promotif2介绍

PROMOTIF v 2.0 E. Gail Hutchinson and Janet M. Thornton, Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street,London WC1E 6BT. e-mail gail@uk.ac.ucl.bioc.bsm, or gail@bsm.bioc.ucl.ac.uk (if mailing from outside uk) PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files. The current version of the program analyses the following structural features: Secondary structure Beta strands Disulphide bridges Beta bulges Beta turns Beta hairpins Gamma turns Beta alpha beta units Helical geometry Psi loops Helical interactions Beta sheet topology Main chain hydrogen bonding patterns The program also produces a summary page, which gives a briefer description of each motif found in the protein. The progran can be used to compare motifs in a group of related structures such as an ensemble of NMR structures. A description of the program and some applications has recently been published (Hutchinson & Thornton, 1996). Sample outputs for the program can be viewed on our World Wide Web page (address: http://www.biochem.ucl.ac.uk ). Availability The program is freely available for academic users. Industrial users should contact the authors directly. The files can be down loaded from our anonymous ftp server (IP address 128.40.46.11). The files are in the /pub/promotif/v2.0 directory. Please read the LICENSE file, sign it and return it to the authors. If you experience problems in accessing the files by ftp contact the authors via e-mail at one of the following addresses: gail@uk.ac.ucl.bioc.bsm or thornton@uk.ac.ucl.bioc.bsm . Installation The programs can be copied either as a single tar file (in /tar directory) or individually. The following are the source code files and their associated "parameters" files which need to be copied and compiled. Source file Parameters file p_bulge2.f p_bulge.par p_disulph2.f p_disulph.par p_hairpin2.f p_hairpin.par p_helix2.f p_helix.par p_hera2.f p_hera.par p_sheet2.f p_sheet.par p_sssum2.f p_sssum.par p_sstruc2.f p_sstruc.par p_turn2.f p_turn.par psplot2.f psplot.par psplotc.f " psrout.f " nmrconvert.f nmrconvert.par There are also a number of additional files as shown below: makefile2 this will compile the above set of programs on a Unix machine promotif2.prm the standard parameters file which can be editied by the user to control which outputs are produced and the colours to be used promotif.scr promotif_multi.scr promotif_nmr.scr these are the script files for running the program. make sure these are 'user-executable' phipsi.mat data file for Ramachandran plot hera_colours colours file for hydrogen bonding diagram It is easiest if you create a directory and copy all the files into there. Compile the programs by typing:- sh makefile2 Set up the following aliases (by adding them to your .cshrc file). setenv motifdir 'directory' alias promotif $motifdir'/promotif.scr' alias promotif_multi $motifdir'/promotif_multi.scr' alias promotif_nmr $motifdir'/promotif_nmr.scr' where directory is the directory in which you have stored the executables of the programs. Once these have been set up the program can be run from any directory. Running the program This documentation describes PROMOTIF v2.0, which can now be run in one of 3 possible modes:- (1) Single protein This takes as input a single Brookhaven format file of protein coordinates and produces a series of output files for each motif. To run this type promotif pdbfile where pdbfile is the full filename of a Brookhaven format file. The output consists of: · Various ASCII text files intended to be machine readable for further automatic processing. · Black and white postscript tables · Colour postscript schematic diagrams (2) Multiple protein This is used for processing a list of Brookhaven coordinate files. The input file is a list of Brookhaven files and this can be processed in 3 ways: Postscript (p) option This produces a series of output text and postscript files as in the single protein version for each of the proteins in the list. To do this type promotif_multi p file where file is the file containing the list of proteins.  List (l) option This produces a text file for each motif. Each file contains a list of all the examples of the particular motif found in the entire list of proteins. To do this type promotif_multi l file The files created using this option have file names in upper case: BETATURNS, GAMMATURNS, DISULPHIDES, HELICES, HELIX_INT, STRANDS, SHEETS, BULGES, HAIRPINS, BETAALPHABETA, PSILOOPS, SSSUM.  