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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git] / help / html / misc / aminoAcids.html
diff --git a/help/html/misc/aminoAcids.html b/help/html/misc/aminoAcids.html
index dbcd13f..d404527 100755 (executable)
--- a/help/html/misc/aminoAcids.html
+++ b/help/html/misc/aminoAcids.html
@@ -1,22 +1,26 @@
 <html>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
---!>
-<head><title>Amino Acids</title>
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Amino Acids</title>
 <style type="text/css">
 <!--
 td {
@@ -30,279 +34,244 @@ td {
 <body>
 
 
-<div align="center">
-  <table width="450" BORDER ="1" cellpadding="3" BGCOLOR="#FFFFFF">
-    <tr> 
-      <td width="15">A</td>
-      <td width="25">Ala</td>
-      <td width="90">Alanine</td>
-      <td width="80">aliphatic<br>
-        hydrophobic<br>
-        neutral </td>
-      <td width="43" valign="middle">GCT<br>
-        GCC<br>
-        GCA<br>
-        GCG</td>
-      <td width="125"><img src="ala.jpg" width="94" height="81"></td>
-    </tr>
-    <tr> 
-      <td>B</td>
-      <td>&nbsp;</td>
-      <td>either aspartic acid or asparagine</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-    </tr>
-    <tr> 
-      <td>C</td>
-      <td>Cys</td>
-      <td>Cysteine</td>
-      <td>polar<br>
-        hydrophobic<br>
-        neutral </td>
-      <td>TGT<br>
-        TGC</td>
-      <td><img src="cys.jpg" width="82" height="95"></td>
-    </tr>
-    <tr> 
-      <td>D</td>
-      <td>Asp</td>
-      <td>Aspartic Acid</td>
-      <td>polar<br>
-        hydrophilic<br>
-        charged (-) </td>
-      <td>GAT<br>
-        GAC</td>
-      <td><img src="aspartate.jpg" width="95" height="103"></td>
-    </tr>
-    <tr> 
-      <td>E</td>
-      <td>Glu</td>
-      <td>Glutamic Acid</td>
-      <td>polar<br>
-        hydrophilic<br>
-        charged (-) </td>
-      <td>GAA<br>
-        GAG</td>
-      <td><img src="glutamate.jpg" width="93" height="128"></td>
-    </tr>
-    <tr> 
-      <td>F</td>
-      <td>Phe</td>
-      <td>Phenylalanine</td>
-      <td>aromatic<br>
-        hydrophobic<br>
-        neutral</td>
-      <td>TTT<br>
-        TTC</td>
-      <td><img src="phe.jpg" width="87" height="134"></td>
-    </tr>
-    <tr> 
-      <td>G</td>
-      <td>Gly</td>
-      <td>Glycine</td>
-      <td>&nbsp;</td>
-      <td>GGT<br>
-        GGC<br>
-        GGA<br>
-        GGG</td>
-      <td><img src="gly.jpg" width="97" height="79"></td>
-    </tr>
-    <tr> 
-      <td>H</td>
-      <td>His</td>
-      <td>Histidine</td>
-      <td>aromatic<br>
-        polar<br>
-        hydrophilic<br>
-        charged (+) </td>
-      <td>CAT<br>
-        CAC</td>
-      <td><img src="his.jpg" width="97" height="142"></td>
-    </tr>
-    <tr> 
-      <td>I</td>
-      <td>Ile</td>
-      <td>Isoleucine</td>
-      <td>aliphatic<br>
-        hydrophobic<br>
-        neutral </td>
-      <td>ATT<br>
-        ATC<br>
-        ATA</td>
-      <td><img src="iso.jpg" width="101" height="125"></td>
-    </tr>
-    <tr> 
-      <td>K</td>
-      <td>Lys</td>
-      <td>Lysine</td>
-      <td>&nbsp;</td>
-      <td>AAA<br>
-        AAG</td>
-      <td><img src="lys.jpg" width="79" height="167"></td>
-    </tr>
-    <tr> 
