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16 <p><em><a name="zappo">Zappo Colour</a>s</em><br>
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18 The residues are coloured according to their physico-chemical properties as
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20 <div align="center">
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21 <table width="400" border="1">
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23 <td > Aliphatic/hydrophobic</td>
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24 <td bgcolor="#ffafaf">ILVAM </td>
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28 <td bgcolor="#ffc800">FWY</td>
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32 <td bgcolor="#6464ff">KRH</td>
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36 <td bgcolor="#ff0000">DE</td>
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39 <td>Hydrophilic</td>
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40 <td bgcolor="#00ff00">STNQ</td>
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43 <td>conformationally special</td>
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44 <td bgcolor="#ff00ff">PG</td>
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48 <td bgcolor="#ffff00">C</td>
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52 <p align="center"></p>
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53 <p><em><a name="taylor">Taylor</a></em></p>
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54 <p>These colours were invented by Willie Taylor and an entertaining description
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55 of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>
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56 <div align="center">
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57 <table width="400" border="1">
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59 <td bgcolor="#ccff00">A</td>
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60 <td bgcolor="#99ff00">V</td>
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61 <td bgcolor="#66ff00">I</td>
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62 <td bgcolor="#33ff00">L</td>
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65 <td bgcolor="#00ff00">M</td>
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66 <td bgcolor="#00ff66">F</td>
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67 <td bgcolor="#00ffcc">Y</td>
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68 <td bgcolor="#00ccff">W</td>
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71 <td bgcolor="#0066ff">H</td>
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72 <td bgcolor="#0000ff">R</td>
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73 <td bgcolor="#6600ff">K</td>
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74 <td bgcolor="#cc00ff">N</td>
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77 <td bgcolor="#ff00cc">Q</td>
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78 <td bgcolor="#ff0066">E</td>
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79 <td bgcolor="#ff0000">D</td>
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80 <td bgcolor="#ff3300">S</td>
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83 <td bgcolor="#ff6600">T</td>
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84 <td bgcolor="#ff9900">G</td>
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85 <td bgcolor="#ffcc00">P</td>
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86 <td bgcolor="#ffff00">C</td>
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90 <p align="center"> </p>
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91 <p><em><a name="hydrophobic">Hydrophobicity</a></em></p>
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92 <p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.
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93 Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this
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94 table are coloured red and the most hydrophilic ones are coloured blue.</p>
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95 <div align="center">
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96 <table width="400" border="1">
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98 <td bgcolor="#ff0000">I</td>
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99 <td bgcolor="#f60009">V</td>
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100 <td bgcolor="#ea0015">L</td>
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101 <td bgcolor="#cb0034">F</td>
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102 <td bgcolor="#c2003d">C</td>
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105 <td bgcolor="#b0004f">M</td>
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106 <td bgcolor="#ad0052">A</td>
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107 <td bgcolor="#6a0095">G</td>
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108 <td bgcolor="#680097">X</td>
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109 <td bgcolor="#61009e">T</td>
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112 <td bgcolor="#5e00a1">S</td>
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113 <td bgcolor="#5b00a4">W</td>
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114 <td bgcolor="#4f00b0">Y</td>
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115 <td bgcolor="#4600b9">P</td>
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116 <td bgcolor="#1500ea">H</td>
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119 <td bgcolor="#0c00f3">E</td>
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120 <td bgcolor="#0c00f3">Z</td>
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121 <td bgcolor="#0c00f3">Q</td>
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122 <td bgcolor="#0c00f3">D</td>
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123 <td bgcolor="#0c00f3">B</td>
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126 <td bgcolor="#0c00f3">N</td>
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127 <td bgcolor="#0000ff">K</td>
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128 <td bgcolor="#0000ff">R</td>
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132 <p align="center"> </p>
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133 <p><em><a name="helix">Helix Propensity</a></em></p>
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134 <div align="center">
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135 <table width="400" border="1">
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137 <td bgcolor="#ff00ff">E</td>
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138 <td bgcolor="#ef10ef">M</td>
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139 <td bgcolor="#e718e7">A</td>
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140 <td bgcolor="#c936c9">Z</td>
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141 <td bgcolor="#ae51ae">L</td>
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144 <td bgcolor="#a05fa0">K</td>
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145 <td bgcolor="#986798">F</td>
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146 <td bgcolor="#926d92">Q</td>
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147 <td bgcolor="#8a758a">I</td>
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148 <td bgcolor="#8a758a">W</td>
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151 <td bgcolor="#857a85">V</td>
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152 <td bgcolor="#778877">D</td>
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153 <td bgcolor="#758a75">X</td>
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154 <td bgcolor="#758a75">H</td>
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155 <td bgcolor="#6f906f">R</td>
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158 <td bgcolor="#49b649">B</td>
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159 <td bgcolor="#47b847">T</td>
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160 <td bgcolor="#36c936">S</td>
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161 <td bgcolor="#23dc23">C</td>
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162 <td bgcolor="#21de21">Y</td>
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165 <td bgcolor="#1be41b">N</td>
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166 <td bgcolor="#00ff00">G</td>
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167 <td bgcolor="#00ff00">P</td>
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171 <p align="center"> </p>
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172 <p><em><a name="strand">Strand propensity</a></em></p>
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173 <div align="center">
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174 <table width="400" border="1">
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176 <td bgcolor="#ffff00">V</td>
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177 <td bgcolor="#ecec13">I</td>
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178 <td bgcolor="#d3d32c">Y</td>
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179 <td bgcolor="#c2c23d">F</td>
