Default 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	R
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	^{^2.014}H	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 ^{^2}H since most deuterium used in the laboratory is of weight 2.014 rather than exactly 2, which is the weight ^{^2}H 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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