Editing Protein primary structure (section)

== Notation ==
Protein sequence is typically notated as a string of letters, listing the amino acids starting at the [[Amine|amino]]-terminal end through to the [[Carboxylic acid|carboxyl]]-terminal end. Either a three letter code or single letter code can be used to represent the 22 naturally encoded amino acids, as well as mixtures or ambiguous amino acids (similar to [[nucleic acid notation]]).<ref name="sanger"/><ref name="letter">{{Cite journal|last1=Aasland|first1=Rein|last2=Abrams|first2=Charles|last3=Ampe|first3=Christophe|last4=Ball|first4=Linda J.|last5=Bedford|first5=Mark T.|last6=Cesareni|first6=Gianni|last7=Gimona|first7=Mario|last8=Hurley|first8=James H.|last9=Jarchau|first9=Thomas|date=2002-02-20|title=Normalization of nomenclature for peptide motifs as ligands of modular protein domains|journal=FEBS Letters|volume=513|issue=1|pages=141–144|doi=10.1016/S0014-5793(01)03295-1|pmid=11911894 |issn=1873-3468|doi-access=free|bibcode=2002FEBSL.513..141A }}</ref><ref>{{Cite journal|date=1968-07-01|title=A One-Letter Notation for Amino Acid Sequences*|journal=European Journal of Biochemistry|volume=5|issue=2|pages=151–153|doi=10.1111/j.1432-1033.1968.tb00350.x|issn=1432-1033|pmid=11911894|vauthors=Aasland R, Abrams C, Ampe C, Ball LJ, Bedford MT, Cesareni G, Gimona M, Hurley JH, Jarchau T, Lehto VP, Lemmon MA, Linding R, Mayer BJ, Nagai M, Sudol M, Walter U, Winder SJ }}</ref>

Peptides can be [[Peptide sequencing|directly sequenced]], or inferred from [[DNA sequence]]s. Large [[sequence database]]s now exist that collate known protein sequences.

{{col-float}}
{| class="wikitable sortable"
|+22 natural amino acid notation
!Amino Acid
!3-Letter<ref name="Hausman">{{Cite book|title=The cell: a molecular approach|publisher=ASM Press|year=2004|isbn=978-0-87893-214-6|location=Washington, D.C.|page=51|author1=Hausman, Robert E.|author2=Cooper, Geoffrey M.}}</ref>
!1-Letter<ref name="Hausman" />
|- style="text-align:center;"
|[[Alanine]]
|Ala
|A
|- style="text-align:center;"
|[[Arginine]]
|Arg
|R
|- style="text-align:center;"
|[[Asparagine]]
|Asn
|N
|- style="text-align:center;"
|[[Aspartic acid]]
|Asp
|D
|- style="text-align:center;"
|[[Cysteine]]
|Cys
|C
|- style="text-align:center;"
|[[Glutamic acid]]
|Glu
|E
|- style="text-align:center;"
|[[Glutamine]]
|Gln
|Q
|- style="text-align:center;"
|[[Glycine]]
|Gly
|G
|- style="text-align:center;"
|[[Histidine]]
|His
|H
|- style="text-align:center;"
|[[Isoleucine]]
|Ile
|I
|- style="text-align:center;"
|[[Leucine]]
|Leu
|L
|- style="text-align:center;"
|[[Lysine]]
|Lys
|K
|- style="text-align:center;"
|[[Methionine]]
|Met
|M
|- style="text-align:center;"
|[[Phenylalanine]]
|Phe
|F
|- style="text-align:center;"
|[[Proline]]
|Pro
|P
|- style="text-align:center;"
|[[Pyrrolysine]]
|Pyl
|O
|- style="text-align:center;"
|[[Selenocysteine]]
|Sec
|U
|- style="text-align:center;"
|[[Serine]]
|Ser
|S
|- style="text-align:center;"
|[[Threonine]]
|Thr
|T
|- style="text-align:center;"
|[[Tryptophan]]
|Trp
|W
|- style="text-align:center;"
|[[Tyrosine]]
|Tyr
|Y
|- style="text-align:center;"
|[[Valine]]
|Val
|V
|}

{{col-float-break}}

{| class="wikitable"
|+Ambiguous amino acid notation
!Symbol
!Description
!Residues represented
|-
|X
|Any amino acid, or unknown
|All
|-
|B
|Aspartate or Asparagine
|D, N
|-
|Z
|Glutamate or Glutamine
|E, Q
|-
| J
|Leucine or Isoleucine
|I, L
|-
|Φ
|[[Hydrophobic]]
|V, I, L, F, W, M
|-
|Ω
|[[Aromatic]]
|F, W, Y, H
|-
|Ψ
|[[Aliphatic]]
|V, I, L, M
|-
|π
|Small
|P, G, A, S
|-
|ζ
|[[Hydrophilic]]
|S, T, H, N, Q, E, D, K, R, Y
|-
| +
|[[Cation|Positively charged]]
|K, R, H
|-
| -
|[[Anion|Negatively charged]]
|D, E
|}
{{col-float-end}}