3 <style type="text/css">
\r
13 <p><em><a name="zappo">Zappo Colour</a>s</em><br>
\r
15 The residues are coloured according to their physico-chemical properties as
\r
17 <div align="center">
\r
18 <table width="400" border="1">
\r
20 <td > Aliphatic/hydrophobic</td>
\r
21 <td bgcolor="#ffafaf">ILVAM </td>
\r
25 <td bgcolor="#ffc800">FWY</td>
\r
29 <td bgcolor="#6464ff">KRH</td>
\r
33 <td bgcolor="#ff0000">DE</td>
\r
36 <td>Hydrophilic</td>
\r
37 <td bgcolor="#00ff00">STNQ</td>
\r
40 <td>conformationally special</td>
\r
41 <td bgcolor="#ff00ff">PG</td>
\r
45 <td bgcolor="#ffff00">C</td>
\r
49 <p align="center"></p>
\r
50 <p><em><a name="taylor">Taylor</a></em></p>
\r
51 <p>These colours were invented by Willie Taylor and an entertaining description
\r
52 of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)</p>
\r
53 <div align="center">
\r
54 <table width="400" border="1">
\r
56 <td bgcolor="#ccff00">A</td>
\r
57 <td bgcolor="#99ff00">V</td>
\r
58 <td bgcolor="#66ff00">I</td>
\r
59 <td bgcolor="#33ff00">L</td>
\r
62 <td bgcolor="#00ff00">M</td>
\r
63 <td bgcolor="#00ff66">F</td>
\r
64 <td bgcolor="#00ffcc">Y</td>
\r
65 <td bgcolor="#00ccff">W</td>
\r
68 <td bgcolor="#0066ff">H</td>
\r
69 <td bgcolor="#0000ff">R</td>
\r
70 <td bgcolor="#6600ff">K</td>
\r
71 <td bgcolor="#cc00ff">N</td>
\r
74 <td bgcolor="#ff00cc">Q</td>
\r
75 <td bgcolor="#ff0066">E</td>
\r
76 <td bgcolor="#ff0000">D</td>
\r
77 <td bgcolor="#ff3300">S</td>
\r
80 <td bgcolor="#ff6600">T</td>
\r
81 <td bgcolor="#ff9900">G</td>
\r
82 <td bgcolor="#ffcc00">P</td>
\r
83 <td bgcolor="#ffff00">C</td>
\r
87 <p align="center"> </p>
\r
88 <p><em><a name="hydrophobic">Hydrophobicity</a></em></p>
\r
89 <p>According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J.
\r
90 Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this
\r
91 table are coloured red and the most hydrophilic ones are coloured blue.</p>
\r
92 <div align="center">
\r
93 <table width="400" border="1">
\r
95 <td bgcolor="#ff0000">I</td>
\r
96 <td bgcolor="#f60009">V</td>
\r
97 <td bgcolor="#ea0015">L</td>
\r
98 <td bgcolor="#cb0034">F</td>
\r
99 <td bgcolor="#c2003d">C</td>
\r
102 <td bgcolor="#b0004f">M</td>
\r
103 <td bgcolor="#ad0052">A</td>
\r
104 <td bgcolor="#6a0095">G</td>
\r
105 <td bgcolor="#680097">X</td>
\r
106 <td bgcolor="#61009e">T</td>
\r
109 <td bgcolor="#5e00a1">S</td>
\r
110 <td bgcolor="#5b00a4">W</td>
\r
111 <td bgcolor="#4f00b0">Y</td>
\r
112 <td bgcolor="#4600b9">P</td>
\r
113 <td bgcolor="#1500ea">H</td>
\r
116 <td bgcolor="#0c00f3">E</td>
\r
117 <td bgcolor="#0c00f3">Z</td>
\r
118 <td bgcolor="#0c00f3">Q</td>
\r
119 <td bgcolor="#0c00f3">D</td>
\r
120 <td bgcolor="#0c00f3">B</td>
\r
123 <td bgcolor="#0c00f3">N</td>
\r
124 <td bgcolor="#0000ff">K</td>
\r
125 <td bgcolor="#0000ff">R</td>
\r
