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IMGT color menu

The IMGT color menu comprises:

Colors are defined according to the RGB decimal color chart.

Color menu for amino acids

  R - Arg - Arginine [230, 6, 6] [#E60606]
  K - Lys - Lysine [198, 66, 0] [#C64200]
  Q - Gln - Glutamine [255, 102, 0] [#FF6600]
  N - Asn - Asparagine [255, 153, 0] [#FF9900]
  E - Glu - Glutamic Acid [255, 204, 0] [#FFCC00]
  D - Asp - Aspartic Acid [255, 204, 153] [#FFCC99]
  H - His - Histidine [255, 255, 153] [#FFFF99]
  P - Pro - Proline [255, 255, 0] [#FFFF00]
  Y - Tyr - Tyrosine [204, 255, 204] [#CCFFCC]
  W - Trp - Tryptophan [204, 153, 255] [#CC99FF]
  S - Ser - Serine [204, 255, 153] [#CCFF99]
  T - Thr - Threonine [0, 255, 153] [#00FF99]
  G - Gly - Glycine [0, 255, 0] [#00FF00]
  A - Ala - Alanine [204, 255, 255] [#CCFFFF]
  M - Met - Methionine [153, 204, 255] [#99CCFF]
  C - Cys - Cysteine [0, 255, 255] [#00FFFF]
  F - Phe - Phenylalanine [0, 204, 255] [#00CCFF]
  L - Leu - Leucine [51, 102, 255] [#3366FF]
  V - Val - Valine [0, 0, 255] [#0000FF]
  I - Ile - Isoleucine [0, 0, 128] [#000080]

The amino acids are colored according to 'Physicochemical' or specific amino acid classes [1].

Color menu for the 11 IMGT amino acid 'Physicochemical' classes

  A,I,L,V- Aliphatic [27, 4, 172] [#1B04AC]
  F- Phe - Phenylalanine [0, 204, 255] [#00CCFF]
  C,M - Sulfur [204, 236, 255] [#CCECFF]
  G - Gly - Glycine [0, 255, 0] [#00FF00]
  S,T - Hydroxyl [137, 248, 139] [#89F88B]
  W - Trp - Tryptophan [204, 153, 255] [#CC99FF]
  Y - Tyr - Tyrosine [204, 255, 204] [#CCFFCC]
  P - Pro - Proline [255, 255, 0] [#FFFF00]
  D,E - Acidic [255, 204, 0] [#FFCC00]
  N,Q - Amide [244, 165, 4] [#CCA504]
  R,H,K - Basic [236, 21, 4] [#EC1504]

IMGT amino acid 'Physicochemical' classes are according to [2].

Color menu for the 3 IMGT amino acid 'Hydropathy' classes

  Hydrophobic (A,C,I,L,M,F,W,V) [51, 102, 255] [#3366FF]
  Neutral (G,H,P,S,T,Y) [255, 255, 0] [#FFFF00]
  Hydrophilic (R,N,D,Q,E,K) [230,6,6] [#E60606]

IMGT amino acid 'Hydropathy' classes are according to [2].

Color menu for the 5 IMGT amino acid 'Volume' classes

  [60-90[ (A,G,S) [255, 153, 153] [#FF9999]
  [108-117[ (N,D,C,P,T) [230, 6, 6] [#E60606]
  [138-154[ (Q,E,H,V) [255, 255, 0] [#FFFF00]
  [162-174[ (R,I,L,K,M) [153, 204, 255] [#99CCFF]
  [189-228[ (F,W,Y) [51, 102, 255] [#3366FF]

IMGT amino acid 'Volume' classes are according to [2].

Color menu for the 7 IMGT amino acid 'Chemical' classes

If tools are limited to 7 choices of colors, the following menu is used.

