X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fmisc%2FaminoAcids.html;h=9e25c35d4427590dd172f0f7e8d869066c209854;hb=f850089f8bc67403194f4a1a3b793a46dbb4224a;hp=f1e597a67c58b07a8e6f7b83186898a7ec9c6eb0;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git

diff --git a/help/html/misc/aminoAcids.html b/help/html/misc/aminoAcids.html
index f1e597a..9e25c35 100755
--- a/help/html/misc/aminoAcids.html
+++ b/help/html/misc/aminoAcids.html
@@ -16,150 +16,276 @@ td {
 <div align="center">
   <h2><br>
   </h2>
-  <table WIDTH="441" BORDER ="5" cellpadding="3" BGCOLOR="#FFFFFF">
-    <tr>
+  <table width="450" BORDER ="5" cellpadding="3" BGCOLOR="#FFFFFF">
+    <tr> 
       <td width="15">A</td>
       <td width="25">Ala</td>
-      <td width="157">Alanine</td>
-      <td width="192">GCT, GCC, GCA, GCG</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="alachem.gif" width="102" height="61"></td>
     </tr>
-    <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>
+    <tr> 
       <td>C</td>
       <td>Cys</td>
       <td>Cysteine</td>
-      <td>TGT, TGC</td>
+      <td>polar<br>
+        hydrophobic<br>
+        neutral </td>
+      <td>TGT<br>
+        TGC</td>
+      <td><img src="cyschem.gif" width="102" height="81"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>D</td>
       <td>Asp</td>
       <td>Aspartic Acid</td>
-      <td>GAT, GAC</td>
+      <td>polar<br>
+        hydrophilic<br>
+        charged (-) </td>
+      <td>GAT<br>
+        GAC</td>
+      <td><img src="aspchem.gif" width="102" height="104"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>E</td>
       <td>Glu</td>
       <td>Glutamic Acid</td>
-      <td>GAA, GAG</td>
+      <td>polar<br>
+        hydrophilic<br>
+        charged (-) </td>
+      <td>GAA<br>
+        GAG</td>
+      <td><img src="gluchem.gif" width="102" height="127"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>F</td>
       <td>Phe</td>
       <td>Phenylalanine</td>
-      <td>TTT, TTC</td>
+      <td>aromatic<br>
+        hydrophobic<br>
+        neutral</td>
+      <td>TTT<br>
+        TTC</td>
+      <td><img src="phechem.gif" width="102" height="125"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>G</td>
       <td>Gly</td>
       <td>Glycine</td>
-      <td>GGT, GGC, GGA, GGG</td>
+      <td>&nbsp;</td>
+      <td>GGT<br>
+        GGC<br>
+        GGA<br>
+        GGG</td>
+      <td><img src="glychem.gif" width="102" height="58"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>H</td>
       <td>His</td>
       <td>Histidine</td>
-      <td>CAT, CAC</td>
+      <td>aromatic<br>
+        polar<br>
+        hydrophilic<br>
+        charged (+) </td>
+      <td>CAT<br>
+        CAC</td>
+      <td><img src="hischem.gif" width="102" height="116"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>I</td>
       <td>Ile</td>
       <td>Isoleucine</td>
-      <td>ATT, ATC, ATA</td>
+      <td>aliphatic<br>
+        hydrophobic<br>
+        neutral </td>
+      <td>ATT<br>
+        ATC<br>
+        ATA</td>
+      <td><img src="ilechem.gif" width="102" height="106"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>K</td>
       <td>Lys</td>
       <td>Lysine</td>
-      <td>AAA, AAG</td>
+      <td>&nbsp;</td>
+      <td>AAA<br>
+        AAG</td>
+      <td><img src="lyschem.gif" width="102" height="152"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>L</td>
       <td>Leu</td>
       <td>Leucine</td>
-      <td>TTG, TTA, CTT, CTC, CTA, CTG</td>
+      <td>aliphatic<br>
+        hydrophobic<br>
+        neutral </td>
+      <td>TTG<br>
+        TTA<br>
+        CTT<br>
+        CTC<br>
+        CTA<br>
+        CTG</td>
+      <td><img src="leuchem.gif" width="102" height="107"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>M</td>