129 <p align="center"> </p>
\r
130 <p><em><a name="helix">Helix Propensity</a></em></p>
\r
131 <div align="center">
\r
132 <table width="400" border="1">
\r
134 <td bgcolor="#ff00ff">E</td>
\r
135 <td bgcolor="#ef10ef">M</td>
\r
136 <td bgcolor="#e718e7">A</td>
\r
137 <td bgcolor="#c936c9">Z</td>
\r
138 <td bgcolor="#ae51ae">L</td>
\r
141 <td bgcolor="#a05fa0">K</td>
\r
142 <td bgcolor="#986798">F</td>
\r
143 <td bgcolor="#926d92">Q</td>
\r
144 <td bgcolor="#8a758a">I</td>
\r
145 <td bgcolor="#8a758a">W</td>
\r
148 <td bgcolor="#857a85">V</td>
\r
149 <td bgcolor="#778877">D</td>
\r
150 <td bgcolor="#758a75">X</td>
\r
151 <td bgcolor="#758a75">H</td>
\r
152 <td bgcolor="#6f906f">R</td>
\r
155 <td bgcolor="#49b649">B</td>
\r
156 <td bgcolor="#47b847">T</td>
\r
157 <td bgcolor="#36c936">S</td>
\r
158 <td bgcolor="#23dc23">C</td>
\r
159 <td bgcolor="#21de21">Y</td>
\r
162 <td bgcolor="#1be41b">N</td>
\r
163 <td bgcolor="#00ff00">G</td>
\r
164 <td bgcolor="#00ff00">P</td>
\r
168 <p align="center"> </p>
\r
169 <p><em><a name="strand">Strand propensity</a></em></p>
\r
170 <div align="center">
\r
171 <table width="400" border="1">
\r
173 <td bgcolor="#ffff00">V</td>
\r
174 <td bgcolor="#ecec13">I</td>
\r
175 <td bgcolor="#d3d32c">Y</td>
\r
176 <td bgcolor="#c2c23d">F</td>
\r
177 <td bgcolor="#c0c03f">W</td>
\r
180 <td bgcolor="#b2b24d">L</td>
\r
181 <td bgcolor="#9d9d62">T</td>
\r
182 <td bgcolor="#9d9d62">C</td>
\r
183 <td bgcolor="#8c8c73">Q</td>
\r
184 <td bgcolor="#82827d">M</td>
\r
187 <td bgcolor="#797986">X</td>
\r
188 <td bgcolor="#6b6b94">R</td>
\r
189 <td bgcolor="#64649b">N</td>
\r
190 <td bgcolor="#60609f">H</td>
\r
191 <td bgcolor="#5858a7">A</td>
\r
194 <td bgcolor="#4949b6">S</td>
\r
195 <td bgcolor="#4949b6">G</td>
\r
196 <td bgcolor="#4747b8">Z</td>
\r
197 <td bgcolor="#4747b8">K</td>
\r
198 <td bgcolor="#4343bc">B</td>
\r
201 <td bgcolor="#2323dc">P</td>
\r
202 <td bgcolor="#2121de">D</td>
\r
203 <td bgcolor="#0000ff">E</td>
\r
207 <p align="center"> </p>
\r
208 <p><em><a name="turn">Turn propensity</a></em></p>
\r
209 <div align="center">
\r
210 <table width="400" border="1">
\r
212 <td bgcolor="#ff0000">N</td>
\r
213 <td bgcolor="#ff0000">G</td>
\r
214 <td bgcolor="#f60909">P</td>
\r
215 <td bgcolor="#f30c0c">B</td>
\r
216 <td bgcolor="#e81717">D</td>
\r
219 <td bgcolor="#e11e1e">S</td>
\r
220 <td bgcolor="#a85757">C</td>
\r
221 <td bgcolor="#9d6262">Y</td>
\r
222 <td bgcolor="#7e8181">K</td>
\r
223 <td bgcolor="#7c8383">X</td>
\r
226 <td bgcolor="#778888">Q</td>
\r
227 <td bgcolor="#738c8c">W</td>
\r
228 <td bgcolor="#738c8c">T</td>
\r
229 <td bgcolor="#708f8f">R</td>
\r
230 <td bgcolor="#708f8f">H</td>
\r
233 <td bgcolor="#5ba4a4">Z</td>
\r
234 <td bgcolor="#3fc0c0">E</td>
\r
235 <td bgcolor="#2cd3d3">A</td>
\r
236 <td bgcolor="#1ee1e1">F</td>
\r
