BioPHP - Protein sequence information (original)
Original code submitted by josebaCode bellow is covered by GNU GPL v2 license.
Description
Last change: 2006/01/13 21:40 | Recent ChangesThe following may be computed: Aminoacid composition, Molecular weight, Molar absorption coefficient, Protein isoelectric point and Charge. It also allows geting a colored sequence based in nature of each aminoacid.
Code
Last change: 2006/01/13 21:40 | Download original | Recent Changes | Original code and
<html>
<head>
<title>Protein sequence information</title>
</head>
<body bgcolor=FFFFFF>
<center>
<?
// author Joseba Bikandi
// license GNU GPL v2
// Developers: consider adding new options to the form
// the code in the top will manipulated the input protein sequence
// in the middle of the file is located the form
// in the bottom are located the functions used in this script
//############################################################################
//################# lets manipulated the sequence #################
//############################################################################
if ($_SERVER["QUERY_STRING"]=="info"){
print_information();die();
}elseif($_POST){
$seq=$_POST["seq"];
$pH=$_POST["pH"];
$data_source=$_POST["data_source"];
$result="";
// remove non coding (works by default)
$seq=remove_non_coding_prot($seq);
// we will save the original sequence, just in case subsequence is used
$original_seq = chunk_split($seq, 70);
// if subsequence is requested
if ($_POST["start"] or $_POST["end"]){
if($_POST["start"]!=""){$start=$_POST["start"]-1;}else{$start=0;}
if($_POST["end"]!=""){$end=$_POST["end"];}else{$end=strlen($seq);}
$seq=substr($seq,$start,$end-$start);
$result.="<p><b>Subsequence used for calculations:</b><br>".chunk_split($seq, 70);
}
// length of sequence
$seqlen=strlen($seq);
// compute requested parameter
if ($_POST["composition"]==1 or $_POST["molweight"]==1 or $_POST["abscoef"]==1 or $_POST["charge"]==1 or $_POST["charge2"]==1){
// calculate nucleotide conposition
$aminoacid_content=aminoacid_content($seq);
// prepare nucleotide composition to be printed out
if ($_POST["composition"]==1){
$result.="<p><b>Aminoacid composition of protein:</b><br>".print_aminoacid_content($aminoacid_content);
}
}
if ($_POST["molweight"]==1 or $_POST["abscoef"]==1){
// calculate molecular weight of protein
$molweight=protein_molecular_weight($seq,$aminoacid_content);
if ($_POST["molweight"]==1){
$result.="<p><b>Molecular weight:</b><br>$molweight Daltons";
}
}
if ($_POST["abscoef"]==1){
$abscoef=molar_absorption_coefficient_of_prot($seq,$aminoacid_content,$molweight);
$result.="<p><b>Molar Absorption Coefficient at 280 nm:</b><br>".round($abscoef,2);
}
if ($_POST["charge"]==1){
// get pk values for charged aminoacids
$pK=pK_values ($data_source);
// calculate isoelectric point of protein
$charge=protein_isoelectric_point($pK,$aminoacid_content);
$result.="<p><b>Isoelectric point of sequence ($data_source):</b><br>".round($charge,2);
}
if ($_POST["charge2"]==1){
// get pk values for charged aminoacids
$pK=pK_values ($data_source);
// calculate charge of protein at requested pH
$charge=protein_charge($pK,$aminoacid_content,$pH);
$result.="<p><b>Charge of sequence at pH = $pH ($data_source):</b><br>".round($charge,2);
}
// colored sequence based in plar/non-plar/charged aminoacids
if ($_POST["3letters"]==1){
// get the colored sequence (html code)
$three_letter_code=seq_1letter_to_3letter($seq);
// add to result
$result.="<p><b>Sequence as three letters aminoacid code:</b><br>".$three_letter_code;
}
// 50 characters per line before output
$seq = chunk_split($seq, 70);
