L I G P L O T
v . 2 . 0
------------------------Operating manual
A program to plot schematic diagrams of protein-ligand interactions
Andrew C Wallace & Roman A Laskowski
C o n t e n t s
--------------1.
2.
3.
4.
5.
Introduction
How to run LIGPLOT
Inputs to LIGPLOT
Outputs produced by LIGPLOT
Customizing LIGPLOT - amending the ligplot.par parameter
file
6. Improving the plots
7. Adding/removing H-bonds and hydrophobic interactions
Appendix A - Brookhaven file format
Appendix B - LIGPLOT file formats
1. INTRODUCTION
--------------These Operating Instructions describe how to run the LIGPLOT program
(Wallace et al., 1995).
The program automatically generates schematic diagrams of interactions in
proteins from the 3D coordinates alone. (Some examples are given here).
It
is particularly useful for comparing different structures, such as the
interactions of different ligands with the same enzyme.
The inputs to LIGPLOT comprise:
*
the PDB file (Bernstein et al., 1977) holding the
coordinates of the structure of interest,
*
a list of hydrogen-bonds and
*
a list of hydrophobic contacts within the structure.
The latter two lists can be automatically generated using the HBPLUS
program which is supplied separately from LIGPLOT, and is described
elsewhere (McDonald & Thornton, 1994). A parameter file, called
ligplot.par can be edited to alter the parameters that control the
appearance of the plot generated - eg colours, text sizes, etc (see
section
5).
The outputs from LIGPLOT include:
* the PostScript file showing the plotted schematic diagram, and
* various files that allow the diagram to be amended to the user's
requirements (see section 6).
The LIGPLOT algorithm is described in detail in Wallace et al. (1995). In
principle, it takes the 3D structure of the ligand and "unrolls" it about
its rotatable bonds, flattening it out onto the 2D page. As it does so,
it
takes with it the hydrogen-bonded sidechains and sidechains involved in
hydrophobic contacts, flattening those out too and placing them so that
the
overlap of atoms and the crossing of bonds in the final diagram is kept
to
a minumum.
2. HOW TO RUN LIGPLOT
--------------------a. To run LIGPLOT with HBPLUS
-------------------------To run LIGPLOT, with all hydrogen bonds and hydrophobic contacts
computed by HBPLUS, type the following:
ligplot filename [residue1] [residue2] [chain_id] [-h]
where:
filename is the name of the file containing your protein structure
and should contain the full path unless your structure is in the
default directory. The file must be in full Brookhaven Format (see
Appendix A).
[residue1] and [residue2] is the residue range for the ligand.
[chain_id] is the ligand's chain identifier (optional).
[-h] indicates that you would like to enter a heading for the
output
plot (the program will prompt you to enter the heading).
This assumes you have installed both LIGPLOT and HBPLUS according to the
installation instructions.
For example, to run a LIGPLOT for 6tmn, in which the ligand has a range
of
1 to 4 with chain identifier I, you might type:
ligplot /data/pdb/p6tmn.pdb 1 4 I
Alternatively, if the ligand range is unknown, you can omit the optional
parameters and enter:
ligplot /data/pdb/p6tmn.pdb
In this case, the program will search through the PDB file 6tmn and will
produce a list of chain and ligand ranges. It will then prompt you to
enter one of these residue ranges as the ligand.
b. LIGONLY - running LIGPLOT on its own
-----------------------------------If you do not have HBPLUS, or wish to use your own list of hydrogen bonds
and hydrophobic contacts (see Appendix B), you can run just LIGPLOT on
its
own by typing:
ligonly filename [residue1] [residue2] [chain_id] [-h]
The parameters are as before.
The LIGONLY script is also useful where you have just run LIGPLOT and now
want to generate a new plot (say having slightly modified the parameters
in
the ligplot.par file - see section 5). This saves running HBPLUS and
recalculating all the hydrogen bonds and hydrophobic contacts.
3. INPUTS TO LIGPLOT
-------------------The input files to LIGPLOT are:
* filename.pdb - Input PDB file holding the coordinates of the protein
and ligand.
* filename.hhb - List of hydrogen bonds, either generated by HBPLUS,
or
supplied in LIGPLOT format (see Appendix B).
* filename.nnb - List of non-bonded, hydrophobic contacts, either
generated by HBPLUS, or supplied in LIGPLOT format (see Appendix B).
* ligplot.par - Parameter file containing parameters governing the
production of the plot (see section 5).
