If after reading this documentation, you are still having difficulties using MC-HELAN, please contact MC-HELAN for support.

If you would like to view MC-HELAN analysis data files of all of the membrane proteins in the PDBTM (Current as of March 4, 2010) please click here.

MC-HELAN accurately detects and characterizes bends and disruptions in helices using a Monte Carlo algorithm. Furthermore there is no dependance on amino acid sequence for kink detection. For a description of the MC-HELAN algorithm please read our publication. If you find MC-HELAN useful for your research, please cite this work.


Preparing the MC-HELAN submission form:

Only the PDB file field  must be filled out. If your protein is transmembrane (TM) and you wish to take advantage of the added features MC-HELAN has for TM proteins, you can provide both a .xml file and PDB file from the PDB_TM. If you only provide a PDBid for MC-HELAN, a .xml file will be searched for automatically. If you supply a .xml file, be sure to supply a transformed pdb file (.trpdb) to ensure proper analysis.

If you wish to select only certain chains or models for analysis indicate this in the appropiate boxes.

If you wish, you can provide user defined helicies as a starting point for MC-HELAN. In some cases this may aid MC-HELAN in detecting a kink (especially in non-canonical helices where poor geometric criteria exclude certain areas of the helix for consideration). Only use this option if you feel it is necessary, not by default. The starting helicies that you supply to MC-HELAN will be analyzed and modified or merged with other helices as the algorithm sees fit. In order to assign starting helices, simply write the first and last residue number separated by '-'. Multiple helices are space delimited. Example input: 180-192 192-200

After you submit your data, you will be forwarded to a confirmation page. If instead you receive an error,  follow the directions of the error and resubmit.


After submission you should soon receive a link and possibly an e-mail from the MC-HELAN e-mail address directing you to a file for you to download. After unpackaging, several types of data should be visible. After submission your file will only be remain on the server for 14 days.


For the topology diagram (only generated for membrane proteins) the user may select between drawing all of the disruptions (extracellular loops) or just the disruptions which occur  within a transmembrane segment of a protein (as defined by TMDET). There is also an option to draw all of the helical segments of a protein instead of just the transmembrane ones. In addition the N-terminus of the protein can be drawn at the bottom or the top of the diagram. Note that by default the TOPDB is used to attempt to determine protein topology. If TOPDB was successfully used, the topology files will have the inside and outside surfaces of the membrane labelled.



Interpreting the MC-HELAN output:


Note that MC-HELAN will automatically analyze each protein that you submit 10 times. This default behaviour allows the user to assess the convergence of the program.

Textfiles: MC-HELAN  provides the user with text files which indicate fundamental information about  the data analyzed. Each file is unique and is summarized below.

AA_legend.txt: A legend file which summarizes all of the different residues types found in the PDB file as well as their one letter abbreviation.

Proteininfo.txt: Information about all of the proteins analyzed.

Helicalregioninfo.txt: Information about each helix found in your data.

HelicalSection_axes.txt: A summary of the helix axes observed.  For each helical section x, y and z coordinates are defined for the beginning and end of the section.

Sectioninfo.txt: Information about all of the helical sections found by MC-HELAN.

Kinkinfo.txt: A list of the kinks and disruptions detected by MC-HELAN for each protein, sorted by individual helix.

Residuefrequencies_solution.txt: Statistics about the numbers of residues found near a bend in solution proteins.

Exactresiduefrequencies_Solution.txt: Similar to above, but split up for each position before, in and after a bend.

Allkinkedsections.txt: Similar to the above file. Except that all disrupted sections are included. (Such as loops)

Residuefrequencies_solution.txt: Statistics about the numbers of residues found near a bend in solution proteins.

Exactresiduefrequencies_Solution.txt: Similar to above, but split up for each position before, in and after a bend.

Residuefrequencies_membrane_70.txt: Statistics about the numbers of residues found near a bend or disruption that is located in the central 70% of the membrane.

Exactresiduefrequencies_Membrane_70.txt: Similar to above, but split up for each position before, in and after a bend or disruption.


Textfile Headers: In each text file, you will find various headers to the columns. Below is an explanation of what each various header means:

#AAinkink: The number of amino acids in a kink.

#Helices: This is the number of helices detected in a partcular protein.

#HelicesinProt: The number of helices in the protein.

#HelSects: The number of helical sections found in this particular helix. There can be any number of helical sections separated by bends and disruptions.

#Kinkedhelices: The number of kinked helices in a particular protein.

#Kinks: The number of kinks found in a particular helix.

AAlength: The number of amino acids in a section.

Angle: In the allkinkedsections.txt file. It is the angle between the helices on either side of the kink.

AnglestoNormal: The angles of each of this helix's sections to the membrane normal. This feature only works for membrane proteins with a PDBTM entry. In the Sectioninfo.txt file this is simple called Angletonormal.

AngstromLength: The length of a section in Angstroms.