// colored sequence based in polar/non-plar/charged aminoacids
if ($_POST["type1"]==1){
// get the colored sequence (html code)
$colored_seq=protein_aminoacid_nature1($seq);
// add to result
$result.="<p><b><font color=Magenta>Polar</font>, <font color=yellow>Nonpolar</font></b> or <b><font color=red>Charged</font></b> aminoacids:<br>".$colored_seq;
}
// colored sequence based in polar/non-plar/charged aminoacids
if ($_POST["type2"]==1){
// get the colored sequence (html code)
$colored_seq=protein_aminoacid_nature2($seq);
// add to result
$result.="<p><b><font color=magenta>Polar</font>, <font color=yellow>small non-polar</font>, <font color=green>hydrophobic</font>, <font color=red>negatively</font></b> or <b><font color=blue>positively</font> charged</b> aminoacids:<br>".$colored_seq;
}
}else{
$seq="ARNDCEQGHILKMFPSTWYVX*";
$original_seq=$seq;
$seqlen=strlen($seq);
$pH=7.0;
}
//############################################################################
//################# we have already manipulated the sequence #################
//############################# bellow is the form ###########################
//############################################################################
?>
<H2>Protein sequence information</H2>
<form method='post' action="<? print $_SERVER["PHP_SELF"]; ?>">
<table cellpadding=5 width=650 border=0 bgcolor=DDFFFF>
<tr><td>
<B>Sequence <?php if($seq){print "(length: $seqlen)";} ?>:</B>
</td></tr>
<tr><td>
<textarea name='seq' rows='4' cols='80'><?php print $original_seq; ?></textarea>
</td></tr>
<tr><td>
Select subsequence from position <input type=text name=start size=4 value="<? if ($_POST["start"]==1){print $_POST["start"];} ?>"> to <input type=text name=end size=4 value="<? if ($_POST["end"]==1){print $_POST["end"];} ?>"> (both included) for computation
<hr><input type=checkbox name=composition value=1<? if ($_POST["composition"]==1){print " checked";} ?>>Aminoacid composition
<br><input type=checkbox name=molweight value=1<? if ($_POST["molweight"]==1){print " checked";} ?>>Molecular weight
<br><input type=checkbox name=abscoef value=1<? if ($_POST["abscoef"]==1){print " checked";} ?>>Molar absorption coefficient
<br><input type=checkbox name=charge value=1<? if ($_POST["charge"]==1){print " checked";} ?>>Protein isoelectric point with pK values from
<select name=data_source>
<option<? if ($data_source=="EMBOSS"){print " selected";} ?>>EMBOSS
<option<? if ($data_source=="DTASelect"){print " selected";} ?>>DTASelect
<option<? if ($data_source=="Solomon"){print " selected";} ?>>Solomon
</select>
<br><input type=checkbox name=charge2 value=1<? if ($_POST["charge2"]==1){print " checked";} ?>>Charge at pH = <input type=text name=pH value="<? print $pH ?>" size=4>
<br><input type=checkbox name=3letters value=1<? if ($_POST["3letters"]==1){print " checked";} ?>>Show sequence as 3 letters aminoacid code
<br><input type=checkbox name=type1 value=1<? if ($_POST["type1"]==1){print " checked";} ?>>Show polar, non-polar and charged nature of aminoacids
<br><input type=checkbox name=type2 value=1<? if ($_POST["type2"]==1){print " checked";} ?>>Show polar, non-polar, Hydrofobic, and negatively or positively charged nature of aminoacids
</td></tr>
<tr><td align=center>
<input type='submit' value='Sutmit'>
<div align=right><a href=?info>Info</a></div>
</td></tr>
<?php if($result!=""){print "<tr><td bgcolor=FFFFFF><pre>$result</pre></td></tr>";} ?>
</table>
</form>
<?php
//############################################################################
//####################### The form is finished ##############################
//############################################################################