Note that, for the PDB file, the file extension does not need to be
.pdb. It can be anything other that .hhb, .nnb or .par. The extensions
for
the .hhb and .nnb files must be as stated, otherwise LIGPLOT will not be
able to find the files.
4. OUTPUTS PRODUCED BY LIGPLOT
-----------------------------The output files produced by LIGPLOT are:
* ligplot.ps - Colour or black-and-white PostScript output
file of the plot.
* ligplot.pdb - Output file in PDB format of the final flattened
molecules (ligand and interacting protein residues) as shown in the
plot.
* ligplot.hhb - Output file, in LIGPLOT format, of just those hydrogen
bonds in the original filename.hhb file that were used by LIGPLOT in
producing the final picture.
* ligplot.nnb - Output file, in LIGPLOT format, of just those
hydrophobic contacts in the original filename.nnb file that were
used
by LIGPLOT in producing the final picture.
* ligplot.bonds - Output file listing of bonds and bond-types in the
final LIGPLOT picture.
* ligplot.frm - Output file in PDB format of the molecules shown in
the
plot, prior to flattening.
5. CUSTOMIZING LIGPLOT - AMENDING THE ligplot.par PARAMETER FILE
---------------------------------------------------------------The plots produced by LIGPLOT can be customised by amending the parameter
file called ligplot.par. The file is created in the default directory
when
you first run LIGPLOT. You can then edit it with any text editor.
The file contains a number of keywords, in capitals, below which the
parameters are entered. The keywords are:-
1. PRINT OPTIONS
2. PLOT PARAMETERS
3. LINKED RESIDUES
4. SIZES
5. TEXT SIZES
6. COLOURS
7. TEXT COLOURS
8. COLOUR DEFINITIONS
9. MINIMIZATION PARAMETERS
Other text can be inserted anywhere in the file and will be ignored
provided that it is not in the block of parameters directly associated
with
one of these keywords.
Throughout the file are various notes to assist you during editing.
1. PRINT OPTIONS
------------There are two print options, as follows:PRINT OPTIONS
------------Y
<- Produce a colour PostScript file (Y/N)?
P
<- Orientation of plot: (P)ortrait or (L)andscape?
Description of options:---------------------Produce a colour PostScript file (Y/N)? - The first option defines
whether
a colour or a black-and-white PostScript file is to be generated.
Orientation of plot: (P)ortrait or (L)andscape? - The second option
defines
whether the orientation of the plot on the page is to be Portrait or
Landscape.
2. PLOT PARAMETERS
--------------There are 16 plot parameters, as follows:-
PLOT PARAMETERS
--------------Y
<- Include: Hydrophobic interactions - (Y/N)?
N
<- Include: Water molecules - (Y/N)?
Y
<- Include: Non-ligand mainchain atoms - (Y/N)?
N
<- Include: Linked residues listed below - (Y/N)?
Y
<- Plot: Hydrogen bonds - (Y/N)?
N
<- Plot: Internal H-bonds in ligand - (Y/N)?
N
<- Plot: Simple ligand representation [see Note 1] - (Y/N)?
N
<- Plot: Accessibility shading [see Note 2] - (Y/N)?
Y
<- Plot: Ligand atoms (as spheres) - (Y/N)?
Y
<- Plot: Nonligand atoms (as spheres) - (Y/N)?
Y
<- Plot: Double- and triple bonds (for ligplot.pdb only) - (Y/N)?
Y
<- Print: Key to symbols in PostScript output - (Y/N)?
Y
<- Print: Residue names/numbers - (Y/N)?
Y
<- Print: Atom names - (Y/N)?
Y
<- Print: H-bond lengths on hydrogen bonds - (Y/N)?
Y
<- Print: Filename as title if title not explicitly defined (Y/N)?
Description of the parameters:----------------------------Include: Hydrophobic interactions - (Y/N)? The first option defines
whether
all hydrophobic interactions between the protein and the ligand are to
be shown on the plot.
Include: Water molecules - (Y/N)? The second option defines whether any
water molecules hydrogen-bonded to the ligand are to be shown on the
plot.
Include: Non-ligand mainchain atoms - (Y/N)? This option defines whether
the mainchain atoms of the non ligand residues are to be shown on the
plot.
Include: Linked residues listed below - (Y/N)? This option allows you to
include any residues that are not directly hydrogen-bonded to the
ligand
but which are indirectly connected via another residue (or water
molecule) which is hydrogen-bonded to the ligand.
