Section 18.3.2.3.1. Peptide parameters: proline, glycine, alanine and CB substitution

Fragments representing five-atom lengths of the backbone currently provide adequate statistics for peptide compositions of varieties including glycine, proline and side chains branched at CB. Peptide cyclicity was generally allowed on the assumption that this does not introduce distortions greater than typical protein secondary-structure interactions. The results are presented in Table 18.3.2.3. With one exception, none of the values deviates from those of 1991 by more than one sample standard deviation. However, the very large σ values for the proline C—N—CA and C—N—CD angles (Table 18.3.2.1) are conspicuous. Using high-resolution protein structures, Lamzin et al. (1995) identified geometries of proline that were inconsistent with high-resolution protein structures and also noted inconsistencies in C—CA—CB angle parameters (see also the sections on individual amino acids below). In the case of proline, a bimodal distribution of these parameters could be resolved with the discrimination between cis and trans forms (Fig. 18.3.2.1). A scatter plot of the angles against ω torsion angle resolves the averages (and σ's) of 122.6 (50) and 125.4 (44)° for C—N—CA and C—N—CD, respectively, into cis- and trans-dependent values with much smaller sample deviations (see Table 18.3.2.2). The large σ value for CB—CG remains, however, particularly for trans-proline. Its origin is unknown, but proline pucker may play a role.

Table 18.3.2.1| top | pdf | Bond lengths of standard amino-acid side chains EH denotes the values of Engh & Huber (1991), which were clustered according to atom type. The EH99 values are taken from recent Cambridge Structural Database releases with clustering of parameters only in the choice of fragments, based on amino acids. Parameters marked with an asterisk involving CA—CB bonds were taken from peptide fragment geometries. Two asterisks mark long-chain aliphatic parameters taken from arginine statistics. The number of fragments and the number of structures containing these fragments are noted after the amino-acid name. The fragments used for generating the statistics are described after the amino-acid name: incomplete valences indicate unspecified substituents with, however, specified orbital hybridization. Alanine, 163/268, CO—NH—CH(CH3)—CO—NH Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.521 0.033 1.520 0.021 Arginine, 71/98, CH—(CH2)3—NH—C(NH2)2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.520 0.030 1.521 0.027 CG—CD 1.520 0.030 1.515 0.025 CD—NE 1.460 0.018 1.460 0.017 NE—CZ 1.329 0.014 1.326 0.013 CZ—NH(1,2) 1.326 0.018 1.326 0.013 Asparagine, 145/247, —C—CH2—CO—NH2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.527 0.026 CB—CG 1.516 0.025 1.506 0.023 CG—OD1 1.231 0.020 1.235 0.022 CG—ND2 1.328 0.021 1.324 0.025 Aspartate, 265/404, C—CH2—CO2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.516 0.025 1.513 0.021 CG—OD(1,2) 1.249 0.019 1.249 0.023 Cysteine, 10/17, N—CH(CO)—CH2—SH Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.526 