| residue | color | symbols | comment |
| <b>residue-type</b> | * | | |
| E | #ffdddd | | |
| D | #ffddde | | |
| KR | #ddddff | | |
| WYF | #ffddff | | |
| LVIMA | #eeffee | | |
| C | #ffffbb | | |
| GHNPQST | #bbffff | | |
| BXZ | #eeeeee | | |
| <b>icm-combo</b> | * | | |
| ED | #ffdddd | | |
| KR | #ddddff | | |
| WYF | #ffddff | | |
| WYF | #ff66ff | WYF | |
| LVIMA | #eeffee | | |
| LVIMA | #66ff66 | LVIMA | |
| G | #99FFFF | G | |
| P | #FF9900 | P | |
| T | #99ffff | tSTnN# | |
| S | #99ffdd | tSTnN#aA | |
| N | #99ffee | tnND-gG | |
| Q | #99ffee | qQE+- | |
| LVIMA | #bbffbb | #WFY | |
| C | #ffffbb | | |
| C | #ffff00 | C | |
| HY | #ffaaff | #ACFHILMVWYPp | |
| E | #ff3366 | -DEqQ | |
| D | #ff6699 | -DEnNt | |
| KR | #33aaff | +KR | |
| <b>consensus-strength</b> | * | | |
| CWYFHP | #00cc99 | CWYFHP | |
| ABDEGIKLMNOQRSTUVXZ | #66ff88 | ABDEGIKLMNOQRSTUVXZ | |
| ABCDEFGHIKLMNOPQRSTUVWXYZ | #eeffcc | tpqden+-g# | |
| <b>greyscale</b> | * | | |
| CWYFHP | #969696 | CWYFHP | |
| ABDEGIKLMNOQRSTUVXZ | #bbbbbb | ABDEGIKLMNOQRSTUVXZ | |
| ABCDEFGHIKLMNOPQRSTUVWXYZ | #e0e0e0 | tpqden+-g# | |
| <b>function</b> | * | | |
| DE | red | | acidic, hydrophilic |
| RKH | blue | | basic hydrophilic |
| GAVILM | green | | neutral, hydrophobic, aliphatic |
| FYW | orange | | neutral, hydrophobic, aromatic |
| STNQ | cyan | | neutral, hydrophilic |
| C | yellow | | thiol containing |
| P | lightgreen | | imino acid |
| <b>Hydrophobicity</b> | * | | |
| DE | red | | acidic |
| RKH | blue | | basic |
| AVILMFWP | green | | hydrophobic |
| GSTNQCY | cyan | | hydrophilic |
| <b>Structural</b> | * | | |
| RNDQEHK | blue | | external |
| ACGPSTWY | grey | | ambivalent |
| ILMFV | orange | | internal |
| <b>Helix Terminators</b> | * | | |
| GTMRKHF | green | | start |
| SNDELWP | red | | end |
| CQAVIY | grey | | ambivalent |
| <b>Helical</b> | * | | (consensus from several scales) |
| AMLEQK | red | | likely to form helix |
| VIFW | magenta | | weak formers |
| CSTNDHR | grey | | ambivalent |
| PGY | blue | | helix breaking |
| <b>Beta Strand</b> | * | | |
| VILMTFWY | blue | | likely to form strand |
| ACSNQHR | grey | | ambivalent |
| DEKGP | red | | beta sheet breaking |
| <b>Turn prediction</b> | * | | |
| GSDNP | cyan | | likely to form turn |
| EQTKRY | grey | | ambivalent |
| AVLIMHFWC | magenta | | turn breaking |
| <b>Steric</b> | * | | (order of increasing side chain length) (color by spectrum) |
| G | red | | |
| A | red | | |
| CS | red | | |
| TV | magenta | | |
| NDIL | magenta | | |
| P | magenta | | |
| M | magenta | | |
| QE | cyan | | |
| K | cyan | | |
| R | cyan | | |
| H | blue | | |
| FY | blue | | |
| W | blue | | |