-      <td>L</td>
-      <td>Leu</td>
-      <td>Leucine</td>
-      <td>aliphatic<br>
-        hydrophobic<br>
-        neutral </td>
-      <td>TTG<br>
-        TTA<br>
-        CTT<br>
-        CTC<br>
-        CTA<br>
-        CTG</td>
-      <td><img src="leu.jpg" width="97" height="120"></td>
-    </tr>
-    <tr> 
-      <td>M</td>
-      <td>Met</td>
-      <td>Methionine</td>
-      <td>hydrophobic<br>
-        neutral </td>
-      <td>ATG</td>
-      <td><img src="met.jpg" width="86" height="151"></td>
-    </tr>
-    <tr> 
-      <td>N</td>
-      <td>Asn</td>
-      <td>Asparagine</td>
-      <td>polar<br>
-        hydrophilic<br>
-        neutral </td>
-      <td>AAT<br>
-        AAC</td>
-      <td><img src="asparagine.jpg" width="84" height="116"></td>
-    </tr>
-    <tr> 
-      <td>P</td>
-      <td>Pro</td>
-      <td>Proline</td>
-      <td>hydrophobic<br>
-        neutral</td>
-      <td>CCT<br>
-        CCC<br>
-        CCA<br>
-        CCG</td>
-      <td><img src="pro.jpg" width="101" height="90"></td>
-    </tr>
-    <tr> 
-      <td>Q</td>
-      <td>Gln</td>
-      <td>Glutamine</td>
-      <td>polar<br>
-        hydrophilic<br>
-        neutral</td>
-      <td>CAA<br>
-        CAG</td>
-      <td><img src="glutamine.jpg" width="81" height="137"></td>
-    </tr>
-    <tr> 
-      <td>R</td>
-      <td>Arg</td>
-      <td>Arginine</td>
-      <td>polar<br>
-        hydrophilic<br>
-        charged (+) </td>
-      <td>CGT<br>
-        CGC<br>
-        CGA<br>
-        CGG<br>
-        AGA<br>
-        AGG</td>
-      <td><img src="arg.jpg" width="95" height="187"></td>
-    </tr>
-    <tr> 
-      <td>S</td>
-      <td>Ser</td>
-      <td>Serine</td>
-      <td>polar<br>
-        hydrophilic<br>
-        neutral </td>
-      <td>TCT<br>
-        TCC<br>
-        TCA<br>
-        TCG<br>
-        AGT<br>
-        AGC</td>
-      <td><img src="ser.jpg" width="96" height="74"></td>
-    </tr>
-    <tr> 
-      <td>T</td>
-      <td>Thr</td>
-      <td>Threonine</td>
-      <td>polar<br>
-        hydrophilic<br>
-        neutral </td>
-      <td>ACT<br>
-        ACC<br>
-        ACA<br>
-        ACG</td>
-      <td><img src="thr.jpg" width="94" height="96"></td>
-    </tr>
-    <tr> 
-      <td>V</td>
-      <td>Val</td>
-      <td>Valine</td>
-      <td>aliphatic<br>
-        hydrophobic<br>
-        neutral </td>
-      <td>GTT<br>
-        GTC<br>
-        GTA<br>
-        GTG</td>
-      <td><img src="val.jpg" width="99" height="98"></td>
-    </tr>
-    <tr> 
-      <td>W</td>
-      <td>Trp</td>
-      <td>Tryptophan</td>
-      <td>aromatic<br>
-        hydrophobic<br>
-        neutral</td>
-      <td>TGG</td>
-      <td><img src="tryp.jpg" width="106" height="173"></td>
-    </tr>
-    <tr> 
-      <td>X</td>
-      <td>&nbsp;</td>
-      <td>UNKNOWN</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-    </tr>
-    <tr> 
-      <td>Y</td>
-      <td>Tyr</td>
-      <td>Tyrosine</td>
-      <td>aromatic<br>
-        polar<br>
-        hydrophobic </td>
-      <td>TAT<br>
-        TAC</td>
-      <td><img src="tyr.jpg" width="85" height="152"></td>
-    </tr>
-    <tr> 
-      <td>Z</td>
-      <td>&nbsp;</td>
-      <td>either glutamic acid or glutamine</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-      <td>&nbsp;</td>