For example, in the enzyme active sites of the serine proteases the
His-Asp pair is essential for catalytic activity. Here the His is
hydrogen bonded to the ligand whereas the Asp is hydrogen bonded to
the
His and not to the ligand (as for His 57 and Asp 102 in chymotrypsin).
By setting the Linked residues to Y here, you can then define which
linked residues you want included in the plot (see LINKED RESIDUES).
Plot: Hydrogen bonds - (Y/N)? This option defines whether hydrogen bond
interactions between the ligand and the protein are to be shown on the
plot.
Plot: Internal H-bonds in ligand - (Y/N)? This option defines whether
internal hydrogen bonds within the ligand itself are to be shown on
the
plot. Generally, however, these comlicate the diagram unnecessarily.
Plot: Simple ligand representation - (Y/N)? This option may be useful if
the ligand is large (for example a peptide). It prints out the ligand
residues as circles and the non ligand residues just have their names
and atom identifiers printed out. Ligand sidechains not involved in
hydrogen bonds are not shown.
Plot: Accessibility shading - (Y/N)? This option defines whether the
solvent accessibilities of the ligand atoms are to be shown on the
plot. The accessibilities are represented by the shading behind each
ligand atom. Solvent accessibilities can be calculated by running the
NACCESS program. This generates an .asa file, and LIGPLOT should then
be
run on this .asa file in place of the original .pdb file. (If LIGPLOT
is
run on an ordinary PDB file, the values in the B-value column will be
taken to be accessibilities).
Plot: Ligand atoms (as spheres) - (Y/N)? This option defines whether the
ligand atoms are to be shown on the plot (if this option is set to N,
only the ligand bonds will be shown).
Plot: Nonligand atoms (as spheres) - (Y/N)? As above, but for the
non-ligand atoms.
Plot: Double- and triple-bonds - (Y/N)? This option defines whether
doubleand triple-bonds are to be plotted. At present, LIGPLOT assumes that
all bonds are single bonds and needs to be told which are double and
which are triple. This is done as follows:First, run LIGPLOT in the usual manner.
Then, edit the ligplot.bonds file and change the "s" in the final
column
of any double-bond to "d", and, for any triple-bond, to "t".
Finally, re-run LIGPLOT with the ligplot.pdb file as the input PDB
file
(ie run: ligplot ligplot.pdb [options], where the options defining the
ligand are as before).
Print: Key to symbols in PostScript output - (Y/N)? This option defines
whether a key explaining the symbols used in the LIGPLOT diagram
produced is to be included in the plot.
Print: Residue names/numbers - (Y/N)? This option defines whether residue
names and numbers are to be printed adjacent to the relevant residues.
Print: Atom names - (Y/N)? This option defines whether atom names are to
be
printed next to each of the atoms.
Print: H-bond lengths on hydrogen bonds - (Y/N)? This option defines
whether the length of each hydrogen bond is to be printed on the plot.
Print: Filename as title if title not explicitly defined - (Y/N)? If the
-h option is omitted when LIGPLOT is run, the program will not prompt
for a title for the plot. In which case, if the "Filename as title"
option is set to "Y", the filename will be printed as the plot title
instead.
3. LINKED RESIDUES
--------------Up to 10 pairs of linked residues can be input, in the form:LINKED RESIDUES
--------------HIS-ASP <- Residue-pair
HOH-*** <- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
<- Residue-pair
1
2
3
4
5
6
7
8
9
10
Description:----------The above list defines which residues, not directly hydrogen-bonded to
the
ligand are to be included in the plot, provided they are hydrogen-bonded
to
a residue that is hydrogen-bonded to the ligand.
Each residue-pair shows: the residue-type hydrogen-bonded to the ligand,
and the residue-type to be plotted if it is hydrogen-bonded to this first
residue.
For example, "HIS-ASP" will include any Asp residues that are H-bonded to
a
His which is H-bonded to the ligand. More generally, "HIS-***" will show
any residue H-bonded to the His. Similarly, "HOH-***" will include any
residues in the protein that are connected to the ligand via a water
molecule.
4. SIZES
----The sizes of the following symbols, plotted on the LIGPLOT diagram, can
be
defined.
