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// ------------------------------------------------------------

// Name, Classification, pKa(COOH), pKa(NH3+), pKa(R), TypeSideChain
var Acids = new Array(21);
var AName=0;
var AClass=1;
var ApKa1=2;
var ApKa2=3;
var ApKa3=4;
var ASide=5;
Acids[1]  = new Array("Alanine",       "N", 2.34, 9.69, 0,    "Aliphatic");
Acids[2]  = new Array("Arginine",      "B", 2.17, 9.04,12.48, "N-containing base");
Acids[3]  = new Array("Asparagine",    "P", 2.02, 8.8,  0,    "Amide");
Acids[4]  = new Array("Aspartate",     "A", 2.09, 9.82, 3.86, "Carboxylic acid");
Acids[5]  = new Array("Cysteine",      "N", 1.71,10.78, 8.33, "Thiol (S-H)");
Acids[6]  = new Array("Glutamate",     "A", 2.19, 9.67, 4.25, "Carboxylic acid");
Acids[7]  = new Array("Glutamine",     "P", 2.17, 9.13, 0,    "Amide");
Acids[8]  = new Array("Glycine",       "N", 2.34, 9.6,  0,    "Single H-atom");
Acids[9]  = new Array("Histidine",     "B", 1.82, 9.17, 6.0,  "Cyclic N-base");
Acids[10] = new Array("Isoleucine",    "N", 2.36, 9.6,  0,    "Aliphatic");
Acids[11] = new Array("Leucine",       "N", 2.36, 9.6,  0,    "Aliphatic");
Acids[12] = new Array("Lysine",        "B", 2.18, 8.95,10.79, "Amine");
Acids[13] = new Array("Methionine",    "N", 2.28, 9.21, 0,    "Thio-ether");
Acids[14] = new Array("Phenylalanine", "N", 1.83, 9.13, 0,    "Aromatic ring");
Acids[15] = new Array("Proline",       "N", 1.99,10.6,  0,    "Cyclic aliphatic");
Acids[16] = new Array("Serine",        "P", 2.21, 9.15, 0,    "Alcohol");
Acids[17] = new Array("Threonine",     "P", 2.63,10.43, 0,    "Alcohol");
Acids[18] = new Array("Tryptophan",    "N", 2.83, 9.39, 0,    "Fused aromatic rings");
Acids[19] = new Array("Tyrosine",      "P", 2.2,  9.11,10.07, "Phenol");
Acids[20] = new Array("Valine",        "N", 2.32, 9.62, 0,    "Aliphatic");


// ----------------------------------------------------------------------
// Function to display 2d picture of amino acids
// ----------------------------------------------------------------------
function Show2D()  {
   newWin = window.open("","2D Structures","status,height=805,width=639")
   newWin.document.open()
   newWin.document.write("<img src='amino20.gif' height='785' width='619'" +
          "alt='2D structure of amino acids'>")
   newWin.document.close();
   newWin.focus();
   }


// ----------------------------------------------------------------------
// Function to show summary information for any one amino acid
// ----------------------------------------------------------------------
function ShowInfo(AcidNum)  {
   var Class = "";
   if (Acids[AcidNum][AClass] == "N")  {
      Class = "Non-polar";
      }
   if (Acids[AcidNum][AClass] == "P")  {
      Class = "Polar";
      }
   if (Acids[AcidNum][AClass] == "A")  {
      Class = "Acidic";
      }
   if (Acids[AcidNum][AClass] == "B")  {
      Class = "Basic";
      }
   newWin = window.open("","InfoBox","status,height=250,width=300")
   newWin.document.open()
   newWin.document.write("<H1>" + Acids[AcidNum][AName] + "</H1>")
   newWin.document.write("<p>This amino acid is classified as <b>" + Class +
                         "</b>.<br>");
   newWin.document.write("Side Chain: <b>" + Acids[AcidNum][ASide] + "</b></p>");
   newWin.document.write("<Table Border='1'><TR Align='Center'>" +
                         "<TD>pK<sub>a</sub>(-COOH)</TD>" +
                         "<TD>pK<sub>a</sub>(-NH<sub>3</sub><sup>+</sup>)</TD>");
   if (Acids[AcidNum][ApKa3] > 0) {
      newWin.document.write("<TD>pK<sub>a</sub>(-R)</TD>");
      }
   newWin.document.write("</TR>");
   newWin.document.write("<TR Align='Center'><TD>" + Acids[AcidNum][ApKa1] +
                         "</TD><TD>" + Acids[AcidNum][ApKa2] + "</TD>");
   if (Acids[AcidNum][ApKa3] > 0) {
      newWin.document.write("<TD>" + Acids[AcidNum][ApKa3] + "</TD>");
      }
   newWin.document.write("</TR></Table>");
   newWin.document.close();
   newWin.focus();
   }


// ----------------------------------------------------------------------
// Function to show pKa values for all amino acids
// ----------------------------------------------------------------------
function ShowpKa()  {
   pKaWin = window.open("","InfoBox","status,scrollbars,resizable,height=550,width=450");
   pKaWin.document.open();
   pKaWin.document.write("<H1>pK<sub>a</sub> values for Amino Acids</H1>");
   pKaWin.document.write("<Table Border='1'><TR Align='Center'>" +
                         "<TD><b>Amino Acid</b></TD>" +
                         "<TD><b>pK<sub>a</sub>(-COOH)</b></TD>" +
                         "<TD><b>pK<sub>a</sub>(-NH<sub>3</sub><sup>+</sup>)</b></TD>");
   pKaWin.document.write("<TD><b>pK<sub>a</sub>(-R)</b></TD>");
   pKaWin.document.write("</TR>");
   for (i=1; i <= 20; i++)  {
      pKaWin.document.write("<TR Align='Center'><TD>" + Acids[i][AName] +
                            "</TD><TD>" + Acids[i][ApKa1] +
                            "</TD><TD>" + Acids[i][ApKa2] + "</TD>");
      if (Acids[i][ApKa3] > 0)  {
         pKaWin.document.write("<TD>" + Acids[i][ApKa3] + "</TD>");
         }
      else  {
         pKaWin.document.write("<TD>&nbsp;</TD>");
         }
      pKaWin.document.write("</TR>");
      }
   pKaWin.document.write("</Table>");
   pKaWin.document.close();
   pKaWin.focus();
   }

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