Default Abbreviations

See also using abbreviations.

Default Abbreviations for Amino Acids

Abbreviation Amino Acid Formula Molecular Weight One Letter Abbreviation
Ala Alanine C3H5NO 71.07794 A
Arg Arginine
(unprotonated NH2)
C6H12N4O 156.1859

Asn Asparagine C4H6N2O2 114.1027 N
Asp Aspartic acid (undissociated COOH) C4H5NO3 115.0874 D
Cys Cysteine (no disulfide link) C3H5NOS 103.1439 C
Gla gamma-Carboxyglutamate C6H7NO5 173.124 U
Gln Glutamine C5H8N2O2 128.1293 Q
Glu Glutamic acid (undissociated COOH) C5H7NO3 129.114 E
Gly Glycine C2H3NO 57.05136 G
His Histidine (unprotonated NH) C6H7N3O 137.1394 H
Hse Homoserine C4H7NO2 101.104  
Hyl Hydroxylysine C6H12N2O2 144.172  
Hyp Hydroxyproline C5H7NO2 113.1146  
Ile Isoleucine C6H11NO 113.1577 I
Leu Leucine C6H11NO 113.1577 L
Lys Lysine (unprotonated NH2) C6H12N2O 128.1742 K
Met Methionine C5H9NOS 131.1971 M
Orn Ornithine C5H10N2O 114.146 O
Phe Phenylalanine C9H9NO 147.1739 F
Pro Proline C5H7NO 97.11522 P
Pyr Pyroglutamic acid C5H5NO2 111.099  
Sar Sarcosine C3H5NO 71.078  
Ser Serine C3H5NO2 87.07734 S
Thr Threonine C4H7NO2 101.1039 T
Trp Tryptophan C11H10N2O 186.210 W
Tyr Tyrosine C9H9NO2 163.1733 Y
Val Valine C5H9NO 99.1311 V
Note: The amino acids are listed as (NH)CH(CO)R (missing an H and an OH) as if they had formed peptide bonds and were in a protein. Be sure to add an H to the first amino acid and an OH to the last amino acid when you type in a complete peptide or protein (for the neutral form).
For example: H-Gly-Ala-Phe-OH is a neutral peptide chain with three amino acids. The zwitterionic (dipolar) form of the peptide would be represented as H2-Gly-Ala-Phe-O though the molecular weight would be the same.

The Amino Acid Notation Converter can be used to convert between 1 and 3 letter abbreviations.

The following is a list of the default abbreviations included with this program. Be aware that BPY is Boron-Phosphorus-Yttrium while Bpy is bipyridine:

Default Abbreviations for Normal Recognition

Abbreviation Name Formula Molecular Weight Charge
Bpy 2,2-Bipyridine (See Note 1) C10H8N2 156.184 0
Bu Butyl CH3CH2CH2 57.11426 1
D (See Note 2) Deuterium ^2.014H 2.0140 1
En Ethylenediamine H2NCH2CH2NH2 60.0984 0
Et Ethyl CH3CH2 29.0611 1
Me Methyl CH3 15.03452 1
Ms Mesyl CH3SOO 79.09932 -1
Oac Acetate CH3COO 59.04402 -1
Otf Triflate OSOOCF3 149.0701 -1
Ox Oxalate C2O4 88.019 -2
Ph Phenyl C6H5 77.1039 1
Phen 1,10-Phenanthroline C12H8N2 180.2054 0
Py Pyridine C5H5N 79.09994 0
Tpp Tetraphenylporphyrin (See Note 3) 612.7201 0
Ts Tosyl CH3C6H4SOO 155.1953 -1
Urea Urea H2NCONH2 60.05534 0

Note 1: 2,2'-Bipyridine is also known as 2,2'-Dipyridyl

Note 2: It is suggested that D be used for deuterium rather than ^2H since most deuterium used in the laboratory is of weight 2.014 rather than exactly 2, which is the weight ^2H would calculate as.

Note 3: Tpp is (C4H2N(C6H5C)C4H2N(C6H5C))2 and is assumed to be bound to a metal. Thus, solid, pure Tpp would be notated H2Tpp to add back the two hydrogens that leave upon complex formation. Tpp is also known as 5,10,15,20-Tetraphenyl-21H,23H-porphine.

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