//############################################################################
//################# Functions used in this script ############################
//############################################################################
function remove_non_coding_prot($seq) {
// change the sequence to upper case
$seq=strtoupper($seq);
// remove non-coding characters([^ARNDCEQGHILKMFPSTWYVX\*])
$seq = preg_replace ("([^ARNDCEQGHILKMFPSTWYVX\*])", "", $seq);
return $seq;
}
function protein_isoelectric_point($pK, $aminoacid_content) {
// At isoelectric point, charge of protein will be 0
// To calculate pH where charge is 0 a loop is required
// The loop will start computing charge of protein at pH=7, and if charge is not 0, new charge value will be computed
// by using a different pH. Procedure will be repeated until charge is 0 (at isoelectric point)
$pH=7; // pH value at start
$delta=4; // this parameter will be used to modify pH when charge!=0. The value of $delta will change during the loop
while(1) {
// compute charge of protein at corresponding pH (uses a function)
$charge=protein_charge($pK,$aminoacid_content,$pH);
// check whether $charge is 0 (consecuentely, pH will be the isoelectric point
if (round($charge,4)==0){break;}
// next line to check how computation is perform
// print "<br>$charge\t$pH";
// modify pH for next round
if ($charge > 0) {$pH = $pH + $delta;}else{$pH = $pH - $delta;}
// reduce value for $delta
$delta = $delta/2;
}
// return pH at which charge=0 (the isoelectric point) with two decimals
return round($pH,2);
}
function partial_charge($val1,$val2){
// compute concentration ratio
$cr=pow(10,$val1-$val2);
// compute partial charge
$pc=$cr/($cr+1);
return $pc;
}
// computes protein charge at corresponding pH
function protein_charge($pK,$aminoacid_content,$pH){
$charge = partial_charge($pK["N_terminus"],$pH);
$charge+= partial_charge($pK["K"],$pH)*$aminoacid_content["K"];
$charge+= partial_charge($pK["R"],$pH)*$aminoacid_content["R"];
$charge+= partial_charge($pK["H"],$pH)*$aminoacid_content["H"];
$charge-= partial_charge($pH,$pK["D"])*$aminoacid_content["D"];
$charge-= partial_charge($pH,$pK["E"])*$aminoacid_content["E"];
$charge-= partial_charge($pH,$pK["C"])*$aminoacid_content["C"];
$charge-= partial_charge($pH,$pK["Y"])*$aminoacid_content["Y"];
$charge-= partial_charge($pH,$pK["C_terminus"]);
return $charge;
}
function pK_values ($data_source){
// pK values for each component (aa)
if ($data_source=="EMBOSS"){
$pK=array(
"N_terminus"=>8.6,
"K"=>10.8,
"R"=>12.5,
"H"=>6.5,
"C_terminus"=>3.6,
"D"=>3.9,
"E"=>4.1,
"C"=>8.5,
"Y"=>10.1
);
}elseif ($data_source=="DTASelect"){
$pK=array(
"N_terminus"=>8,
"K"=>10,
"R"=>12,
"H"=>6.5,
"C_terminus"=>3.1,
"D"=>4.4,
"E"=>4.4,
"C"=>8.5,
"Y"=>10
);
}elseif ($data_source=="Solomon"){
$pK=array(
"N_terminus"=>9.6,
"K"=>10.5,
"R"=>125,
"H"=>6.0,
"C_terminus"=>2.4,
"D"=>3.9,
"E"=>4.3,
"C"=>8.3,
"Y"=>10.1
);
}
return $pK;
}
function print_aminoacid_content($aminoacid_content) {
$results="";
foreach($aminoacid_content as $aa => $count){
$results.="$aa\t".seq_1letter_to_3letter ($aa)."\t$count\n";
}
return $results;
}
function aminoacid_content($seq) {
$array=array("A"=>0,"R"=>0,"N"=>0,"D"=>0,"C"=>0,"E"=>0,"Q"=>0,"G"=>0,"H"=>0,"I"=>0,"L"=>0,
"K"=>0,"M"=>0,"F"=>0,"P"=>0,"S"=>0,"T"=>0,"W"=>0,"Y"=>0,"V"=>0,"X"=>0,"*"=>0);
for($i=0; $i<strlen($seq);$i++){
$aa=substr($seq,$i,1);
$array[$aa]++;
}
return $array;
}
function molar_absorption_coefficient_of_prot($seq,$aminoacid_content,$molweight) {
// Prediction of the molar absorption coefficient of a protein
// Pace et al. . Protein Sci. 1995;4:2411-23.