237 <td bgcolor="#1ee1e1">M</td>
\r
240 <td bgcolor="#1ce3e3">L</td>
\r
241 <td bgcolor="#07f8f8">V</td>
\r
242 <td bgcolor="#00ffff">I</td>
\r
246 <p align="center"> </p>
\r
247 <p><em><a name="buried"></a>Buried index</a></em></p>
\r
248 <div align="center">
\r
249 <table width="400" border="1">
\r
251 <td bgcolor="#0000ff">C</td>
\r
252 <td bgcolor="#0054ab">I</td>
\r
253 <td bgcolor="#005fa0">V</td>
\r
254 <td bgcolor="#007b84">L</td>
\r
255 <td bgcolor="#008778">F</td>
\r
258 <td bgcolor="#009768">M</td>
\r
259 <td bgcolor="#009d62">G</td>
\r
260 <td bgcolor="#00a35c">A</td>
\r
261 <td bgcolor="#00a857">W</td>
\r
262 <td bgcolor="#00b649">X</td>
\r
265 <td bgcolor="#00d52a">S</td>
\r
266 <td bgcolor="#00d52a">H</td>
\r
267 <td bgcolor="#00db24">T</td>
\r
268 <td bgcolor="#00e01f">P</td>
\r
269 <td bgcolor="#00e619">Y</td>
\r
272 <td bgcolor="#00eb14">N</td>
\r
273 <td bgcolor="#00eb14">B</td>
\r
274 <td bgcolor="#00eb14">D</td>
\r
275 <td bgcolor="#00f10e">Q</td>
\r
276 <td bgcolor="#00f10e">Z</td>
\r
279 <td bgcolor="#00f10e">E</td>
\r
280 <td bgcolor="#00fc03">R</td>
\r
281 <td bgcolor="#00ff00">K</td>
\r
285 <p align="center"> </p>
\r
286 <p><em></em><a name="nucleotide">Nucleotide Colours</a></em></p>
\r
287 <div align="center">
\r
288 <table width="200" border="1">
\r
290 <td bgcolor="#64F73F">A</td>
\r
291 <td bgcolor="#FFB340">C</td>
\r
292 <td bgcolor="#EB413C">G</td>
\r
293 <td bgcolor="#3C88EE">T</td>
\r
297 <p align="center"> </p>
\r
298 <p><em><a name="blosum"></a>Blosum62</a></em></p>
\r
299 <p>Gaps are coloured white. If a residue matchs the consensus sequence residue
\r
300 at that position it is colored dark blue. If it does not match the consensus
\r
301 residue but the 2 residues have a positive Blosum62 score, it is colored light
\r
304 <p><em><a name="pid">Colouring above a percentage identity threshold</a></em><br>
\r
305 Selecting this option causes the colour scheme to be applied to only those residues
\r
306 that occur in that column more than a certain percentage of the time. For instance
\r
307 selecting the threshold to be 100 will only colour those columns with 100 %
\r
308 identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity
\r
309 and User colour schemes. <br>
\r
310 This option depends on a consensus calculation having been performed. If no
\r
311 consensus exists (e.g. after a copy or a clustalw alignment) then no residues
\r
313 <p><em>PID Colours</em><br>
\r
314 This depends on the applet having performed a consensus calculation on the alignment.<br>
\r
315 The PID option colours the residues (boxes and/or text) according to the percentage
\r
316 of the residues in each column that agree with the consensus sequence. Only
\r
317 the residues that agree with the consensus residue for each column are coloured.<br>
\r