  Aliphatic (A,G,I,L,P,V) [27, 4, 172] [#1B04AC]
  Aromatic (F,W,Y) [204, 153, 255] [#CC99FF]
  Sulfur (C,M) [0, 130, 255] [#0082FF]
  Hydroxyl (S,T) [137, 248, 139] [#89F88B]
  Basic (R,H,K) [236, 21, 4] [#EC1504]
  Acidic (D,E) [255, 204, 0] [#FFCC00]
  Amide (N,Q) [244, 165, 4] [#CCA504]

Color menu for nucleotides

  A [0, 204, 0] [#00CC00]
  T [204, 0, 0] [#CC0000]
  G [255, 179, 0] [#FFB300]
  C [0, 0, 204] [#0000CC]

Color menu for CDR-IMGT

  IG heavy chain
TR beta chain
TR delta chain 		    IG light chain
TR alpha chain
TR gamma chain
  CDR1-IMGT [200, 0, 0] [#C80000]     CDR1-IMGT [0, 0, 228] [#0000E4]
  CDR2-IMGT [255, 169, 0] [#FFA900]     CDR2-IMGT [70, 213, 0] [#46D500]
  CDR3-IMGT [156, 65, 215] [#9C41D7]     CDR3-IMGT [0, 122, 0] [#007A00]

Color menu for FR-IMGT

Framework amino acids delimiting the CDR-IMGT:
  [200, 200, 200] [#C8C8C8] in CDR-IMGT 3D structures
  [238, 238, 238] [#EEEEEE] in 3D representations
Amino acids at the end of a polypeptide region:
  C (carboxy) end of a polypeptide [204, 0, 204] [#CC00CC] in 3D representations
  N (amino) end of a polypeptide [72, 241, 241] [#48F1F1] in 3D representations

Color menu for tables

IG
TR alpha-beta
TR gamma-delta 		IG heavy chain
TR beta chain
TR delta chain 		IG light chain
TR alpha chain
TR gamma chain
  header [255, 153, 102] [#FF9966]     header [255, 153, 153] [#FF9999]     header [0, 204, 153] [#00CC99]
  rows [255, 204, 153] [#FFCC99]     rows [255, 204, 204] [#FFCCCC]     rows [209, 247, 237] [#D1F7ED]

Color menu for genes

The color menu for genes is used in Locus representation.

  V-GENE Functionnal [0,238,0] [#00EE00]
  V-GENE ORF [255, 255, 0] [#FFFF00]
  V-GENE Pseudogene [255, 51, 0] [#FF3300]
  V-GENE Vestigial [169, 169, 169] [#A9A9A9]
  D-GENE Functionnal [0, 0, 228] [#0000E4]
  D-GENE ORF [0, 0, 228] [#0000E4]
  D-GENE Pseudogene [128, 0, 128] [#800080]
  J-GENE Functionnal [255, 204, 0] [#FFE400]
  J-GENE ORF [255, 204, 0] [#FFE400]
  J-GENE Pseudogene [255, 106, 0] [#FF6A00]
  C-GENE Functionnal [0, 153, 250] [#0099FA]
  C-GENE ORF [0, 153, 250] [#0099FA]
  C-GENE Pseudogene [0, 153, 250] [#0099FA]
  Genes not related Functionnal [204, 0, 204] [#E400E4]
  Genes not related Pseudogene [204, 0, 204] [#E400E4]

Color menu for regions and domains

The color menu for regions and domains is used in figures.

  L-REGION [255, 255, 0] [#FFFF00]     D-REGION [255, 51, 0] [#FF3300]
  V-REGION [0, 238, 0] [#00EE00]     J-REGION [255, 204, 0] [#FFCC00]
  C-REGION [0, 153, 255] [#0099FF]     HINGE-REGION [0, 117, 255] [#0075FF]
  C-DOMAIN [0, 153, 255] [#0099FF]     CH-S [0, 153, 0] [#009900]
  V-LIKE-DOMAIN [161, 238, 161] [#A1EEA1]     CONNECTING-REGION [255, 204, 150] [#FFCC96]
  C-LIKE-DOMAIN [190, 228, 234] [#BEE4EA]     TRANSMEMBRANE-REGION [212, 202, 217] [#D4CAD9]
  GROOVE-DOMAIN [254, 234, 200] [#FEEAC8]     CYTOPLASMIC-REGION [255, 204, 204] [#FFCCCC]
  FIBRONECTIN-DOMAIN [255, 255, 223] [#FFFFDF]  

Color menu for mutations

  [255, 0, 0] [#FF0000]

Color menu for sequence alignments

The color menu for sequence alignments is used in:

  CONNECTING-REGION [255, 155, 45] [#FF9B2D]
  TRANSMEMBRANE-REGION [169, 149, 179] [#A995A9]
  CYTOPLASMIC-REGION [255, 170, 170] [#FFAAAA]
  CDR-IMGT [128, 0, 0] [#800000]
C 1st-CYS; 2nd-CYS (intrachain disulfide bridge) [204, 51, 204] (bold) [#CC33CC] (bold)
W CONSERVED-TRP [0, 0, 255] [#0000FF]
A,C,F,I,L,M,V,W conserved hydrophobic amino acids [0, 0, 255] [#0000FF]
N N (Asn, asparagine) from a N-glycosylation site (NXS/T where X is different from P) [0, 255, 0] [#00FF00]

Color menu for splicing types

The color menu for splicing types is used in IMGT Repertoire (RPI):

Color menu for splicing types identify the nucleotides and amino acids resulting from the splicing (splicing frames 1 and 2) or next to the splicing (splicing frame 0).

The last nucleotide of the upstream 5' exon is shown in bold and is colored in purple (splicing frame 1), green (splicing frame 2) or blue (splicing frame 0).
The first amino acid the downstream (3') exon is in bold and is colored in purple (splicing frame 1), green (splicing frame 2) or blue (splicing frame 0). For the splicing frames 1 and 2, that amino acid results from the splicing.

Splicing frame 1 codon_start3 (purple/mauve) [204, 51, 204] [#CC33CC]
splicing frame 1 L-REGION (yellow/jaune)
V-DOMAIN (green/vert)		 [255, 255, 0]
[161, 238, 161]		 [#FFFF00]
[#00EE00]

Splicing frame 2
codon_start2 (green/vert)
[0, 255, 0]
[#00FF00]
splicing frame 2 CONNECTING-REGION (salmon/saumon) [255, 204, 150] [#FFCC96]

Splicing frame 0
codon_start1 (blue/bleu)
[50, 50, 205]
[#3232CD]
splicing frame 0 INTRACYTOPLAMIC-REGION (pink/rose) [255, 204, 204] [#FFCCCC]

Splicing site examples are from TREML1.

Note that in IMGT Protein displays, amino acids resulting from the splicing frames 1 and 2 are colored in purple and green respectively, and are underlined.

Color menu for splicing representation

Spliced intron
Splicing frame 1
  (purple/mauve) [204, 51, 204] [#CC33CC]
Splicing frame 2
  (green/vert) [0, 255, 0] [#00FF00]
Splicing frame 0
  (blue/bleu) [50, 50, 205] [#3232CD]

Exon or intron not included in transcript
  (grey/gris) [103, 103, 103] [#676767]

Exon or intron modified length due to an alternative splicing
  (red/rouge) [255, 10, 22] [#FF0A16]

Color menu for IMGT pMHC contact sites

Between parentheses, colors as described in text (English/French).

CS1 (red/rouge) [1,0,0] [#FF0000]
CS2 (grey/gris) [0.5,0.5,0.5] [#808080]
CS3 (blue/bleu) [0,0,1] [#0000FF]
CS4 (lawn green/vert) [0,1,0] [#00FF00]
CS5 (royal blue/bleu royal) [0,0.5,1] [#0080FF]
CS6 (yellow/jaune) [1,1,0] [#FFFF00]
CS7 (light green/vert pâle) [0.6,1,0.2] [#99FF33]
CS8 (aqua/aqua) [0,1,1] [#00FFFF]
CS9 (lavender/lavande) [0.5,0.5,1] [#8080FF]
CS10 (orange/orange) [1,0.7,0] [#FFB300]
CS11 (pink/rose) [1,0.5,1] [#FF80FF]

The color menu for IMGT pMHC contact sites is according to [3].

References:
[1] Ruiz, M. and Lefranc, M.-P., Currents in Computational Molecular Biology, Frontiers Science Series n°30, Universal Academy Press, Tokyo, pp 126-127 (2000)
[2] Pommié, C., Levadoux, S., Sabatier, R., Lefranc, G. and Lefranc, M.-P. "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". Journal of Molecular Recognition, 17, 17-32 (2004) PMID: 14872534 LIGM:284 pdf
[3] Kaas, Q. and Lefranc, M.-P. "T cell receptor/peptide/MHC molecular characterization and standardized pMHC contact sites in IMGT/3Dstructure-DB". In Silico Biology, 2005, 5, 505-528. Epub 2005, 5, 0046, Oct 20. PMID: 16268793 LIGM:306 pdf