Compare (c) option This will generate all the motifs for each protein in the list and, in addition produce a postscript file in which the motifs in the different proteins are compared. To run this type promotif_multi c file Note: In the current version the program assumes that the structures in the data set are aligned with identical sequence numbers at equivalent positions in all structures. If you run this option on a list of unrelated proteins the results of the comparison will be meaningless. (3) NMR ensemble This is used for processing a file containing an ensemble of NMR structures. The program generates individual coordinate files for each of the members of the ensemble and these are then treated as in the multiple protein mode above.  Postscript (p) option This will produce a set of output postscript files giving details of the motifs in each of the members of the ensemble. To do this type promotif_nmr p nmrfile where nmrfile is a Brookhaven file containing an ensemble of NMR structures.  List (l) option This produces a flat file for each motif. Each file contains a list of all the examples of the particular motif found in the NMR ensemble. To do this type promotif_nmr l nmrfile  Compare (c) option This will generate all the motifs for each member of the ensemble and, in addition, produce a postscript file in which the motifs in the different members of the ensemble are compared. To run this type promotif_nmr c nmrfile Options The user can control which outputs are produced and the colours to be used by editing the standard parameters file promotif2.prm. There is also the option to produce all the outputs in black and white only. See Appendix I for details of how to modify this file. Details of PROMOTIF Output Most of the motifs are identified and classified according to rules defined in published papers. A more detailed description of the analysis and output for each motif follows below. Secondary Structure The program calculates the secondary structure of the protein using a local implementation (D. K. Smith, unpublished data) of the DSSP algorithm of Kabsch and Sander (1983). In the standard DSSP algorithm, a residue is included in a secondary structure only if its NH and CO groups form the appropriate hydrogen bonds or alternatively, for beta sheets only, if the CO(i-1) and NH(i+1) groups are involved in the appropriate hydrogen bonds. This gives assignments which broadly agree with IUPAC rule 6.2 (1970), which states that, to be involved in a particular secondary structure, a residue should have phi and psi values close to the ideal values for that secondary structure. The slightly modified algorithm used in this suite of programs conforms to IUPAC convention rule 6.3, according to which a residue is considered part of a beta sheet or alpha helix if either its NH or CO groups are involved in the appropriate hydrogen bonds. In practice this means that one extra residue is added to the ends of each strand and helix where possible. These extra residues are classified using lower case letters for the secondary structure, while the remainder of the residues in secondary structures are indicated using upper case letters (E for beta strands, H for alpha helices and G for 3,10 helices.). This rule is that most commonly used amongst crystallographers. The secondary structure output is given in the file pdbn.sst, where 'pdbn' represents the characters preceding the decimal point in the Brookhaven file name (i.e. usually the Brookhaven code). This secondary structure file provides the raw data used for the remainder of the analyses. Beta Turns A beta turn is defined for 4 consecutive residues (denoted by i, i+1, i+2 and i+3) if the distance between the Calpha atom of residue i and the Calpha atom of residue i+3 is less than 7 Angstroms and if the central two residues are not helical (either using the Kabsch and Sander criteria or using author defined criteria) (Lewis, 1973). The turns are assigned to one of 9 classes on the basis of the phi, psi angles of residues i+1 and i+2. The ideal angles for each of the turn types are as follows: Type Phi(i+1) Psi(i+1) Phi(i+2) Psi(i+2) I -60 -30 -90 0 II -60 120 80 0 VIII -60 -30 -120 120 I' 60 30 90 0 II' 60 -120 -80 0 VIa1 -60 120 -90 0 cis-proline(i+2) VIa2 -120 120 -60 0 cis-proline(i+2) VIb -135 135 -75 160 cis-proline(i+2) IV turns excluded from all the above categories With the exception of the type VI turns these angles were originally defined by Venkatachalam (1968). The angles for the type VI turns were originally defined by Richardson (1981). We have used the nomenclature VIa1 and VIa2 to distinguish between two subclasses of type VIa turns with the phi, psi angles of residue i+1 in the beta and polyproline region of the Ramachandran plot (Hutchinson and Thornton 1994). The phi and psi angles are allowed to vary by +/- 30 degrees from these ideal values with the added flexibility of one angle being allowed to deviate by as much as 40 degrees. Types VIa1, VIa2 and VIb turns are subject to the additional condition that residue i must be a cis-proline. Turns