0.013 CB—SG 1.808 0.033 1.812 0.016 Disulfides, 53/68, C—CH2—S—S—CH2—C Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—SG 1.808 0.033 1.818 0.017 SG—SG 2.030 0.008 2.033 0.016 Glutamate, 74/88, C—CH2—CH2—CO2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.520 0.030 1.517 0.019 CG—CD 1.516 0.025 1.515 0.015 CD—OE(1,2) 1.249 0.019 1.252 0.011 Glutamine, 145/247, —C—CH2—CO—NH2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.520 0.030 1.521 0.027 CG—CD 1.516 0.025 1.506 0.023 CD—OE1 1.231 0.020 1.235 0.022 CD—NE2 1.328 0.021 1.324 0.025 Glycine: see peptide parameters, Table 18.3.2.3 Histidine (HISE), 35/37, C—CH2—imidazole; NE protonated Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.497 0.014 1.496 0.018 CG—ND1 1.371 0.017 1.383 0.022 CG—CD2 1.356 0.011 1.353 0.014 ND1—CE1 1.319 0.013 1.323 0.015 CD2—NE2 1.374 0.021 1.375 0.022 CE1—NE2 1.345 0.020 1.333 0.019 Histidine (HISD), 10/12, C—CH2—imidazole; ND protonated Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.497 0.014 1.492 0.016 CG—ND1 1.378 0.011 1.369 0.015 CG—CD2 1.356 0.011 1.353 0.017 ND1—CE1 1.345 0.020 1.343 0.025 CD2—NE2 1.382 0.030 1.415 0.021 CE1—NE2 1.319 0.013 1.322 0.023 Histidine (HISH), 50/54, C—CH2—imidazole; NE, ND protonated Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.497 0.014 1.492 0.010 CG—ND1 1.378 0.011 1.380 0.010 CG—CD2 1.354 0.011 1.354 0.009 ND1—CE1 1.321 0.010 1.326 0.010 CD2—NE2 1.374 0.011 1.373 0.011 CE1—NE2 1.321 0.010 1.317 0.011 Isoleucine, 54/80, NH—CH(CO)—CH(CH3)—CH2—CH3 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.540 0.027 1.544 0.023 CB—CG1 1.530 0.020 1.536 0.028 CB—CG2 1.521 0.033 1.524 0.031 CG1—CD1 1.513 0.039 1.500 0.069 Leucine, 178/288, NH—CH(CO)—CH2—CH(CH3)2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.533 0.023 CB—CG 1.530 0.020 1.521 0.029 CG—CD(1,2) 1.521 0.033 1.514 0.037 Lysine, 232/380, —(CH2)3—NH3 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.520 0.030 1.521 0.027 CG—CD 1.520 0.030 1.520 0.034 CD—CE 1.520 0.030 1.508 0.025 CE—NZ 1.489 0.030 1.486 0.025 Methionine, 37/49, C—(CH2)2—S—CH3 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.520 0.030 1.509 0.032 CG—SD 1.803 0.034 1.807 0.026 SD—CE 1.791 0.059 1.774 0.056 Phenylalanine, 1076/1616, C—CH2—phenyl Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.502 0.023 1.509 0.017 CG—CD(1,2) 1.384 0.021 1.383 0.015 CD(1,2)—CE(1,2) 1.382 0.030 1.388 0.020 CE(1,2)—CZ 1.382 0.030 1.369 0.019 Proline, 262/255, trans, C—CO—pyrrolidine—CO—N Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.531 0.020 CB—CG 1.492 0.050 1.495 0.050 CG—CD 1.503 0.034 1.502 0.033 CD—N 1.473 0.014 1.474 0.014 Proline, 262/158, cis, C—CO—pyrrolidine—CO—N Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.533 0.018 CB—CG 1.492 0.050 1.506 0.039 CG—CD 1.503 0.034 1.512 0.027 CD—N 1.473 0.014 1.474 0.014 Serine, 33/39, NH—CH(CO)—CH2—OH Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.525 0.015 CB—OG 1.417 0.020 1.418 0.013 Threonine, 20/25, NH—CH(CO)—CH(OH)—CH3 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.540 