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COO- HN—C—H € Ô Y B a 5 6 4 3 2 1 que — CH o CH, o CH, o CH Ob” *NH, *NH, Lysine POOr C00 EE da L-Alanine D-Alanine (b) 'CHO HO-2C—H 3CH,0H L-Glyceraldehyde COo HN— CH CH, L-Alanine CHO H— C —=0OH CH,0H D-Glyceraldehyde COO H— CNH, CH, D-Alanine Aromatic R groups coo” coo” coo” HC HS é-H HN-C-H NE CH, CH, C=cH NH 0H S Phenylalanine Tyrosine Tryptophan Polar, uncharged R groups Coo” 4 HsN—C—H CcH,0H Serine Coo” H ud Holt HoC E CH, Proline coo- HN—C—H H-C—0H cm, Threonine Asparagine Coo” + BN OE CH; | SH Cysteine Glutamine Negatively charged R groups (6/00 coo” HAN—-C—-H HN-C-H CH, CH, Coo- CH, Coo” Aspartate Glutamate table 5-1 Properties and Conventions Associated with the Standard Amino Acids pk, values Abbreviated pk PK PKR Hydropathy Occurrence Amino acid names M, (—CooH) (—NH3) (R group) pl index* in proteins (%) Nonpolar, aliphatic R groups Glycine Gly G 75 2.34 9.60 5.97 -0.4 TA Alanine Ala A 89 2.34 9.69 6.01 1.8 78 Valine Val V 117 2.32 9.62 5.97 4.2 6.6 Leucine Leu L 131 2.36 9.60 5.98 3.8 9.1 Isoleucine le 131 2.36 9.68 6.02 4.5 5.3 Methionine Met M 149 2.28 9.21 5.74 1.9 2.3 Aromatic R groups Phenylalanine Phe F 165 1.83 9.13 548 2.8 3.9 Tyrosine Tyr Y 181 2.20 9.11 10.07 5.66 =1.3 3.2 Tryptophan Tp W 204 2.38 9.39 5.89 —0.9 1.4 Polar, uncharged R groups Serine Ser S 105 2.21 9.15 5.68 -0.8 6.8 Proline Pro P 115 1.99 10.96 6.48 1.6 5.2 Threonine Thr T 119 Bl 9.62 5.87 -0.7 5.9 Cysteine Cys C 121 1.96 10.28 8.18 5.07 2.5 1.9 Asparagine Asn N 132 2.02 8.80 5.41 RS AS Glutamine Gin Q 146 217 9.13 5.65 -3.5 4.2 Positively charged R groups Lysine lys K 146 2.18 8.95 10.53 9.74 -3.9 5.9 Histidine His H 155 1.82 9.17 6.00 7.59 -3.2 2.3 Arginine Arg R 174 Dal 9.04 12.48 10.76 -4.5 na Negatively charged R groups Aspartate Asp D 133 1.88 9.60 3.65 DITA —3.5 5.3 Glutamate Glu E 147 219 9.67 4.25 3.22 -3.5 6.3 *A scale combining hydrophobicity and hydrophilicity of R groups; it can be used to measure the tendency of an amino acid to seek an aqueous environment (— values) or a hydrophobic environment (+ values). See Chapter 12. From Kyte, J. & Doolittle, R.F. (1982) J. Mol. Biol. 157, 105- 132. 'Average occurrence in over 1150 proteins. From Doolittle, R.F. (1989) Redundancies in protein sequences. In Prediction of Protein Structure and the Principles of Protein Conformation (Fasman, G.D., ed) Plenum Press, NY, pp. 599-623. COoo” Coo” + | + H;N—CH HaN—CH Cysteine bH CH ; 2H? + Ze” : = Cystine EH 2H? + Ze” cH CH Cysteine | ? + | ? + CH—NH; CH—NH; | | Coo” Coo” L HO-C—cH, HC. . CH-C00) H” DH 4-Hydroxyproline H;N-CH;—CH-CH,—CH;—CH-—C00 oH *NH; 5-Hydroxylysine tt DE Ma 6 HCl HED *NH; 6-N-Methyllysine + HAN. “"00C Ccoo” O0€—CH—CH:—CH-COO “NH, y-Carboxyglutamate HN. C00 A xá ch (CHo)s | , | (CH | cH EN” Scoo Desmosine s SHCHo ME CH -01E--CiOO” *NHs Selenocysteine N NH; (CH Cf coo” (a) O | MOo—6 daN R Nonionic form l OC o H;N— T —H R fwitterionic form + NH; NH, NH, | PK, | PK, | GH — Ho — GH CcooH Ccoo” Coo” 13 H Glycine pH OH” (equivalents) + | + + | HoN-CH ENC HoN-GH HoN-GE GHo H GHo H GHo H GHo E Cc Cc C— Cc N IN N N | Pd pKy J Foda pk | Adi pk | ZM H H H 10 + Histidine pk, = a y 8: q pKr = 6.0 ! pHOj a | o l I af | Da pk, — | | 9º 1.82 | É ii | | I I I à | à É 1 l 1 l 0 1.0 2.0 3.0 OH (equivalents) (b) a UT HaN CH li OH + H-—N—CH—COO. udjm Toi HaN CH-C—N—CH—COO 