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180 <td bgcolor="#c0c03f">W</td>
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183 <td bgcolor="#b2b24d">L</td>
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184 <td bgcolor="#9d9d62">T</td>
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185 <td bgcolor="#9d9d62">C</td>
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186 <td bgcolor="#8c8c73">Q</td>
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187 <td bgcolor="#82827d">M</td>
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190 <td bgcolor="#797986">X</td>
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191 <td bgcolor="#6b6b94">R</td>
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192 <td bgcolor="#64649b">N</td>
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193 <td bgcolor="#60609f">H</td>
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194 <td bgcolor="#5858a7">A</td>
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197 <td bgcolor="#4949b6">S</td>
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198 <td bgcolor="#4949b6">G</td>
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199 <td bgcolor="#4747b8">Z</td>
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200 <td bgcolor="#4747b8">K</td>
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201 <td bgcolor="#4343bc">B</td>
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204 <td bgcolor="#2323dc">P</td>
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205 <td bgcolor="#2121de">D</td>
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206 <td bgcolor="#0000ff">E</td>
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210 <p align="center"> </p>
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211 <p><em><a name="turn">Turn propensity</a></em></p>
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212 <div align="center">
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213 <table width="400" border="1">
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215 <td bgcolor="#ff0000">N</td>
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216 <td bgcolor="#ff0000">G</td>
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217 <td bgcolor="#f60909">P</td>
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218 <td bgcolor="#f30c0c">B</td>
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219 <td bgcolor="#e81717">D</td>
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222 <td bgcolor="#e11e1e">S</td>
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223 <td bgcolor="#a85757">C</td>
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224 <td bgcolor="#9d6262">Y</td>
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225 <td bgcolor="#7e8181">K</td>
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226 <td bgcolor="#7c8383">X</td>
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229 <td bgcolor="#778888">Q</td>
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230 <td bgcolor="#738c8c">W</td>
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231 <td bgcolor="#738c8c">T</td>
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232 <td bgcolor="#708f8f">R</td>
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233 <td bgcolor="#708f8f">H</td>
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236 <td bgcolor="#5ba4a4">Z</td>
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237 <td bgcolor="#3fc0c0">E</td>
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238 <td bgcolor="#2cd3d3">A</td>
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239 <td bgcolor="#1ee1e1">F</td>
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240 <td bgcolor="#1ee1e1">M</td>
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243 <td bgcolor="#1ce3e3">L</td>
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244 <td bgcolor="#07f8f8">V</td>
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245 <td bgcolor="#00ffff">I</td>
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249 <p align="center"> </p>
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250 <p><em><a name="buried"></a>Buried index</a></em></p>
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251 <div align="center">
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252 <table width="400" border="1">
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254 <td bgcolor="#0000ff">C</td>
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255 <td bgcolor="#0054ab">I</td>
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256 <td bgcolor="#005fa0">V</td>
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257 <td bgcolor="#007b84">L</td>
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258 <td bgcolor="#008778">F</td>
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261 <td bgcolor="#009768">M</td>
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262 <td bgcolor="#009d62">G</td>
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263 <td bgcolor="#00a35c">A</td>
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264 <td bgcolor="#00a857">W</td>
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265 <td bgcolor="#00b649">X</td>
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268 <td bgcolor="#00d52a">S</td>
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269 <td bgcolor="#00d52a">H</td>
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270 <td bgcolor="#00db24">T</td>
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271 <td bgcolor="#00e01f">P</td>
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272 <td bgcolor="#00e619">Y</td>
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275 <td bgcolor="#00eb14">N</td>
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276 <td bgcolor="#00eb14">B</td>
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277 <td bgcolor="#00eb14">D</td>
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278 <td bgcolor="#00f10e">Q</td>
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279 <td bgcolor="#00f10e">Z</td>
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282 <td bgcolor="#00f10e">E</td>
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283 <td bgcolor="#00fc03">R</td>
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284 <td bgcolor="#00ff00">K</td>
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288 <p align="center"> </p>
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289 <p><em></em><a name="nucleotide">Nucleotide Colours</a></em></p>
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290 <div align="center">
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291 <table width="200" border="1">
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293 <td bgcolor="#64F73F">A</td>
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294 <td bgcolor="#FFB340">C</td>
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295 <td bgcolor="#EB413C">G</td>
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296 <td bgcolor="#3C88EE">T</td>
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300 <p align="center"> </p>
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301 <p><em><a name="blosum"></a>Blosum62</a></em></p>
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302 <p>Gaps are coloured white. If a residue matchs the consensus sequence residue
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303 at that position it is colored dark blue. If it does not match the consensus
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304 residue but the 2 residues have a positive Blosum62 score, it is colored light
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307 <p><em><a name="pid">Colouring above a percentage identity threshold</a></em><br>
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308 Selecting this option causes the colour scheme to be applied to only those residues
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309 that occur in that column more than a certain percentage of the time. For instance
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310 selecting the threshold to be 100 will only colour those columns with 100 %
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311 identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity
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312 and User colour schemes. <br>
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313 This option depends on a consensus calculation having been performed. If no
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314 consensus exists (e.g. after a copy or a clustalw alignment) then no residues
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316 <p><em>PID Colours</em><br>
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317 This depends on the applet having performed a consensus calculation on the alignment.<br>
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318 The PID option colours the residues (boxes and/or text) according to the percentage
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319 of the residues in each column that agree with the consensus sequence. Only
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320 the residues that agree with the consensus residue for each column are coloured.<br>
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