0.027 1.529 0.026 CB—OG1 1.433 0.016 1.428 0.020 CB—CG2 1.521 0.033 1.519 0.033 Tryptophan, 123/135, CH2—indole Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.498 0.031 1.498 0.018 CG—CD1 1.365 0.025 1.363 0.014 CG—CD2 1.433 0.018 1.432 0.017 CD1—NE1 1.374 0.021 1.375 0.017 NE1—CE2 1.370 0.011 1.371 0.013 CD2—CE2 1.409 0.017 1.409 0.012 CD2—CE3 1.398 0.016 1.399 0.015 CE2—CZ2 1.394 0.021 1.393 0.017 CE3—CZ3 1.382 0.030 1.380 0.017 CZ2—CH2 1.368 0.019 1.369 0.019 CZ3—CH2 1.400 0.025 1.396 0.016 Tyrosine, 124/161, para-(—C—CH2)—phenol Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.530 0.020 1.535 0.022 CB—CG 1.512 0.022 1.512 0.015 CG—CD(1,2) 1.389 0.021 1.387 0.013 CD(1,2)—CE(1,2) 1.382 0.030 1.389 0.015 CE(1,2)—CZ 1.378 0.024 1.381 0.013 CZ—OH 1.376 0.021 1.374 0.017 Valine, 198/313, N—CH(CO)—CH—(CH3)2 Bond EH (Å) σ EH (Å) EH99 (Å) σ EH99 (Å) CA—CB 1.540 0.027 1.543 0.021 CB—CG(1,2) 1.521 0.033 1.524 0.021

Table 18.3.2.2| top | pdf | Bond angles of standard amino-acid side chains For details see Table 18.3.2.1. Alanine, 163/268, CO—NH—CH(CH3)—CO—NH Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.4 1.5 110.1 1.4 CB—CA—C 110.5 1.5 110.1 1.5 Arginine, 71/98, CH—(CH2)3—NH—C(NH2)2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 114.1 2.0 113.4 2.2 CB—CG—CD 111.3 2.3 111.6 2.6 CG—CD—NE 112.0 2.2 111.8 2.1 CD—NE—CZ 124.2 1.5 123.6 1.4 NE—CZ—NH(1,2) 120.0 1.9 120.3 0.5 NH1—CZ—NH2 119.7 1.8 119.4 1.1 Asparagine, 145/247, —C—CH2—CO—NH2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 112.6 1.0 113.4 2.2 CB—CG—ND2 116.4 1.5 116.7 2.4 CB—CG—OD1 120.8 2.0 121.6 2.0 ND2—CG—OD1 122.6 1.0 121.9 2.3 Aspartate, 265/404, C—CO2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 112.6 1.0 113.4 2.2 CB—CG—OD(1,2) 118.4 2.3 118.3 0.9 OD1—CG—OD2 122.9 2.4 123.3 1.9 Cysteine, 10/17, N—CH(CO)—CH2—SH Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.8 1.5 CB—CA—C 110.1 1.9 111.5 1.2 CA—CB—SG 114.4 2.3 114.2 1.1 Disulfides, 53/68, C—CH2—S—S—CH2—C Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—SG 114.4 2.3 114.0 1.8 CB—SG—SG 103.8 1.8 104.3 2.3 Glutamate, 74/88, C—CH2—CH2—CO2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 114.1 2.0 113.4 2.2 CB—CG—CD 112.6 1.7 114.2 2.7 CG—CD—OE(1,2) 118.4 2.3 118.3 2.0 OE1—CD—OE2 122.9 2.4 123.3 1.2 Glutamine, 145/247, —C—CH2—CO—NH2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 114.1 2.0 113.4 2.2 CB—CG—CD 112.6 1.7 111.6 2.6 CG—CD—OE1 120.8 2.0 121.6 2.0 CG—CD—NE2 116.4 1.5 116.7 2.4 OE1—CD—NE2 122.6 1.0 121.9 2.3 Glycine: see Table 18.3.2.3 Histidine (HISE), 35/37, C—CH2—imidazole; NE protonated Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.8 1.0 113.6 1.7 CB—CG—ND1 121.6 1.5 121.4 1.3 CB—CG—CD2 129.1 1.3 129.7 1.6 CG—ND1—CE1 105.6 1.0 105.7 1.3 ND1—CE1—NE2 111.7 1.3 111.5 1.3 CE1—NE2—CD2 106.9 1.3 107.1 1.1 NE2—CD2—CG 106.5 1.0 106.7 1.2 CD2—CG—ND1 109.2 0.7 108.8 1.4 Histidine (HISD), 10/12, C—CH2— imidazole; ND protonated Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.8 1.0 113.6 1.7 CB—CG—ND1 122.7 1.5 123.2 2.5 CB—CG—CD2 129.1 1.3 130.8 