International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 18.3, pp. 385-386   | 1 | 2 |

Table 18.3.2.1 

R. A. Engha* and R. Huberb

a Pharmaceutical Research, Roche Diagnostics GmbH, Max Planck Institut für Biochemie, 82152 Martinsried, Germany, and bMax-Planck-Institut für Biochemie, 82152 Martinsried, Germany
Correspondence e-mail:  engh@biochem.mpg.de

Table 18.3.2.1 | top | pdf |
Bond lengths of standard amino-acid side chains

EH denotes the values of Engh & Huber (1991)[link], 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[link]

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