aa.table
This data set provides the atomic masses of a selection of amino acids regularly occuring in proteins.
A data frame with the following components.
aa3aa1massformulanameGrant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
data(aa.table) aa.tableaa3 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 G 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