which do not fit any of the above criteria are classified as type IV. Promotif output data for beta turns  pdbn_bturn_tab01.ps where pdbn represents the characters before the decimal point in the file name i.e. usually the Brookhaven code of the protein. A postscript table giving details of each beta turn in the protein. From left to right are listed the sequence numbers of the first (i) and last (i+3) residues in each turn, the one-letter amino acid codes for each of the four residues in the turn, the turn type, the phi and psi angles of residues i+1 and i+2, the regions of the Ramachandran plot occuped by residues i+1 and i+2 (Appendix II). The final columns show the chi1 angles of residues i+1 and i+2 and the distance between the Calpha atoms of residues i and i+3. Once this page is full, subsequent turns are recorded in files named pdbn_bturn_tab02.ps, pdbn_bturn_tab03.ps etc.  pdbn_bturns_01.ps A set of colour postscript schematic diagrams, one for each turn. This provides a Ramachandran plot with residues i+1 and i+2 plotted on it, as well as a schematic plot of the turn with the 4 residues and the Calpha(i) to Calpha(i+3) distance marked and arrows to indicate whether or not residue i donates a hydrogen bond to residues i+3. The residue numbers and turn type are indicated above the Ramachandran plot. 16 beta turns are plotted on each page; subsequent turns are plotted in file pdbn_bturns_02.ps etc.  pdbn.bturns A flat file containing the same information as in pdbn_bturn_tab01.ps. The information is in the order: residue number and one-letter amino acid code of residues i, i+1, i+2 and i+3; turn type, Ramachandran regions of residues i+1 and i+2, phi(i+1), psi(i+1), phi(i+2), psi(i+2); Y or N to indicate whether or not a hydrogen bond is formed between the NH of residue i+3 and the CO of residue i; chi1(i+1), chi1(i+2); logical sequence number corresponding to the first residue in the turn.  BETATURNS This is the corresponding flat file created when promotif_multi or promotif_nmr is run using the list (l) option. The data are the same as above, but in addition the protein structure from which each turn was derived is given in the first column. Gamma Turns A Gamma turn is defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees of one of the following 2 classes (Rose et al., 1985, Milner-White et al, 1988): turn type phi(i+1) psi(i+1) classic 75.0 -64.0 inverse -79.0 69.0 Promotif output data for gamma turns  pdbn_gturn_tab01.ps where pdbn represents the characters before the decimal point in the file name i.e. usually the Brookhaven code of the protein. A postscript table giving details of each gamma turn in the protein. From left to right are listed the sequence numbers of the first (i) and last (i+2) residues in the turn, the one-letter amino acid codes for each of the three residues in the turn, the turn type (classic or inverse), the phi and psi angles of residue i+1 and the distance between the Calpha atoms of residues i and i+2. Once this page is full, subsequent turns are recorded in files named pdbn_gturn_tab02.ps, pdbn_gturn_tab03.ps etc.  pdbn_gturns_01.ps A set of colour postscript schematic diagrams, one for each turn. This provides a Ramachandran plot with residue i+1 plotted on it, and a schematic plot of the turn with the 3 residues and the Calpha(i)-Calpha(i+2) distance marked and arrows to indicate the i to i+2 hydrogen bond. The residue numbers and turn type are indicated above the Ramachandran plot.  pdbn.gturns A flat file containing the same information as in pdbn_gturn_tab01.ps. The information is in the order: residue number and one-letter amino acid code of residues i, i+1 and i+2, turn type, Ramachandran region of residue i+1, phi(i+1), psi(i+1); distance between the Calpha atoms of residues i and i+2; chi1(i+1); logical sequence number corresponding to the first residue in the turn.  GAMMATURNS This is the corresponding flat file created when promotif_multi or promotif_nmr is run using the list (l) option. The data are the same as above, but in addition the name of the structure in which the turn was found is recorded in the first column. Beta Bulges A beta bulge is a region of irregularity in a beta sheet, where the normal pattern of hydrogen bonding is disrupted e.g. by the insertion of an extra residue. Using the definition of beta strands and main-chain hydrogen bonds provided by the Kabsch and Sander algorithm the program identifies such irregularities and classifies them as described in Chan et al. (1993). The bulges are defined as parallel or antiparallel depending on whether they occur in parallel or antiparallel regions of beta sheet. Within each of these categories bulges are further subdivided into classic, wide, bent, G1 and special types depending