-    </tr>
-    <tr> 
-      <td>&nbsp;</td>
-      <td>End</td>
-      <td>Terminator</td>
-      <td>&nbsp;</td>
-      <td>TAA<br>
-        TAG<br>
-        TGA</td>
-      <td>&nbsp;</td>
-    </tr>
-  </table>
+  <div align="center">
+    <table width="450" BORDER="1" cellpadding="3" BGCOLOR="#FFFFFF">
+      <tr>
+        <td width="15">A</td>
+        <td width="25">Ala</td>
+        <td width="90">Alanine</td>
+        <td width="80">aliphatic<br> hydrophobic<br>
+          neutral
+        </td>
+        <td width="43" valign="middle">GCT<br> GCC<br>
+          GCA<br> GCG
+        </td>
+        <td width="125"><img src="ala.jpg" width="94" height="81"></td>
+      </tr>
+      <tr>
+        <td>B</td>
+        <td>&nbsp;</td>
+        <td>either aspartic acid or asparagine</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+      </tr>
+      <tr>
+        <td>C</td>
+        <td>Cys</td>
+        <td>Cysteine</td>
+        <td>polar<br> hydrophobic<br> neutral
+        </td>
+        <td>TGT<br> TGC
+        </td>
+        <td><img src="cys.jpg" width="82" height="95"></td>
+      </tr>
+      <tr>
+        <td>D</td>
+        <td>Asp</td>
+        <td>Aspartic Acid</td>
+        <td>polar<br> hydrophilic<br> charged (-)
+        </td>
+        <td>GAT<br> GAC
+        </td>
+        <td><img src="aspartate.jpg" width="95" height="103"></td>
+      </tr>
+      <tr>
+        <td>E</td>
+        <td>Glu</td>
+        <td>Glutamic Acid</td>
+        <td>polar<br> hydrophilic<br> charged (-)
+        </td>
+        <td>GAA<br> GAG
+        </td>
+        <td><img src="glutamate.jpg" width="93" height="128"></td>
+      </tr>
+      <tr>
+        <td>F</td>
+        <td>Phe</td>
+        <td>Phenylalanine</td>
+        <td>aromatic<br> hydrophobic<br> neutral
+        </td>
+        <td>TTT<br> TTC
+        </td>
+        <td><img src="phe.jpg" width="87" height="134"></td>
+      </tr>
+      <tr>
+        <td>G</td>
+        <td>Gly</td>
+        <td>Glycine</td>
+        <td>&nbsp;</td>
+        <td>GGT<br> GGC<br> GGA<br> GGG
+        </td>
+        <td><img src="gly.jpg" width="97" height="79"></td>
+      </tr>
+      <tr>
+        <td>H</td>
+        <td>His</td>
+        <td>Histidine</td>
+        <td>aromatic<br> polar<br> hydrophilic<br>
+          charged (+)
+        </td>
+        <td>CAT<br> CAC
+        </td>
+        <td><img src="his.jpg" width="97" height="142"></td>
+      </tr>
+      <tr>
+        <td>I</td>
+        <td>Ile</td>
+        <td>Isoleucine</td>
+        <td>aliphatic<br> hydrophobic<br> neutral
+        </td>
+        <td>ATT<br> ATC<br> ATA
+        </td>
+        <td><img src="iso.jpg" width="101" height="125"></td>
+      </tr>
+      <tr>
+        <td>K</td>
+        <td>Lys</td>
+        <td>Lysine</td>
+        <td>&nbsp;</td>
+        <td>AAA<br> AAG
+        </td>
+        <td><img src="lys.jpg" width="79" height="167"></td>
+      </tr>
+      <tr>
+        <td>L</td>
+        <td>Leu</td>
+        <td>Leucine</td>
+        <td>aliphatic<br> hydrophobic<br> neutral
+        </td>
+        <td>TTG<br> TTA<br> CTT<br> CTC<br> CTA<br>
+          CTG
+        </td>
+        <td><img src="leu.jpg" width="97" height="120"></td>
