<HTML> <HEAD> <TITLE> WHE, WHEEL </TITLE> </HEAD> <BODY BACKGROUND="garlic.gif"> <FONT FACE="Times, Helvetica"> <H1 ALIGN=CENTER> <FONT SIZE=5> <B> WHE, WHEEL </B> </FONT> </H1> <HR SIZE="3"> <FONT SIZE=3 COLOR=#880000> <B> NAME <BR> </B> </FONT> <FONT SIZE=2> <B> WHE, WHEEL - draw helical wheel plot. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> SYNOPSIS <BR> </B> </FONT> <TABLE BORDER=1 CELLSPACING=1 CELLPADING=0> <TD ALIGN="left"> <FONT SIZE=2 COLOR=#004400> <B> SHORT FORM </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2 COLOR=#004400> <B> LONG FORM </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> WHE <BR> WHE CLO <BR> WHE start_index end_index <BR> WHE start_index end_index CLO <BR> WHE OFF </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> WHEEL <BR> WHEEL CLOCKWISE <BR> WHEEL start_index end_index <BR> WHEEL start_index end_index CLOCKWISE <BR> WHEEL OFF </B> </FONT> </TD> </TABLE> <BR> <FONT SIZE=3 COLOR=#880000> <B> DESCRIPTION <BR> </B> </FONT> <FONT SIZE=2> <B> Draw helical wheel plot for the given sequence or sequence fragment. Helical wheel may be used to recognize the amphiphilic character of the specified sequence fragment. The sequence from the main sequence buffer (or part of it) is used as input. Additional input: the rotation angle between adjacent residues and hydrophobicity values. The angle should correspond to certain structural motif. Default (hard-coded) angle is 100 degrees, which corresponds to alpha helix, but this may be changed to some arbitrary value, using the command ANGLE. The value of 160 degrees is suitable for beta strand and 115 or 125 is suitable for 3-10 helix. <BR><BR> While helical wheel may be drawn for any sequence length, it makes sense only for short sequence fragments (up to about twenty residues). Hydrophobic residues will be colored in shades of red, while hydrophilic residues will be colored blue. Color intensity depends on the hydrophobicity: very hydrophobic residues will be intensely red and weakly hydrophobic residues will be almost white. Very hydrophilic residues will be intensely blue and weakly hydrophilic residues will be almost white. The command SCALE may be used to select the hydrophobicity scale. <BR><BR> The command WHEEL is usually used in combination with some other commands. See the examples below. <BR><BR> <IMG SRC="wheel.gif"> <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> KEYWORDS AND PARAMETERS <BR> </B> </FONT> <FONT SIZE=2> <B> The command WHEEL may be used alone, combined with one of two keywords (OFF and CLOCKWISE) or with two residue serial indices. If used alone, the helical wheel will be drawn for the entire sequence stored in the main sequence buffer. If this sequence is large the plot will be useless. Two residue serial indices may be used to specify the residue range. <BR><BR> By default, residues are drawn counterclockwise. This arrangement of residues gives the top view of a helix. The keyword CLO (long form: CLOCKWISE) may be used to force clockwise arrangement of residues (the bottom view of a helix). <BR><BR> The keyword OFF is used to return to the main drawing mode (the structure drawing mode). <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> EXAMPLES <BR> </B> </FONT> <TABLE BORDER=2 CELLSPACING=2 CELLPADING=0> <TD ALIGN="left"> <FONT SIZE=2> <B> COMMAND </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> DESCRIPTION </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> seq = asp ile met ala glu ile <BR> scale eis <BR> angle 100 <BR> wheel </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Initialize the sequence fragment, <BR> select Eisenberg hydrophobicity scale, <BR> set angle to 100 degrees and draw <BR> helical wheel. It is assumed that <BR> that the specified sequence fragment <BR> belongs to alpha helix. </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> load 2por.pdb <BR> seq from 1 <BR> scale eis <BR> angle 160 <BR> wheel 2-10 </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Load porin coordinates, copy the sequence <BR> of this protein to the main sequence <BR> buffer, select Eisenberg hydrophobicity <BR> scale, set angle to 160 degrees and draw <BR> helical wheel for residues from 2 to 10. <BR> It is assumed that the specified sequence <BR> fragment belongs to beta strand. </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> whe clo </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Draw residues clockwise. This <BR> gives the bottom view of a helix, <BR> which is more common in books. </B> </FONT> </TD> <TR> <TD ALIGN="left"> <FONT SIZE=2> <B> whe off </B> </FONT> </TD> <TD ALIGN="left"> <FONT SIZE=2> <B> Return to default drawing mode. <BR> Instead using this command, <BR> you can hit the ESCAPE key. </B> </FONT> </TD> </TABLE> <BR> <FONT SIZE=3 COLOR=#880000> <B> NOTES <BR> </B> </FONT> <FONT SIZE=2> <B> (1) Instead using the command WHEEL OFF, the ESCAPE key may be pressed to return to the main drawing mode. <BR><BR> (2) Don't forget that WHEEL uses only the sequence stored to the main sequence buffer. Read description of the command SEQ (SEQUENCE) to learn how to initialize this buffer. <BR><BR> </B> </FONT> <FONT SIZE=3 COLOR=#880000> <B> RELATED COMMANDS <BR> </B> </FONT> <FONT SIZE=2> <B> SEQUENCE is used to copy, define or load the sequence. ANGLE defines the rotation angle between adjacent residues. SCALE is used to specify the hydrophobicity scale. <BR><BR> </B> </FONT> <HR SIZE="3"> </FONT> </BODY> </HTML>