on the number of residues involved and the hydrogen bonding pattern. Classic and wide bulges both involve an extra residue on one beta strand relative to its neighbouring strand. In antiparallel beta sheet the classic bulges occur where the extra residue is between two narrowly spaced pairs of hydrogen bonds, whilst in the case of the wide bulges the extra residue is between the widely spaced pairs of hydrogen bonds. Corresponding hydrogen bonding patterns for parallel classic and wide bulges can be found in Chan et al. (1993). Bent bulges occur much less frequently, and have one extra residue on both strand partners. The term special bulges is used to refer to several possible situations where there can be up to 3 extra residues in one strand. G1 bulges occur only in antiparallel sheets; in these cases residue 1 is in the alpha left conformation and is therefore usually glycine. This usually occurs at the end of a beta strand. Promotif output data for beta bulges  pdbn_bulge_tab01.ps where pdbn represents the characters before the decimal point in the file name i.e. usually the Brookhaven code of the protein. A postscript table giving details of each beta bulge in the protein. From left to right are residue numbers of residue X (on the normal strand), and residues 1 and 2 (on the bulged strand) and one letter amino acid code for each of these residues. The bulge type is described using two letters: the first letter is P or A depending on whether the bulge involves parallel or antiparallel beta strands; the second letter can be Classic, Wide, G1, Bent or Special. The final columns list the phi and psi angles of residues X, 1 and 2. At the moment just these residues are represented in the table, although there may be some additional residues involved in special bulges. These are listed in the flat file described below.  pdbn_bulges_01.ps etc Colour postscript schematic diagrams for each bulge in the protein. For each bulge there is a Ramachandran plot displaying the phi,psi angles of the residues involved in the bulge. The 'normal' residues in the bulge (X, 1 and 2) are indicated by one colour (pink in the default setting of the program), and any remaining residues (3 and 4 if they occur) are displayed in a second colour (sky blue as a default). The type of bulge is indicated above the Ramachandran plot. To the right of the Ramachandran plot there is a schematic diagram indicating the residues and hydrogen bonding in and around the beta bulge. There are 10 bulges per page; further bulges, where present are represented in subsequent files: pdbn_bulges_02.ps etc.  pdbn.blg A flat file containing the same information as in pdbn_bulge_tab01.ps.The information is in the order: bulge type indicated by two letters; (residue number, one letter amino acid code, phi, psi) of residues X, 1, 2, 3 and 4. Most of the bulges will have just residues X, 1 and 2; the special bulges may have one or more of residues 3 and 4, and the bent bulges will just have residues 1 and 2. If the residues are not present in a given bulge their phi and psi angles are given as -999.9. (The final numbers in each row give sequential numbering of the residues in the bulge, for use by the plotting program).  BULGES This is the corresponding flat file created when promotif_multi or promotif_nmr is run using the list (l) option. The data are the same as above, but in addition the name of the structure in which the bulge was found is recorded in the first column. Helices The helix terminii and helix type are identified directly from the secondary structure assignment program. Promotif output data for helices  pdbn_helix_tab01.ps where pdbn represents the characters before the decimal point in the file name i.e. usually the Brookhaven code of the protein. A postscript table giving details of each helix in the protein. The helices are numbered consecutively from the N-terminus to allow helix interactions to be described. The start and end residues of each helix, helix type (alpha or 3,10), number of residues and amino acid sequence are given for each helix.  pdbn_helix_geom01.ps A postscript table giving details of the geometry of each alpha helix. From left to right are the helix number, the length and unit rise (both in Angstroms), the number of residues per turn (ideally 3.6 for alpha helices), the helix pitch in Angstroms and a measure of the deviation of the helix geometry from an ideal helix (in degrees). This latter value should be 0 for a perfect helix. These parameters are not calculated for helices with less than four residues.  pdbn_helix_diag01.ps A colour postscript file providing schematic diagrams - helical wheels and helical nets for each helix. The residues are colour coded for hydrophobic (green as default), polar (blue) and ch