+      </tr>
+      <tr>
+        <td>M</td>
+        <td>Met</td>
+        <td>Methionine</td>
+        <td>hydrophobic<br> neutral
+        </td>
+        <td>ATG</td>
+        <td><img src="met.jpg" width="86" height="151"></td>
+      </tr>
+      <tr>
+        <td>N</td>
+        <td>Asn</td>
+        <td>Asparagine</td>
+        <td>polar<br> hydrophilic<br> neutral
+        </td>
+        <td>AAT<br> AAC
+        </td>
+        <td><img src="asparagine.jpg" width="84" height="116"></td>
+      </tr>
+      <tr>
+        <td>P</td>
+        <td>Pro</td>
+        <td>Proline</td>
+        <td>hydrophobic<br> neutral
+        </td>
+        <td>CCT<br> CCC<br> CCA<br> CCG
+        </td>
+        <td><img src="pro.jpg" width="101" height="90"></td>
+      </tr>
+      <tr>
+        <td>Q</td>
+        <td>Gln</td>
+        <td>Glutamine</td>
+        <td>polar<br> hydrophilic<br> neutral
+        </td>
+        <td>CAA<br> CAG
+        </td>
+        <td><img src="glutamine.jpg" width="81" height="137"></td>
+      </tr>
+      <tr>
+        <td>R</td>
+        <td>Arg</td>
+        <td>Arginine</td>
+        <td>polar<br> hydrophilic<br> charged (+)
+        </td>
+        <td>CGT<br> CGC<br> CGA<br> CGG<br> AGA<br>
+          AGG
+        </td>
+        <td><img src="arg.jpg" width="95" height="187"></td>
+      </tr>
+      <tr>
+        <td>S</td>
+        <td>Ser</td>
+        <td>Serine</td>
+        <td>polar<br> hydrophilic<br> neutral
+        </td>
+        <td>TCT<br> TCC<br> TCA<br> TCG<br> AGT<br>
+          AGC
+        </td>
+        <td><img src="ser.jpg" width="96" height="74"></td>
+      </tr>
+      <tr>
+        <td>T</td>
+        <td>Thr</td>
+        <td>Threonine</td>
+        <td>polar<br> hydrophilic<br> neutral
+        </td>
+        <td>ACT<br> ACC<br> ACA<br> ACG
+        </td>
+        <td><img src="thr.jpg" width="94" height="96"></td>
+      </tr>
+      <tr>
+        <td>V</td>
+        <td>Val</td>
+        <td>Valine</td>
+        <td>aliphatic<br> hydrophobic<br> neutral
+        </td>
+        <td>GTT<br> GTC<br> GTA<br> GTG
+        </td>
+        <td><img src="val.jpg" width="99" height="98"></td>
+      </tr>
+      <tr>
+        <td>W</td>
+        <td>Trp</td>
+        <td>Tryptophan</td>
+        <td>aromatic<br> hydrophobic<br> neutral
+        </td>
+        <td>TGG</td>
+        <td><img src="tryp.jpg" width="106" height="173"></td>
+      </tr>
+      <tr>
+        <td>X</td>
+        <td>&nbsp;</td>
+        <td>UNKNOWN</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+      </tr>
+      <tr>
+        <td>Y</td>
+        <td>Tyr</td>
+        <td>Tyrosine</td>
+        <td>aromatic<br> polar<br> hydrophobic
+        </td>
+        <td>TAT<br> TAC
+        </td>
+        <td><img src="tyr.jpg" width="85" height="152"></td>
+      </tr>
+      <tr>
+        <td>Z</td>
+        <td>&nbsp;</td>
+        <td>either glutamic acid or glutamine</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+        <td>&nbsp;</td>
+      </tr>
+      <tr>
+        <td>&nbsp;</td>
+        <td>End</td>
+        <td>Terminator</td>
+        <td>&nbsp;</td>
+        <td>TAA<br> TAG<br> TGA
+        </td>
+        <td>&nbsp;</td>
+      </tr>
+    </table>
   </div>
 </body>
 </html>