$abscoef = ($aminoacid_content["A"]*5500 + $aminoacid_content["Y"]*1490 + $aminoacid_content["C"]*125)/$molweight;
return $abscoef;
}
// molecular weight calculation
function protein_molecular_weight ($seq,$aminoacid_content){
$molweight = $aminoacid_content["A"]*71.07; // for Alanine
$molweight+= $aminoacid_content["R"]*156.18; // for Arginine
$molweight+= $aminoacid_content["N"]*114.08; // for Asparagine
$molweight+= $aminoacid_content["D"]*115.08; // for Aspartic Acid
$molweight+= $aminoacid_content["C"]*103.10; // for Cysteine
$molweight+= $aminoacid_content["Q"]*128.13; // for Glutamine
$molweight+= $aminoacid_content["E"]*129.11; // for Glutamic Acid
$molweight+= $aminoacid_content["G"]*57.05; // for Glycine
$molweight+= $aminoacid_content["H"]*137.14; // for Histidine
$molweight+= $aminoacid_content["I"]*113.15; // for Isoleucine
$molweight+= $aminoacid_content["L"]*113.15; // for Leucine
$molweight+= $aminoacid_content["K"]*128.17; // for Lysine
$molweight+= $aminoacid_content["M"]*131.19; // for Methionine
$molweight+= $aminoacid_content["F"]*147.17; // for Phenylalanine
$molweight+= $aminoacid_content["P"]*97.11; // for Proline
$molweight+= $aminoacid_content["S"]*87.07; // for Serine
$molweight+= $aminoacid_content["T"]*101.10; // for Threonine
$molweight+= $aminoacid_content["W"]*186.20; // for Tryptophan
$molweight+= $aminoacid_content["Y"]*163.17; // for Tyrosine
$molweight+= $aminoacid_content["Z"]*99.13; // for Valine
$molweight+= 18.02; // water
$molweight+= $aminoacid_content["X"]*114.822; // for unkwon aminoacids, add avarage of all aminoacids
return $molweight;
}
// this function has not been used in this script, but may be interesting for you
function identify_aminoacid_complete_name ($aa){
$aa=strtoupper($aa);
if (strlen($aa)==1){
if ($aa=="A"){return "Alanine";}
if ($aa=="R"){return "Arginine";}
if ($aa=="N"){return "Asparagine";}
if ($aa=="D"){return "Aspartic Acid";}
if ($aa=="C"){return "Cysteine";}
if ($aa=="E"){return "Glutamic Acid";}
if ($aa=="Q"){return "Glutamine";}
if ($aa=="G"){return "Glycine";}
if ($aa=="H"){return "Histidine";}
if ($aa=="I"){return "Isoleucine";}
if ($aa=="L"){return "Leucine";}
if ($aa=="K"){return "Lysine";}
if ($aa=="M"){return "Methionine";}
if ($aa=="F"){return "Phenylalanine";}
if ($aa=="P"){return "Proline";}
if ($aa=="S"){return "Serine";}
if ($aa=="T"){return "Threonine";}
if ($aa=="W"){return "Tryptophan";}
if ($aa=="Y"){return "Tyrosine";}
if ($aa=="V"){return "Valine";}
}elseif (strlen($aa)==3){
if ($aa=="ALA"){return "Alanine";}
if ($aa=="ARG"){return "Arginine";}
if ($aa=="ASN"){return "Asparagine";}
if ($aa=="ASP"){return "Aspartic Acid";}
if ($aa=="CYS"){return "Cysteine";}
if ($aa=="GLU"){return "Glutamic Acid";}
if ($aa=="GLN"){return "Glutamine";}
if ($aa=="GLY"){return "Glycine";}
if ($aa=="HIS"){return "Histidine";}