SIZES
----0.33
0.33
0.40
1.15
1.00
0.19
0.07
0.07
(All sizes are relative sizes given in Angstroms)
<<<<<<<<-
Radius: Ligand atoms
Radius: Non-ligand atoms
Radius: Water molecules
Radius: Hydrophobic contact residues
Radius: Ligand residues in simple-residue representation
Line-thickness: Ligand bonds
Line-thickness: Non-ligand bonds
Line-thickness: Hydrogen bonds
5. TEXT SIZES
---------The text sizes of the various labels plotted on the LIGPLOT diagram can
be
defined as follows:TEXT SIZES (Relative sizes in Angstroms)
---------0.80 <- Residue names: Ligand residues
0.63 <- Residue names: Non-ligand residues
0.50 <- Residue names: Water molecule IDs
0.50 <- Residue names: Hydrophobic-interaction residues
0.25 <- Residue names: in simple-residue representation
0.31 <- Atom names: Ligand atoms
0.31 <- Atom names: Non-ligand atoms
0.44 <- Hydrogen-bond lengths
6. COLOURS
------The colours of the background to the plot, and of various symbols,
plotted
on the LIGPLOT diagram, can be defined as follows:COLOURS
------CREAM
PURPLE
BLACK
SKY BLUE
BRICK RED
ORANGE
YELLOW
<<<<<<<-
Background colour of page
Ligand bonds [or ATOM - see Note]
Non-ligand bonds [or ATOM - see Note]
Hydrogen bonds
Hydrophobic interactions
Accessibility shading: Buried atoms
Accessibility shading: Accessible atoms
BLUE
RED
BLACK
YELLOW
TURQUOISE
PURPLE
PINK
LIME GREEN
BLACK
BLACK
<<<<<<<<<<-
Nitrogen atoms
Oxygen atoms
Carbon atoms
Sulphur atoms
Water atoms
Phosphorus atoms
Iron atoms
All other atoms
Atom edges
Circles in simple-residue representation
The definitions of the different colours are given at end of file (see
8. COLOUR DEFINITIONS).
Note that, if "ATOM" is entered as the colour of the ligand- or nonligand
bonds, the bonds will be coloured such that each half is of the colour of
the atom bonded at that end.
7. TEXT COLOURS
-----------The colours of the various labels plotted on the LIGPLOT diagram can be
defined as follows:TEXT COLOURS
-----------BLACK
BLACK
BLUE
BRICK RED
PURPLE
BLACK
BLACK
BLACK
SKY BLUE
<<<<<<<<<-
Plot title
Legends in key to symbols
Residue names: Ligand residues
Residue names: Non-ligand residues
Residue names: Water molecule IDs
Residue names: Hydrophobic-interaction residues
Atom names: Ligand atoms
Atom names: Non-ligand atoms
Hydrogen bond lengths
The definitions of the different colours are given at end of file (see
8. COLOUR DEFINITIONS).
8. COLOUR DEFINITIONS
-----------------The colour definitions table allows you to modify any of the default
colour
definitions. You can also set up new colours of your own (up to 20
different colours are allowed).
Each entry contains three numbers, each between 0.0 and 1.0, giving the
ratios of red, green and blue, respectively, making up the given colour.
Each colour also has a 'name', in single quotes, by which the colour is
referred to when defining COLOURS and TEXT COLOURS.
The default colours and their corresponding RGB values are:COLOUR DEFINITIONS
-----------------0.0000 0.0000 0.0000
1.0000 1.0000 1.0000
1.0000 0.0000 0.0000
0.0000 1.0000 0.0000
0.0000 0.0000 1.0000
1.0000 1.0000 0.0000
0.8000 0.5000 0.0000
0.5000 1.0000 0.0000
0.5000 0.0000 1.0000
0.5000 1.0000 1.0000
1.0000 0.5000 1.0000
0.3000 0.8000 1.0000
1.0000 1.0000 0.7000
0.0000 1.0000 1.0000
1.0000 0.0000 1.0000
0.8000 0.0000 0.0000
0.5000 0.0000 0.0000
0.9700 0.9700 0.9700
1.0000 1.0000 1.0000
1.0000 1.0000 1.0000
'BLACK
'WHITE
'RED
'GREEN
'BLUE
'YELLOW
'ORANGE
'LIME GREEN
'PURPLE
'CYAN
'PINK
'SKY BLUE
'CREAM
'TURQUOISE
'LILAC
'BRICK RED
'BROWN
'LIGHT GREY
'WHITE
'WHITE
'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<'<-
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
Colour
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
9. MINIMIZATION PARAMETERS
----------------------The parameters that control the way that LIGPLOT minimizes a given plot
(in
terms of reducing the numbers of atom-atom, bond-bond and atom-bond
overlaps) are given at the end of the ligplot.par file.
It is unlikely you will need to alter these values, although sometimes
you
might get a better plot by altering the parameters by trial-and-error.
A far better way of improving a cluttered or unclear plot is by modifying
the ligplot.pdb file, as described in section 6.
MINIMIZATION PARAMETERS
----------------------0.25
<- Atom-atom clash parameter
0.25
<- Bond-atom clash parameter
10.0
<- Bond-overlap score
1.00
<- Weight for bond-overlap term, relative to atom-clash term
50.0
<- Weight for term giving H-bond deviation from ideal value
7.0
<- Blow-distance for H-bonded groups (in Angstroms)
15.0
<- Furthest move-distance for H-bonded groups (in Angstroms)
6. IMPROVING THE PLOTS
---------------------The plots produce by LIGPLOT can be improved in one of two ways.
a. Editing the PostScript file
--------------------------If you are familiar with PostScript files, you can make simple amendments
to the plot produced by LIGPLOT by editing the ligplot.ps file.
The file is an ASCII text file, and so can be modified using any text
editor. The sorts of amendments you can make are: changes to labels (in
terms of size, colour and text), addition of other text, changes to
colours, sizes, etc.
Some changes, of course, can be made simply by altering the ligplot.par
parameter file (see section 5) and re-running LIGPLOT.
b. Editing the ligplot.pdb file using interactive computer graphics
software
---------------------------------------------------------------For more radical changes (say to change the positions or orientations of
sidechains/residues on the plot), you can use standard interactive
computer
graphics software, such as QUANTA to edit the output ligplot.pdb file.
The ligplot.pdb file contains the coordinates of the flattened molecules,
exactly as seen on the plot. You can read it in as a standard PDB file
and
then use standard molecular modelling operations to modify the structure
in
any way that will make the final plot clearer.
For example, if you are using QUANTA, you might modify the plot as
follows:1. First, import the ligplot.pdb file as a PDB file.
2. Then, use the "Distance" option of the "Geometry" panel to add
dotted lines between hydrogen-bonded atoms. Click first on one,
and then the other, of each hydrogen-bonded atom pair. A dotted
line will be drawn between the two atoms, showing their distance
apart in Angstroms. This will reproduce the hydrogen bonds shown
on the LIGPLOT diagram, and will be useful in getting the
distances between them to match the actual distances (printed on
the plot) as closely as possible.
3. Use the "Move Fragment" option of the "Modelling" panel to
manually move any of the non-ligand residues around the screen.
Note that the residues corresponding to hydrophobic contacts
will
be represented by one (or sometimes more) single carbon
atoms. These, too, can be moved around the screen to more
favourable positions.
4. Use the "Torsions" option of the "Modelling" panel to rotate any
of the residues or sidechains about any of their rotatable
bonds. You can use the torsion angle monitors to ensure that the
final torsion angle is always either 0 or 180 degrees (otherwise
the molecule will lose its flatness, and subsequent operations
may
result in greater and greater distortions to the final picture).
5. Once all the required amendment have been made, save the file as
ligplot.pdb, overwriting the previous version. (See note below).
6. Re-run LIGPLOT, this time using ligplot.pdb as the input file
(ie
run: ligplot ligplot.pdb [options], where the options defining
the
ligand are as before). This should produce a new LIGPLOT diagram
with all residues laid out as defined on screen.
Note that, when the ligplot.pdb file is saved by QUANTA, any blank chain
ID's are replaced by the chain identifier "A". In this case, the
residues
in the ligplot.pdb file will no longer match the data in the ligplot.hhb,
ligplot.nnb and ligplot.bonds files.Thus you will need to edit
ligplot.pdb
to convert the chain "A" back to chain " " (blank).
7. ADDING/REMOVING H-BONDS AND HYDROPHOBIC INTERACTIONS
------------------------------------------------------LIGPLOT uses the list of hydrogen bonds supplied in the file
filename.hhb,
and the list of hydrophobic contacts supplied in the file filename.nnb
(where filename is the name of the original PDB file).
These files can be automatically generated using the HBPLUS program, or
otherwise supplied in LIGPLOT-format (see Appendix B). In the former
case,
using HBPLUS sometimes gives incorrect results as, when HBPLUS encounters
a
ligand it does not recognize, it may be unable to correctly calculate all
the hydrogen bonds the ligand makes with the protein.
For this reason, or otherwise, you may want to add or remove interactions
from either the .hhb or .nnb files.
One way, is to run LIGPLOT, edit the .hhb and .nnb files, and then run
LIGONLY. However, the format of these files is a trifle cumbersome and
awkward to edit.