3.1 CG—ND1—CE1 109.0 1.7 108.2 1.4 ND1—CE1—NE2 111.7 1.3 109.9 2.2 CE1—NE2—CD2 107.0 3.0 106.6 2.5 NE2—CD2—CG 109.5 2.3 109.2 1.9 CD2—CG—ND1 105.2 1.0 106.0 1.4 Histidine (HISH), 50/54, C—CH2—imidazole; NE, ND protonated Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.8 1.0 113.6 1.6 CB—CG—ND1 122.7 1.5 122.5 1.3 CB—CG—CD2 131.2 1.3 131.4 1.2 CG—ND1—CE1 109.3 1.7 109.0 1.0 ND1—CE1—NE2 108.4 1.0 108.5 1.1 CE1—NE2—CD2 109.0 1.0 109.0 0.7 NE2—CD2—CG 107.2 1.0 107.3 0.7 CD2—CG—ND1 106.1 1.0 106.1 0.8 Isoleucine, 54/80, NH—CH(CO)—CH(CH3)—CH2—CH3 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 111.5 1.7 110.8 2.3 CB—CA—C 109.1 2.2 111.6 2.0 CA—CB—CG1 110.4 1.7 111.0 1.9 CB—CG1—CD1 113.8 2.1 113.9 2.8 CA—CB—CG2 110.5 1.7 110.9 2.0 CG1—CB—CG2 110.7 3.0 111.4 2.2 Leucine, 178/288, NH—CH(CO)—CH2—CH(CH3)2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.4 2.0 CB—CA—C 110.1 1.9 110.2 1.9 CA—CB—CG 116.3 3.5 115.3 2.3 CB—CG—CD(1,2) 110.7 3.0 111.0 1.7 CD1—CG—CD2 110.8 2.2 110.5 3.0 Lysine, 232/380, —(CH2)3—NH3 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 114.1 2.0 113.4 2.2 CB—CG—CD 111.3 2.3 111.6 2.6 CG—CD—CE 111.3 2.3 111.9 3.0 CD—CE—NZ 111.9 3.2 111.7 2.3 Methionine, 37/49, C—(CH2)2—S—CH3 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 114.1 2.0 113.3 1.7 CB—CG—SD 112.7 3.0 112.4 3.0 CG—SD—CE 100.9 2.2 100.2 1.6 Phenylalanine, 1076/1616, C—CH2—phenyl Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.8 1.0 113.9 2.4 CB—CG—CD(1,2) 120.7 1.7 120.8 0.7 CD(1,2)—CG—CD(2,1) 118.6 1.5 118.3 1.3 CG—CD(1,2)—CE(1,2) 120.7 1.7 120.8 1.1 CD(1,2)—CE(1,2)—CZ 120.0 1.8 120.1 1.2 CE(1,2)—CZ—CE(2,1) 120.0 1.8 120.0 1.8 Proline, 262/255, trans, C—CO—pyrrolidine—CO—N Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 103.0 1.1 103.3 1.2 CB—CA—C 110.1 1.9 111.7 2.1 CA—CB—CG 104.5 1.9 104.8 1.9 CB—CG—CD 106.1 3.2 106.5 3.9 CG—CD—N 103.2 1.5 103.2 1.5 CA—N—CD 112.0 1.4 111.7 1.4 C—N—CA 122.6 5.0 119.3 1.5 C—N—CD 125.0 4.1 128.4 2.1 Proline, 262/158, cis, C—CO—pyrrolidine—CO—N Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 103.0 1.1 102.6 1.1 CB—CA—C 110.1 1.9 112.0 2.5 CA—CB—CG 104.5 1.9 104.0 1.9 CB—CG—CD 106.1 3.2 105.4 2.3 CG—CD—N 103.2 1.5 103.8 1.2 CA—N—CD 112.0 1.4 111.5 1.4 C—N—CA 122.6 5.0 127.0 2.4 C—N—CD 125.0 4.1 120.6 2.2 Serine, 33/39, NH—CH(CO)—CH2—OH Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.5 1.5 CB—CA—C 110.1 1.9 110.1 1.9 CA—CB—OG 111.1 2.0 111.2 2.7 Threonine, 20/25, NH—CH(CO)—CH(OH)—CH3 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 111.5 1.7 110.3 1.9 CB—CA—C 109.1 2.2 111.6 2.7 CA—CB—OG1 109.6 1.5 109.0 2.1 CA—CB—CG2 110.5 1.7 112.4 1.4 OG1—CB—CG2 109.3 2.0 110.0 2.3 Tryptophan, 123/135, CH2—indole Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.6 1.9 113.7† 1.9† CB—CG—CD1 126.9 1.5 127.0 1.3 CB—CG—CD2 126.8 1.4 126.6 1.3 CD1—CG—CD2 106.3 1.6 106.3 0.8 CG—CD1—NE1 110.2 1.3 110.1 1.0 CD1—NE1—CE2 108.9 1.8 109.0 0.9 NE1—CE2—CD2 107.4 1.3 107.3 1.0 CE2—CD2—CG 107.2 1.2 107.3 0.8 CG—CD2—CE3 133.9 1.0 133.9 0.9 NE1—CE2—CZ2 130.1 1.5 130.4 1.1 CE3—CD2—CE2 118.8 1.0 118.7 1.2 