if ($aa=="ILE"){return "Isoleucine";}
if ($aa=="LEU"){return "Leucine";}
if ($aa=="LYS"){return "Lysine";}
if ($aa=="MET"){return "Methionine";}
if ($aa=="PHE"){return "Phenylalanine";}
if ($aa=="PRO"){return "Proline";}
if ($aa=="SER"){return "Serine";}
if ($aa=="THR"){return "Threonine";}
if ($aa=="TRP"){return "Tryptophan";}
if ($aa=="TYR"){return "Tyrosine";}
if ($aa=="VAL"){return "Valine";}
}
}
function seq_1letter_to_3letter ($seq){
$seq = chunk_split($seq,1,'#');
$seq = chunk_split($seq, 40);
for($i=0; $i<strlen($seq); $i++){
$seq = preg_replace ("(A\#)","Ala", $seq);
$seq = preg_replace ("(R\#)","Arg", $seq);
$seq = preg_replace ("(N\#)","Asp", $seq);
$seq = preg_replace ("(D\#)","Asn", $seq);
$seq = preg_replace ("(C\#)","Cys", $seq);
$seq = preg_replace ("(E\#)","Glu", $seq);
$seq = preg_replace ("(Q\#)","Gln", $seq);
$seq = preg_replace ("(G\#)","Gly", $seq);
$seq = preg_replace ("(H\#)","His", $seq);
$seq = preg_replace ("(I\#)","Ile", $seq);
$seq = preg_replace ("(L\#)","Leu", $seq);
$seq = preg_replace ("(K\#)","Lys", $seq);
$seq = preg_replace ("(M\#)","Met", $seq);
$seq = preg_replace ("(F\#)","Phe", $seq);
$seq = preg_replace ("(P\#)","Pro", $seq);
$seq = preg_replace ("(S\#)","Ser", $seq);
$seq = preg_replace ("(T\#)","Thr", $seq);
$seq = preg_replace ("(W\#)","Trp", $seq);
$seq = preg_replace ("(Y\#)","Tyr", $seq);
$seq = preg_replace ("(V\#)","Val", $seq);
$seq = preg_replace ("(X\#)","XXX", $seq);
$seq = preg_replace ("(\*\#)","*** ", $seq);
}
return $seq;
}
function protein_aminoacid_nature1($seq){
$result="";
for($i=0; $i<strlen($seq); $i++){
// non-polar aminoacids, magenta
if (strpos(" GAPVILFM",substr($seq,$i,1))>0){$result.="<font color=yellow>".substr($seq,$i,1)."</font>";continue;}
// polar aminoacids, magenta
if (strpos(" SCTNQHYW",substr($seq,$i,1))>0){$result.="<font color=magenta>".substr($seq,$i,1)."</font>";continue;}
// charged aminoacids, red
if (strpos(" DEKR",substr($seq,$i,1))>0){$result.="<font color=red>".substr($seq,$i,1)."</font>";continue;}
}
return $result;
}
function protein_aminoacid_nature2($seq){
$result="";
for($i=0; $i<strlen($seq); $i++){
// Small nonpolar (yellow)
if (strpos(" GAST",substr($seq,$i,1))>0){$result.="<font color=yellow>".substr($seq,$i,1)."</font>";continue;}
// Small hydrophobic (green)
if (strpos(" CVILPFYMW",substr($seq,$i,1))>0){$result.="<font color=green>".substr($seq,$i,1)."</font>";continue;}
// Polar
if (strpos(" DQH",substr($seq,$i,1))>0){$result.="<font color=magenta>".substr($seq,$i,1)."</font>";continue;}
// Negatively charged
if (strpos(" NE",substr($seq,$i,1))>0){$result.="<font color=red>".substr($seq,$i,1)."</font>";continue;}
// Positively charged
if (strpos(" KR",substr($seq,$i,1))>0){$result.="<font color=red>".substr($seq,$i,1)."</font>";continue;}
}
return $result;
}
// Chemical group/aminoacids:
// L/GAVLI Amino Acids with Aliphatic R-Groups
// H/ST Non-Aromatic Amino Acids with Hydroxyl R-Groups
// M/NQ Acidic Amino Acids
// R/FYW Amino Acids with Aromatic Rings
// S/CM Amino Acids with Sulfur-Containing R-Groups
// I/P Imino Acids
// A/DE Acidic Amino Acids
// C/KRH Basic Amino Acids
// */*
// X/X
function protein_aminoacids_chemical_group($amino_seq){
$chemgrp_seq = "";
$ctr = 0;
while(1)
{
$amino_letter = substr($amino_seq, $ctr, 1);
if ($amino_letter == "") break;
if (strpos(" GAVLI", $amino_letter)>0) $chemgrp_seq .= "L";
elseif (($amino_letter == "S") or ($amino_letter == "T")) $chemgrp_seq .= "H";
elseif (($amino_letter == "N") or ($amino_letter == "Q")) $chemgrp_seq .= "M";
elseif (strpos(" FYW", $amino_letter)>0) $chemgrp_seq .= "R";
elseif (($amino_letter == "C") or ($amino_letter == "M")) $chemgrp_seq .= "S";
elseif ($amino_letter == "P") $chemgrp_seq .= "I";
elseif (($amino_letter == "D") or ($amino_letter == "E")) $chemgrp_seq .= "A";
elseif (($amino_letter == "K") or ($amino_letter == "R") or ($amino_letter == "H"))
$chemgrp_seq .= "C";
elseif ($amino_letter == "*") $chemgrp_seq .= "*";
elseif ($amino_letter == "X" or $amino_letter == "N") $chemgrp_seq .= "X";
else die("Invalid amino acid symbol in input sequence.");
$ctr++;
}
return $chemgrp_seq;
}
function print_information (){
?>
<table width=600><tr><td>
<b>NOTES</b>:
<br>Non-coding characters will be removed by default.
<br><a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7957164&dopt=abstract>NC-UIBMB</a> codes are used as a reference.
<p>
<b>Computation</b>:
<br>Molecular Weight:
<pre> MW =(A*71.07)+(R*156.18)+(nN*114.08)+(nD*115.08)+(nC*103.10)+
+(nQ*128.13)+(nE*129.11)+(nG*57.05)+(nH*137.14)+(nI*113.15)+
+(nL*113.15)+(nK*128.17)+(nM*131.19)+(nF*147.17)+(nP*97.11)+
+(nS*87.07)+(nT*101.10)+(nW*186.20)+(nY*163.17)+(nV*99.13)+18.02</pre>
<p>Molar absorption coefficient: <a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8563639>Pace et al., 1995</a>
<p>Isoelectric point estimation: <a href=http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf>Tabb D., 2003</a>
<p>Type of aminoacid (1):
<br> Polar: SCTNQHYW
<br> Non-Polar: GAPVILFM
<br> Charged: DEKR
<p>Type of aminoacid (2):
<br> Small non-polar: SCTNQHYW (Yellow)
<br> Hydrophobic: CVILPFYMW (Green)
<br> Polar: DQH (Magenta)
<br> Negatively charged: NE (Red)
<br> Positively charged: KR (Blue)
<hr>
<a href="<? print $_SERVER["PHP_SELF"]; ?>">Use the tool</a>
</td></tr></table>
<?
}
//############################################################################
//############################### End of fuctions ############################
//############################################################################
?>
<br>Source code is available at <a href=http://www.biophp.org/minitools/protein_properties>BioPHP.org</a>
</center>
</body>
</html>