Biological Magnetic Resonance Data Bank

A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data.

D.S. Wishart and B.D. Sykes

Department of Biochemistry, University of Alberta, Edmonton, Canada.

Abstract: A simple technique for identifying protein secondary structures through the analysis of backbone 13C chemical shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647-1651] which was originally developed for the analysis of 1Ha chemical shifts. By extending the Chemical-Shift Index to include 13Ca, 13Cb and carbonyl 13C chemical shifts, it is now possible to use four independent chemical-shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C chemical-shift indices to produce a 'consensus' estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C chemical shifts, without recourse to NOE measurements.

J Biomol NMR 1994 Mar;4(2):171-80

Below is the updated table of proteins from the BMRB database that comprise the 13C  Chemical Shift Index

Protein BMRB code:
Interleukin-1beta 1061
Ovomucoid third domain 1375
Cytochrome c 1404
Micrococcal nuclease 1581
Tendamistat 1642
Ribonuclease H 1657
Ribonuclease T1 1658
Flavodoxin 1673
Thioredoxin 1812
Interleukin 4 2031
Phosphocarrier protein HPr 2060
Cyclophilin 2208
Phosphocarrier protein HPr 2371
Lysozyme 2542
Basic pancreatic trypsin inhibitor 262
Thioredoxin 283
Transcriptional regulator ner 287
OB-fold sub-domain of staphylococcal nuclease' 4010
Plastocyanin 4019
Human carbonic anhydrase I 4022
RNA-binding Interface to the Multiple-RBD ProteinSex-Lethal 4028
Bovine Pancreatic Ribonuclease A 4031
Apokedarcidin 4036
Component IV glycera dibranchiata monomerichemoglobin-CO 4038
Calcium-free form of the first C2-domain ofsynaptotagmin I 4039
Escherichia Coli Topoisomerase I 4045
Drosophila Heat Shock Factor 4046
Urokinase-type plasminogen activator 4049
Rubredoxin 4050
Coiled Coil domain of Chicken Cartilage MatrixProtein 4055
Calmodulin W-7 complex 4056
Myoglobin carbon monoxide complex 4061
Human fibroblast collagenase 4064
Turkey ovomucoid third domain 4068
FimC 4070
RNA-1_Modulator_Protein 4072
Oxidized human ferredoxin 4073
DnaB helicase 4075
Outer Surface Protein A 4076
Group II Phospholipase A2 4078
A-Domain of HMG1 4079
Interferon-alpha-2a 4081
Human Profilin 4082
RNA Binding Domain of Mammalian hnRNP A1 Protein 4084
Tumor Suppressor p16ink4a 4086
E2 4087
peptide deformylase 4089
Basic fibroblast growth factor 4091
Core binding factor b subunit 4092
Human Interleukin 4 4094
SacY(1-55) 4095
RNase H domain of HIV-1 RVT strain BH10 4097
Liver Fatty Acid-Binding Protein 4098
S100B-Ca(2+)-p53_peptide_complex 4099
Mrf-2 4100
Cutinase 4101
Metallo-beta-lactamase 4102
Rat CD2 domain 1 4109
IM9 E9-complex 4115
Human Elongation Factor-1beta 4117
Isl-1 homeodomain 4121
Second PDZ domain from human phosphatase hPTP1E 4123
hPTP1E-Fas receptor complex 4124
Single chain three helix bundle' 4126
Origin DNA-binding domain of SV40 T-antigen 4127
Cyanobacterial metallothionein gene repressor 4128
Human ubiquitin-conjugating enzyme 4132
Den-LysN 4134
EH1 domain of mouse Eps15 4140
Neural cell adhesion molecule module 2 4143
F1Fo ATP Synthase Subunit c 4146
Gallium putidaredoxin 4149
Adenylate kinase from E. coli 4152
Eotaxin 4155
Protein Disulfide Isomerase 4156
Tn916 integrase subunit 1 4160
Neural cell adhesion molecule module 1 4162
Tn916 integrase DNA complex 4165
eps15 homology domain 4184
CRABPII system 4186
Adenylate kinase/AP5A complex 4193
M13 major coat protein 4197
N-terminal domain of syntaxin 1A 4198
N-term linker Type III Antifreeze protein RD3 4199
Ets-1 Pointed 4205
fibronectin 4206
M13 major coat protein 4209
TATA box binding protein associated factorII 230 4223
Glutaredoxin 3 system 4225
Calcium binding subunit of troponin TnC monomer 4232
  Internal xylan binding domain from XYLD 4241
Major Sperm Protein 4242
Lymphoid enhancer-binding factor 4248
Human NER factor XPA 4249
Src homology domain 3 and 2 4251
Mbp1 4254
Mbp1(2-124) 4256
RNAse-SA 4259
Dihydrofolate reductase                   4262
PTB domain of Drosophila Numb protein/GPpY_peptidecomplex' 4263
Ca2+/calmodulin - 26-residue peptide from ratCa2+/calmodulin dependent protein kinase 4270
Methyl binding domain of MeCP2 4280
EDB 4283
Calmodulin-Ca2+-Pump-Peptide Complex 4284
DNase domain of colicin E9 4293
Titin type I domain 4295
Major cold shock protein from E. coli 4296
DnaB helicase N-terminal domain 4297
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase 4299
Pathogenesis-related Protein P14a 4301
Cytokine receptor common beta chain domain4 4308
HasA 4309
Bromodomain 4312
Iron-containing superoxide dismutase 4315
NS1(1-73) dimer 4317
N-Terminal Domain of DNA Polymerase B 4326
N-terminal inhibitory domain of human tissueinhibitor of metalloproteinases-1 4327
Streptomyces subtilisin inhibitor 4331
ARID domain of dead-ringer protein 4334
Methylamine loaded form of the Glycine CleavageSystem H-protein 4336
Interleukin 1-beta 4341
Iron-containing superoxide dismutase 4342
Frataxin 4344
CopZ 4348
Nitrogen Regulatory protein C-C-term-3Ala 4349
Inhibitor (Im9)-bound DNase domain of colicinE9 4352
E. coli maltose binding protein 4354
Pbx1 homeodomain 4357
S19 4369
Recombinant Onconase/P30 protein 4371
VATN VCP-like ATPase of Thermoplasma N-domain 4376
Human prion protein fragment 121-230 4379
Epithelial Cadherin 4380
Capsid protein from Rous Sarcoma Virus 4384
Translation initiation factor IF3 4394
Ribosomal protein L25 4395
Fractalkine 4397
Skeletal N-troponin C 4401
Human prion protein hPrP(23-230) 4402
hnRNP K 4405
GATA-1 N-terminal zinc finger 4423
Ribonuclease HI 4424
Methane monooxygenase regulatory protein B 4431
Human prion protein fragment 90-230 4434
Merozoite Surface Protein 1 4437
Sea raven Type II antifreeze protein 4452
CD58 adhesion domain, 1dCD58 4455
Hen Egg White Lysozyme 4562
Ribosomal Protein S4 Delta 41 4577
Basic pancreatic trypsin inhibitor 4661
Apoptotic protease activating factor 1 46
Basic pancreatic trypsin inhibitor 485
Micrococcal nuclease 497
Calmodulin 547
T4 lysozyme 915
Cytochrome c551 968