# Correlation of hydrogen atom naming systems, including diastereotopic # protons. The original version of this table was created by Charles # Hoogstraten. # # BMRB = System in use at BioMagResBank (IUPAC/IUB Biochemistry 9, 3471-3479 # [1970]). # # SC = Stereochemical designations # # UCSF = Mardigras-type software (peptide protonated with newhyd utility). # # XPLOR = Peptide protonated with XPLOR 3.1. Atom nomenclature is derived # from the X-PLOR topology file topallhdg.pro. # # MSI = Artificial peptide created with InsightII. For the side chain # protons attached to nitrogen in ASN, GLN, and ARG, the atom # nomenclature does not reflect the potential stereoisomerism of the # planar amide and guanidinium groups. The correlation with Z and E # nomenclature listed here simply reflects the state of the artificial # peptide generated as an example. The CG1 and CG2 atoms for VAL in a # peptide generated by InsightII are not labeled according to IUPAC # rules, while the CD1 and CD2 atoms for LEU are. # # PDB = PDB nomenclature (Taken from PDB entry 6I1B REVDAT 15-OCT-92.) # # SYBYL = The atom nomenclature was taken from the xxx.res files supplied with # the software package Sybyl version 6.2 from Tripos, Inc. # # MIDAS = MidasPlus from the Computer Graphics Laboratory at UCSF. The atom # nomenclature has been taken from the XXX.ins files supplied with the # software. The prochiral atoms have not been correlated with the # BMRB assignments at this time. Hydrogens are not included in the # XXX.ins template files. # # Note-1: The prochiral methyl group names may reflect convention of code # generating heavy atom names if protons are added later. # # Note-2: '*' The stereochemical assignments for the named atoms have not been # determined for these software systems. # # Note-3: The Z and E nomenclature is defined in the paper by Blackwood, J.E., # Gladys, C.L., Loening, K.L., Petrarca, A.E., and Rush, J.E., # "Unambiguous Specification of Stereoisomerism about a Double Bond," # J. Amer. Chem. Soc. 90, 509-510 (1968). # # Note-3: For the terminal amine and carboxyl atoms, 'X' has been used as a # dummy value for the amino acid type. # # Note-4: The terminal secondary amine protons for PRO have been included # with the other PRO atoms. # # Note-5: Fields in the table are separated by tabs. # # Note-6: Please report errors, updates, or extensions to Eldon Ulrich # (elu@nmrfam.wisc.edu) # A.A. BMRB SC PDB UCSF MSI XPLOR SYBYL* MIDAS* DIANA # ---- ---- ---- ---- ---- ---- ----- ----- ----- ----- # Terminal amine protons X H1 1H HN1 HN1 HT1 HNCAP X H2 2H HN2 HN2 HT2 X H3 3H HN3 HN3 HT3 # Terminal carboxyl atoms X H'' HOCAP X O' O O OT1 O O X O'' OXT OXT OT2 OXT OXT # Residue atoms A H H HN HN HN H HN A HA HA HA HA HA HA HA A HB1 1HB HB1 HB1 HB1 HB1 HB1 A HB2 2HB HB2 HB2 HB2 HB2 HB2 A HB3 3HB HB3 HB3 HB3 HB3 HB3 A C C C C C C C A CA CA CA CA CA CA CA A CB CB CB CB CB CB CB A N N N N N N N A O O O O O O O R H H HN HN HN H HN R HA HA HA HA HA HA HA R HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 R HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 R HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2 R HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3 R HD2 pro-S 1HD HD1 HD1 HD2 HD2 HD2 R HD3 pro-R 2HD HD2 HD2 HD1 HD1 HD3 R HE HE HNE HE HE HE HE R HH11 Z 1HH1 HN11 HH11 HH11 HH11 HH11 R HH12 E 2HH1 HN12 HH12 HH12 HH12 HH12 R HH21 Z 1HH2 HN21 HH22 HH21 HH21 HH21 R HH22 E 2HH2 HN22 HH21 HH22 HH22 HH22 R C C C C C C C R CA CA CA CA CA CA CA R CB CB CB CB CB CB CB R CG CG CG CG CG CG CG R CD CD CD CD CD CD CD R CZ CZ CZ CZ CZ CZ CZ R N N N N N N N R NE NE NE NE NE NE NE R NH1 Z NH1 NH1 NH1 NH1 NH1 NH1 R NH2 E NH2 NH2 NH2 NH2 NH2 NH2 R O O O O O O O D H H HN HN HN H HN D HA HA HA HA HA HA HA D HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 D HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 D HD2 HD2 HD2 D C C C C C C C D CA CA CA CA CA CA CA D CB CB CB CB CB CB CB D CG CG CG CG CG CG CG D N N N N N N N D O O O O O O O D OD1 OD1 OD1 OD1 OD1 OD1 OD1 D OD2 OD2 OD2 OD2 OD2 OD2 OD2 N H H HN HN HN H HN N HA HA HA HA HA HA HA N HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 N HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 N HD21 E 1HD2 HN21 HD21 HD21 HD21 HD21 N HD22 Z 2HD2 HN22 HD22 HD22 HD22 HD22 N C C C C C C C N CA CA CA CA CA CA CA N CB CB CB CB CB CB CB N CG CG CG CG CG CG CG N N N N N N N N N ND2 ND2 ND2 ND2 ND2 ND2 ND2 N O O O O O O O N OD1 OD1 OD1 OD1 OD1 OD1 OD1 C H H HN HN HN H HN C HA HA HA HA HA HA HA C HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 C HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 C HG HG HSG HG HG HG HG C C C C C C C C C CA CA CA CA CA CA CA C CB CB CB CB CB CB CB C N N N N N N N C O O O O O O O C SG SG SG SG SG SG SG E H H HN HN HN H HN E HA HA HA HA HA HA HA E HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 E HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 E HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2 E HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3 E HE2 HE2 HE2 E C C C C C C C E CA CA CA CA CA CA CA E CB CB CB CB CB CB CB E CG CG CG CG CG CG CG E CD CD CD CD CD CD CD E N N N N N N N E O O O O O O O E OE1 OE1 OE1 OE1 OE1 OE1 OE1 E OE2 OE2 OE2 OE2 OE2 OE2 OE2 Q H H HN HN HN H HN Q HA HA HA HA HA HA HA Q HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 Q HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 Q HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2 Q HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3 Q HE21 E 1HE2 HN21 HE21 HE21 HE21 HE21 Q HE22 Z 2HE2 HN22 HE22 HE22 HE22 HE22 Q C C C C C C C Q CA CA CA CA CA CA CA Q CB CB CB CB CB CB CB Q CG CG CG CG CG CG CG Q CD CD CD CD CD CD CD Q N N N N N N N Q NE2 NE2 NE2 NE2 NE2 NE2 NE2 Q O O O O O O O Q OE1 OE1 OE1 OE1 OE1 OE1 OE1 G H H HN HN HN H HN G HA2 pro-R 1HA HA1 HA1 HA2 HA2 HA1 G HA3 pro-S 2HA HA2 HA2 HA1 HA1 HA2 G C C C C C C C G CA CA CA CA CA CA CA G N N N N N N N G O O O O O O O H H H HN HN HN H HN H HA HA HA HA HA HA HA H HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 H HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 H HD1 HD1 HND1 HD1 HD1 HD1 HD1 H HD2 HD2 HD2 HD2 HD2 HD2 HD2 H HE1 HE1 HE1 HE1 HE1 HE1 HE1 H HE2 HNE2 HE2 HE2 H C C C C C C C H CA CA CA CA CA CA CA H CB CB CB CB CB CB CB H CG CG CG CG CG CG CG H CD2 CD2 CD2 CD2 CD2 CD2 CD2 H CE1 CE1 CE1 CE1 CE1 CE1 CE1 H N N N N N N N H ND1 ND1 ND1 ND1 ND1 ND1 ND1 H NE2 NE2 NE2 NE2 NE2 NE2 NE2 H O O O O O O O I H H HN HN HN H HN I HA HA HA HA HA HA HA I HB HB HB HB HB HB HB I HG12 pro-R 1HG1 HG11 HG11 HG12 HG12 HG12 I HG13 pro-S 2HG1 HG12 HG12 HG11 HG11 HG13 I HG21 1HG2 HG21 HG21 HG21 HG21 HG21 I HG22 2HG2 HG22 HG22 HG22 HG22 HG22 I HG23 3HG2 HG23 HG23 HG23 HG23 HG23 I HD11 1HD1 HD11 HD11 HD11 HD11 HD11 I HD12 2HD1 HD12 HD12 HD12 HD12 HD12 I HD13 3HD1 HD13 HD13 HD13 HD13 HD13 I C C C C C C C I CA CA CA CA CA CA CA I CB CB CB CB CB CB CB I CG1 CG1 CG1 CG1 CG1 CG1 CG1 I CG2 CG2 CG2 CG2 CG2 CG2 CG2 I CD1 CD1 CD1 CD1 CD1 CD1 CD1 I N N N N N N N I O O O O O O O L H H HN HN HN H HN L HA HA HA HA HA HA HA L HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 L HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 L HG HG HG HG HG HG HG L HD11 1HD1 HD11 HD11 HD11 HD11 HD11 L HD12 2HD1 HD12 HD12 HD12 HD12 HD12 L HD13 3HD1 HD13 HD13 HD13 HD13 HD13 L HD21 1HD2 HD21 HD21 HD21 HD21 HD21 L HD22 2HD2 HD22 HD22 HD22 HD22 HD22 L HD23 3HD2 HD23 HD23 HD23 HD23 HD23 L C C C C C C C L CA CA CA CA CA CA CA L CB CB CB CB CB CB CB L CG CG CG CG CG CG CG L CD1 pro-R CD1 CD1 CD1 CD1 CD1 CD1 L CD2 pro-S CD2 CD2 CD2 CD2 CD2 CD2 L N N N N N N N L O O O O O O O K H H HN HN HN H HN K HA HA HA HA HA HA HA K HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 K HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 K HG2 pro-R 1HG HG1 HG1 HG2 HG2 HG2 K HG3 pro-S 2HG HG2 HG2 HG1 HG1 HG3 K HD2 pro-S 1HD HD1 HD1 HD2 HD2 HD2 K HD3 pro-R 2HD HD2 HD2 HD1 HD1 HD3 K HE2 pro-S 1HE HE1 HE1 HE2 HE2 HE2 K HE3 pro-R 2HE HE2 HE2 HE1 HE1 HE3 K HZ1 1HZ HNZ1 HZ1 HZ1 HZ1 HZ1 K HZ2 2HZ HNZ2 HZ2 HZ2 HZ2 HZ2 K HZ3 3HZ HNZ3 HZ3 HZ3 HZ3 HZ3 K C C C C C C C K CA CA CA CA CA CA CA K CB CB CB CB CB CB CB K CG CG CG CG CG CG CG K CD CD CD CD CD CD CD K CE CE CE CE CE CE CE K N N N N N N N K NZ NZ NZ NZ NZ NZ NZ K O O O O O O O M H H HN HN HN H HN M HA HA HA HA HA HA HA M HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 M HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 M HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2 M HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3 M HE1 1HE HE1 HE1 HE1 HE1 HE1 M HE2 2HE HE2 HE2 HE2 HE2 HE2 M HE3 3HE HE3 HE3 HE3 HE3 HE3 M C C C C C C C M CA CA CA CA CA CA CA M CB CB CB CB CB CB CB M CG CG CG CG CG CG CG M CE CE CE CE CE CE CE M N N N N N N N M O O O O O O O M SD SD SD SD SD SD SD F H H HN HN HN H HN F HA HA HA HA HA HA HA F HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 F HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 F HD1 HD1 HD1 HD1 HD1 HD1 HD1 F HD2 HD2 HD2 HD2 HD2 HD2 HD2 F HE1 HE1 HE1 HE1 HE1 HE1 HE1 F HE2 HE2 HE2 HE2 HE2 HE2 HE2 F HZ HZ HZ HZ HZ HZ HZ F C C C C C C C F CA CA CA CA CA CA CA F CB CB CB CB CB CB CB F CG CG CG CG CG CG CG F CD1 CD1 CD1 CD1 CD1 CD1 CD1 F CD2 CD2 CD2 CD2 CD2 CD2 CD2 F CE1 CE1 CE1 CE1 CE1 CE1 CE1 F CE2 CE2 CE2 CE2 CE2 CE2 CE2 F CZ CZ CZ CZ CZ CZ CZ F N N N N N N N F O O O O O O O P H2 pro-R H2 HN2 HT2 P H3 pro-S H1 HN1 HT1 P HA HA HA HA HA HA HA P HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 P HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 P HG2 pro-S 1HG HG1 HG1 HG2 HG2 HG2 P HG3 pro-R 2HG HG2 HG2 HG1 HG1 HG3 P HD2 pro-S 1HD HD2 HD1 HD2 HD2 HD2 P HD3 pro-R 2HD HD1 HD2 HD1 HD1 HD3 P C C C C C C C P CA CA CA CA CA CA CA P CB CB CB CB CB CB CB P CG CG CG CG CG CG CG P CD CD CD CD CD CD CD P N N N N N N N P O O O O O O O S H H HN HN HN H HN S HA HA HA HA HA HA HA S HB2 pro-S 1HB HB1 HB1 HB2 HB2 HB2 S HB3 pro-R 2HB HB2 HB2 HB1 HB1 HB3 S HG HG HOG HG HG HG HG S C C C C C C C S CA CA CA CA CA CA CA S CB CB CB CB CB CB CB S N N N N N N N S O O O O O O O S OG OG OG OG OG OG OG T H H HN HN HN H HN T HA HA HA HA HA HA HA T HB HB HB HB HB HB HB T HG1 HG1 HOG1 HG1 HG1 HG1 HG1 T HG21 1HG2 HG21 HG21 HG21 HG21 HG21 T HG22 2HG2 HG22 HG22 HG22 HG22 HG22 T HG23 3HG2 HG23 HG23 HG23 HG23 HG23 T C C C C C C C T CA CA CA CA CA CA CA T CB CB CB CB CB CB CB T CG2 CG2 CG2 CG2 CG2 CG2 CG2 T N N N N N N N T O O O O O O O T OG1 OG1 OG1 OG1 OG1 OG1 OG1 W H H HN HN HN H HN W HA HA HA HA HA HA HA W HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 W HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 W HD1 HD1 HD1 HD1 HD1 HD1 HD1 W HE1 HE1 HNE1 HE1 HE1 HE1 HE1 W HE3 HE3 HE3 HE3 HE3 HE3 HE3 W HZ2 HZ2 HZ2 HZ2 HZ2 HZ2 HZ2 W HZ3 HZ3 HZ3 HZ3 HZ3 HZ3 HZ3 W HH2 HH2 HH2 HH2 HH2 HH2 HH2 W C C C C C C C W CA CA CA CA CA CA CA W CB CB CB CB CB CB CB W CG CG CG CG CG CG CG W CD1 CD1 CD1 CD1 CD1 CD1 CD1 W CD2 CD2 CD2 CD2 CD2 CD2 CD2 W CE2 CE2 CE2 CE2 CE2 CE2 CE2 W CE3 CE3 CE3 CE3 CE3 CE3 CE3 W CZ2 CZ2 CZ2 CZ2 CZ2 CZ2 CZ2 W CZ3 CZ3 CZ3 CZ3 CZ3 CZ3 CZ3 W CH2 CH2 CH2 CH2 CH2 CH2 CH2 W N N N N N N N W NE1 NE1 NE1 NE1 NE1 NE1 NE1 W O O O O O O O Y H H HN HN HN H HN Y HA HA HA HA HA HA HA Y HB2 pro-R 1HB HB1 HB1 HB2 HB2 HB2 Y HB3 pro-S 2HB HB2 HB2 HB1 HB1 HB3 Y HD1 HD1 HD1 HD1 HD1 HD1 HD1 Y HD2 HD2 HD2 HD2 HD2 HD2 HD2 Y HE1 HE1 HE1 HE1 HE1 HE1 HE1 Y HE2 HE2 HE2 HE2 HE2 HE2 HE2 Y HH HH HOH HH HH HH HH Y C C C C C C C Y CA CA CA CA CA CA CA Y CB CB CB CB CB CB CB Y CG CG CG CG CG CG CG Y CD1 CD1 CD1 CD1 CD1 CD1 CD1 Y CD2 CD2 CD2 CD2 CD2 CD2 CD2 Y CE1 CE1 CE1 CE1 CE1 CE1 CE1 Y CE2 CE2 CE2 CE2 CE2 CE2 CE2 Y CZ CZ CZ CZ CZ CZ CZ Y N N N N N N N Y O O O O O O O Y OH OH OH OH OH OH OH V H H HN HN HN H HN V HA HA HA HA HA HA HA V HB HB HB HB HB HB HB V HG11 1HG1 HG11 HG21 HG11 HG11 HG11 V HG12 2HG1 HG12 HG22 HG12 HG12 HG12 V HG13 3HG1 HG13 HG23 HG13 HG13 HG13 V HG21 1HG2 HG21 HG11 HG21 HG21 HG21 V HG22 2HG2 HG22 HG12 HG22 HG22 HG22 V HG23 3HG2 HG23 HG13 HG23 HG23 HG23 V C C C C C C C V CA CA CA CA CA CA CA V CB CB CB CB CB CB CB V CG1 pro-R CG1 CG2 CG1 CG1 CG1 CG1 V CG2 pro-S CG2 CG1 CG2 CG2 CG2 CG2 V N N N N N N N V O O O O O O O