       <td>Met</td>
       <td>Methionine</td>
+      <td>hydrophobic<br>
+        neutral </td>
       <td>ATG</td>
+      <td><img src="metchem.gif" width="102" height="130"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>N</td>
       <td>Asn</td>
       <td>Asparagine</td>
-      <td>AAT, AAC</td>
+      <td>polar<br>
+        hydrophilic<br>
+        neutral </td>
+      <td>AAT<br>
+        AAC</td>
+      <td><img src="asnchem.gif" width="102" height="106"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>P</td>
       <td>Pro</td>
       <td>Proline</td>
-      <td>CCT, CCC, CCA, CCG</td>
+      <td>hydrophobic<br>
+        neutral</td>
+      <td>CCT<br>
+        CCC<br>
+        CCA<br>
+        CCG</td>
+      <td><img src="prochem.gif" width="65" height="93"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>Q</td>
       <td>Gln</td>
       <td>Glutamine</td>
-      <td>CAA, CAG</td>
+      <td>polar<br>
+        hydrophilic<br>
+        neutral</td>
+      <td>CAA<br>
+        CAG</td>
+      <td><img src="gluchem.gif" width="102" height="127"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>R</td>
       <td>Arg</td>
       <td>Arginine</td>
-      <td>CGT, CGC, CGA, CGG, AGA, AGG</td>
+      <td>polar<br>
+        hydrophilic<br>
+        charged (+) </td>
+      <td>CGT<br>
+        CGC<br>
+        CGA<br>
+        CGG<br>
+        AGA<br>
+        AGG</td>
+      <td><img src="argchem.gif" width="102" height="175"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>S</td>
       <td>Ser</td>
       <td>Serine</td>
-      <td>TCT, TCC, TCA, TCG, AGT, AGC</td>
+      <td>polar<br>
+        hydrophilic<br>
+        neutral </td>
+      <td>TCT<br>
+        TCC<br>
+        TCA<br>
+        TCG<br>
+        AGT<br>
+        AGC</td>
+      <td><img src="serchem.gif" width="102" height="81"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>T</td>
       <td>Thr</td>
       <td>Threonine</td>
-      <td>ACT, ACC, ACA, ACG</td>
+      <td>polar<br>
+        hydrophilic<br>
+        neutral </td>
+      <td>ACT<br>
+        ACC<br>
+        ACA<br>
+        ACG</td>
+      <td><img src="thrchem.gif" width="102" height="84"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>V</td>
       <td>Val</td>
       <td>Valine</td>
-      <td>GTT, GTC, GTA, GTG</td>
+      <td>aliphatic<br>
+        hydrophobic<br>
+        neutral </td>
+      <td>GTT<br>
+        GTC<br>
+        GTA<br>
+        GTG</td>
+      <td><img src="valchem.gif" width="102" height="84"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>W</td>
       <td>Trp</td>
       <td>Tryptophan</td>
+      <td>aromatic<br>
+        hydrophobic<br>
+        neutral</td>
       <td>TGG</td>
+      <td><img src="trpchem.gif" width="125" height="125"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>X</td>
       <td>&nbsp;</td>
       <td>UNKNOWN</td>
       <td>&nbsp;</td>
+      <td>&nbsp;</td>
+      <td>&nbsp;</td>
     </tr>
-    <tr>
+    <tr> 
       <td>Y</td>
       <td>Tyr</td>
       <td>Tyrosine</td>
-      <td>TAT, TAC</td>
+      <td>aromatic<br>
+        polar<br>
+        hydrophobic </td>
+      <td>TAT<br>
+        TAC</td>
+      <td><img src="tyrchem.gif" width="102" height="149"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>Z</td>
       <td>&nbsp;</td>
       <td>either glutamic acid or glutamine</td>
       <td>&nbsp;</td>
+      <td>&nbsp;</td>
+      <td><img src="glnchem.gif" width="102" height="130"></td>
     </tr>
-    <tr>
+    <tr> 
       <td>&nbsp;</td>
       <td>End</td>
       <td>Terminator</td>
-      <td>TAA, TAG, TGA</td>
+      <td>&nbsp;</td>
+      <td>TAA<br>
+        TAG<br>
+        TGA</td>
+      <td>&nbsp;</td>
     </tr>
   </table>
   <h2><br>