CD2—CE2—CZ2 122.4 1.0 122.3 1.2 CE2—CZ2—CH2 117.5 1.3 117.4 1.0 CZ2—CH2—CZ3 121.5 1.3 121.6 1.2 CH2—CZ3—CE3 121.1 1.3 121.2 1.1 CZ3—CE3—CD2 118.6 1.3 118.8 1.3 Tyrosine 124/161, para—C—CH2—phenyl—OH Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 110.5 1.7 110.6 1.8 CB—CA—C 110.1 1.9 110.4 2.0 CA—CB—CG 113.9 1.8 113.4 1.9 CB—CG—CD(1,2) 120.8 1.5 121.0 0.6 CD(1,2)—CG—CD(2,1) 118.1 1.5 117.9 1.1 CG—CD(1,2)—CE(1,2) 121.2 1.5 121.3 0.8 CD(1,2)—CE(1,2)—CZ 119.6 1.8 119.8 0.9 CE(1,2)—CZ—CE(2,1) 120.3 2.0 119.8 1.6 CE(1,2)—CZ—OH 119.9 3.0 120.1 2.7‡ Valine, 198/313, N—CH(CO)—CH—(CH3)2 Angle EH (°) σ EH (°) EH99 (°) σ EH99 (°) N—CA—CB 111.5 1.7 111.5 2.2 CB—CA—C 109.1 2.2 111.4 1.9 CA—CB—CG(1,2) 110.5 1.7 110.9 1.5 CG1—CB—CG2 110.8 2.2 110.9 1.6 †Alternate fragment definition including CA. ‡Bimodal distribution (see text).

Figure 18.3.2.1| top | pdf | Torsion dependence of proline angle geometry. A one-dimensional frequency plot of either C—N—Cα or C—N—Cδ angles shows a broad and bimodal distribution. (a) A scatter plot of the two angles shows a very strong anticorrelation and suggests two minima. (b) Plotting either angle against the ω torsion angle resolves the broad distribution into two separate peaks.

Glycine, with its unique CH₂ as CA, required new atom-type definitions for Engh & Huber (EH) (1991) parameterization to account for parameter-average differences of about one-half of a sample standard deviation. These also included C—N—CA, for which the average angles were 120.6° for glycine and 121.7° for the rest. The new statistics with 83 C—CO—NH—CH₂—C fragments estimate a larger value of 122.3° for the glycine C—N—CA angle.

`Extended atom'-type parameterizations, which cluster carbon atoms according to the number of bound hydrogen atoms, naturally separate parameters involving CB into values representing alanine and branched and unbranched side chains. Separate analyses of the bonds and angles for fragments depending on the number of hydrogen atoms at CB (1, 2 or 3) revealed significant variation for the C—CA—CB and N—CA—CB angles. The fragments chosen for peptide parameterization did not cover all possibilities for the peptide chain. In particular, effects of charges at the termini were not analysed. Also, specific residue sequences likely to have statistical effects, such as Pro-Pro (Bansal & Ananthanarayanan, 1988), were not analysed here. With 50–60 relevant fragments from the predominantly α-helical ROP protein, Vlassi et al. (1998) were able to compile statistics for main-chain bonds and angles and compare them with protein refinement parameters. Differences from EH were particularly significant for CO and CA—C bonds (1.237 and 1.508 Å, respectively) and for the O—C—N angle (121.35°). Excepting the proline O—C—N angle, for which the new CSD statistics predict an average value lowered to 121.1°, these values remained relatively unchanged. A likely source of the difference might be the predominantly helical structure of the ROP protein; the helical hydrogen bonding directly involves the C—O group in a systematic way.