aa.table.RdThis data set provides the atomic masses of a selection of amino acids regularly occuring in proteins.
aa.table
A data frame with the following components.
aa3a character vector containing three-letter amino acid code.
aa1a character vector containing one-letter amino acid code.
massa numeric vector containing the mass of the respective amino acids.
formulaa character vector containing the formula of the amino acid in which the mass calculat was based.
namea character vector containing the full names of the respective amino acids.
aa2mass, aa.index,
atom.index, elements,
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
#> 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