 O1 Arginine #> ASN ASN N 114.103 C4 H6 N2 O2 Asparagine #> ASP ASP D 114.079 C4 H4 N O3 Aspartic Acid #> CYS CYS C 103.143 C3 H5 N O1 S Cystein #> GLN GLN Q 117.126 C4 H9 N2 O2 Glutamine #> GLU GLU E 128.106 C5 H6 N O3 Glutamic Acid #> GLY GLY G 57.051 C2 H3 N O1 Glycine #> HIS HIS H 137.139 C6 H7 N3 O1 Histidine #> ILE ILE I 113.158 C6 H11 N O1 Isoleucine #> LEU LEU L 113.158 C6 H11 N O1 Leucine #> LYS LYS K 129.180 C6 H13 N2 O1 Lysine #> MET MET M 131.196 C5 H9 N O1 S Methionine #> PHE PHE F 147.174 C9 H9 N O1 Phenylalanine #> PRO PRO P 97.115 C5 H7 N O1 Proline #> SER SER S 87.077 C3 H5 N O2 Serine #> THR THR T 101.104 C4 H7 N O2 Threonine #> TRP TRP W 186.210 C11 H10 N2 O1 Tryptophan #> TYR TYR Y 163.173 C9 H9 N O2 Tyrosine #> VAL VAL V 99.131 C5 H9 N O1 Valine #> ABA ABA X 85.104 C4 H7 N1 O1 alpha-aminobutyric acid #> ASH ASH D 115.087 C4 H5 N O3 Aspartic acid Neutral #> CIR CIR R 157.170 C6 H11 N3 O2 citrulline #> CME CME C 179.260 C5 H9 N O2 S2 s,s-(2-hydroxyethyl)thiocysteine #> CMT CMT C 115.154 C4 H5 N O1 S o-methylcysteine #> CSD CSD C 134.134 C3 H4 N O3 S s-cysteinesulfinic acid #> CSO CSO C 119.142 C3 H5 N O2 S s-hydroxycysteine #> CSW CSW C 135.142 C3 H5 N O3 S cysteine-s-dioxide #> CSX CSX C 119.142 C3 H5 N O2 S s-oxy cysteine #> CYM CYM C 102.135 C3 H4 N O1 S Cystein Negative #> CYX CYX C 102.135 C3 H4 N O1 S Cystein SSbond #> DDE DDE H 280.346 C13 H22 N5 O2 diphthamide #> GLH GLH E 129.114 C5 H7 N O3 Glutatmic acid Neutral #> HID HID H 137.139 C6 H7 N3 O1 Histidine #> HIE HIE H 137.139 C6 H7 N3 O1 Histidine #> HIP HIP H 138.147 C6 H8 N3 O1 Histidine Positive #> HSD HSD H 137.139 C6 H7 N3 O1 Histidine #> HSE HSE H 137.139 C6 H7 N3 O1 Histidine #> HSP HSP H 138.147 C6 H8 N3 O1 Histidine Positive #> IAS IAS D 115.087 C4 H5 N O3 beta-aspartyl #> KCX KCX K 172.182 C7 H12 N2 O3 lysine nz-carboxylic acid #> LYN LYN K 129.180 C6 H13 N2 O1 Lysine Neutral #> MHO MHO M 147.195 C5 H9 N O2 S s-oxymethionine #> MLY MLY K 156.225 C8 H16 N2 O1 n-dimethyl-lysine #> MSE MSE M 178.091 C5 H9 N O1 SE selenomethionine #> OCS OCS C 151.141 C3 H5 N O4 S cysteinesulfonic acid #> PFF PFF F 165.164 C9 H8 F N O1 4-fluoro-l-phenylalanine #> PTR PTR Y 243.153 C9 H10 N O5 P o-phosphotyrosine #> SEP SEP S 167.057 C3 H6 N O5 P phosphoserine #> TPO TPO T 181.084 C4 H8 N O5 P phosphothreonine
## table look up aa.table["HIS", ]
#> aa3 aa1 mass formula name #> HIS HIS H 137.139 C6 H7 N3 O1 Histidine
## read PDB, and fetch residue masses pdb <- read.pdb(system.file("examples/1hel.pdb", package="bio3d")) aa2mass(pdb)
#> [1] 130.1879 99.1310 147.1740 57.0510 157.1940 103.1430 128.1060 113.1580 #> [9] 71.0780 71.0780 71.0780 131.1960 129.1800 157.1940 137.1390 57.0510 #> [17] 113.1580 114.0790 114.1030 163.1730 157.1940 57.0510 163.1730 87.0770 #> [25] 113.1580 57.0510 114.1030 186.2100 99.1310 103.1430 71.0780 71.0780 #> [33] 129.1800 147.1740 128.1060 87.0770 114.1030 147.1740 114.1030 101.1040 #> [41] 117.1260 71.0780 101.1040 114.1030 157.1940 114.1030 101.1040 114.0790 #> [49] 57.0510 87.0770 101.1040 114.0790 163.1730 57.0510 113.1580 113.1580 #> [57] 117.1260 113.1580 114.1030 87.0770 157.1940 186.2100 186.2100 103.1430 #> [65] 114.1030 114.0790 57.0510 157.1940 101.1040 97.1150 57.0510 87.0770 #> [73] 157.1940 114.1030 113.1580 103.1430 114.1030 113.1580 97.1150 103.1430 #> [81] 87.0770 71.0780 113.1580 113.1580 87.0770 87.0770 114.0790 113.1580 #> [89] 101.1040 71.0780 87.0770 99.1310 114.1030 103.1430 71.0780 129.1800 #> [97] 129.1800 113.1580 99.1310 87.0770 114.0790 57.0510 114.1030 57.0510 #> [105] 131.1960 114.1030 71.0780 186.2100 99.1310 71.0780 186.2100 157.1940 #> [113] 114.1030 157.1940 103.1430 129.1800 57.0510 101.1040 114.0790 99.1310 #> [121] 117.1260 71.0780 186.2100 113.1580 157.1940 57.0510 103.1430 157.1940 #> [129] 130.1653