Convergence: The percentage of times that the 10 identical MC-HELAN analyses produce the same value.

CtermKink: The residue which is C-terminal to the kink.

Distfromcenter: The distance of a kink from the estimated center of the membrane. This only works for membrane proteins with a PDBTM entry.

Firstresi: The first residue of a section.

HelixID: Contains the information in the protein header plus the first and last residue numbers of the helical section.

InKink: The residues which are in the kink.

Kinkangle: The angle of a bend or disruption from being a straight line. A small angles indicates a very slight bend or disruption.

KinkID: The header of a kink. Contains the same information as the protein header plus the residues of the kink.

Kinklocation: Whether a kink is located in a globular protein (SOLUTION), in the center 70% of the membrane of a membrane protein (MEMBRANE) or near the lipid headgroup region (outer 30%) of a membrane protein (HEADGROUP).

Lastresi: The last residue of a section.

Length: The length of  a helix in angstroms.

Lengthofkink: The length of a kink in angstroms.

LocalSequence: The local sequence around the kink (4 residues on either side).

MembWidth: The membrane width based from a PDBTM entry for a protein.

Nterm: The side of the membrane that the N-terminus of the protein located on as determined by TOPDB.

Ntermkink: The residue which in N-terminal to the kink.

Protein: This identifier is the protein PDBID followed by the chain ID and model number of your protein.

ProteinType: Whether or not MC-HELAN as analyzed a protein as being membrane spanning (MEMBRANE) or globular (SOLUTION).

Side: The side of the membrane that a kink is located on as determined by TOPDB.

STDev: The standard deviation of values from 10 identical MC-HELAN analyses.

Type: The category of a helix or a kink. For helices  'GOOD' means that there are no kinks present in the helix 'BENT' means that there is at least one bend in the helix and 'DISRUPTED' meanThe number of times a residue is within one turn of a bend or in the bend.s that there is at least one disruption in the helix (and any number of bends). For kinks, the type is either a bend (change in helix axis without loss of helical character) or a disruption (change in helix axis and loss of helical character).

Headers for the residue frequency files:

#Bends_local: The number of bends with a particular residue at or within 4 residues of the bend.

#Bends_with: The number of bends which contain a particular residue.

#Bent: The number of times a residue is in a bend.

#Bent_1turn: The number of times a residue is within one turn of a bend or in the bend.

#Disrupted: The number of times a residue in in a disruption.

#Disrup_1turn: The number of times a residue is within one turn of a disruption or in the disruption.

#Disruptions_local: The number of disruptions with a particular residue at or within 4 residues of the disruption.

#Disruptions_with: The number of disrutions chich contain a particular residue.

i-4bent: The # of times a residue is at the i-4 position to a bend.

i-4disrupted: The # of time a residue is at the i-4 position to a disruption.

Residue: The residue type.

Total#: The total # of residues found in all of the helices analyzed.


Directories: Below is a description of the types of files found in each directory of the MC-HELAN analysis

disrupted/ Contains all helices which MC-HELAN has determined to have a disruption of one or more residues. Helix axes are indicated. Note that disruptions can only occur in TM helices, and show up as a separate model in the PDB file.

FullProteins/ In this directory are full length protein .pdb files. They are annotated as models, such that at each separate section (helical or ortherwise) found by MC-HELAN is its own model. Also, for sections which are helical, white points indicate the calculated helix axis of the helix.

head-bent/ In this directory are all individual helices which MC-HELAN has determined to have a definite bend which are not in the central 70% of the membrane. Each section of the helix is its own model. Also, for helical sections the calculated helix axis is indicated. To determine the location of a bend from a .pdb file, look for two adjoining secitions which share a residue. The residue which is shared is the residue assigned as bent by MC-HELAN.

good/ Conatins all helices which have neither a bend or disruption. Helix axes are indicated.

memb-bent/ In this directory are all individual helices which MC-HELAN has determined to have a definite bend in the central 70% of the membrane. Each section of the helix is its own model. Also, for helical sections the calculated helix axis is indicated. To determine the location of a bend from a .pdb file, look for two adjoining secitions which share a residue. The residue which is shared is the residue assigned as bent by MC-HELAN.
nonhelical/ Contains all membrane spanning regions defined by TMDET which do not actually have any helices in them.

Struct_summary/ Contains an alignment file of secondary structure elements for each protein. Alignment is made over all of the various models of a particular PDB. 'H' represents a helical residue while 'D' represents anything else.

topology/ Contains an output topology file from each membrane protein analyzed. In the file, each section is drawn with an accurate angle to the membrane normal. The bend angles are annotated, since these can not be acccurately represented along with the angle to the membrane normal. Helices are colored by membrane spanning section. If a helix does not belong to any membrane spanning section, it is colored black.


Topology Diagram: Each detected transmembrane helix in the protein is shown with a different color. Bends are shown as a black circle while disruptions are a line. If a helx is not transmembrane, it is colored black.