A simpler way is to use the files ligplot.hhb and ligplot.nnb, generated
in
the LIGPLOT format when LIGPLOT is run. The file format is a great deal
simpler, and also has the advantage of showing only those interactions
that
were actually plotted, rather than all possible interactions in the
original PDB file.
Having edited in, or removed, the relevant interactions into either
ligplot.hhb or ligplot.nnb, overwrite the original filename.hhb and
filename.nnb files before running LIGONLY to regenerate the plot - this
time with all the correct interactions shown.
---------------------------------------------------------------------------APPENDIX A - BROOKHAVEN FILE FORMAT
----------------------------------The table below shows the Brookhaven file format for the coordinate
records
(ie ATOM and HETATM) of your PDB file. Each record holds the coordinates
and other details of a single atom.
-------------------------------------------------------------------------Field |
Column
| FORTRAN |
No. |
range
| format | Description
-------------------------------------------------------------------------1. |
1 - 6
|
A6
| Record ID (eg ATOM, HETATM)
2. |
7 - 11
|
I5
| Atom serial number
- |
12 - 12
|
1X
| Blank
3. |
13 - 16
|
A4
| Atom name (eg " CA " , " ND1")
4. |
17 - 17
|
A1
| Alternative location code (if any)
5. |
18 - 20
|
A3
| Standard 3-letter amino acid code for
residue
- |
21 - 21
|
1X
| Blank
6. |
22 - 22
|
A1
| Chain identifier code
7. |
23 - 26
|
I4
| Residue sequence number
8. |
27 - 27
|
A1
| Insertion code (if any)
- |
28 - 30
|
3X
| Blank
9. |
31 - 38
| F8.3
| Atom's x-coordinate
10. |
39 - 46
| F8.3
| Atom's y-coordinate
11. |
47 - 54
| F8.3
| Atom's z-coordinate
12. |
55 - 60
| F6.2
| Occupancy value for atom
13. |
61 - 66
| F6.2
| B-value (thermal factor)
- |
67 - 67
|
1X
| Blank
14. |
68 - 68
|
I3
| Footnote number
-------------------------------------------------------------------------Example:Four sample records are shown below:1
2
3
4
5
6
12345678901234567890123456789012345678901234567890123456789012345678
-------------------------------------------------------------------ATOM
1751 N
GLY C 250
32.286
1.882 43.206 1.00 22.00
ATOM
1752 CA GLY C 250
32.365
1.086 41.969 1.00 21.39
ATOM
1753 C
GLY C 250
31.538
1.735 40.864 1.00 20.79
ATOM
1754 O
GLY C 250
30.621
2.527 41.152 1.00 21.58
APPENDIX B - LIGPLOT FILE FORMATS
--------------------------------a. Hydrogen-bonds file, .hhb
------------------------The table below shows the LIGPLOT file format for the .hhb file
containing
the listing of hydrogen bonds to be plotted.
Line 1: 'ligplot.hhb'
Line 2: (blank)
Line 3: '
Donor
Acceptor
Distance'
Lines 4 to end:-------------------------------------------------------------------------Field |
Column
| FORTRAN |
No. |
range
| format | Description
-------------------------------------------------------------------------1. |
1 - 3
|
A3
| Acceptor residue standard 3 letter code
- |
4 - 4
|
1X
| Blank
2. |
5 - 5
|
A1
| Acceptor chain identifier
- |
6 - 6
|
1X
| Blank
3. |
7 - 11
|
A5
| Acceptor residue sequence number
- |
12 - 13
|
2X
| Blank
4. |
14 - 16
|
A3
| Acceptor residue atom name (eg CA or
ND1)
- |
17 - 21
|
5X
| Blank
5. |
22 - 24
|
A3
| Donor residue standard 3 letter code
- |
25 - 25
|
1X
| Blank
6. |
26 - 26
|
A1
| Donor chain identifier
- |
27 - 27
|
1X
| Blank
7. |
28 - 32
|
A5
| Donor residue sequence number
- |
33 - 34
|
2X
| Blank
8. |
35 - 37
|
A3
| Donor residue atom name (eg CA or ND1)
- |
38 - 41
|
4X
| Blank
9. |
42 - 45
| F4.2
| Hydrogen bond distance
-------------------------------------------------------------------------Example of .hhb file
A sample ligplot.hhb file is given below:1
2
3
4
123456789012345678901234567890123456789012345
--------------------------------------------ligplot.hhb output:
Donor
HIS
57
GLY
193
SER
195
TRP C 252
GLY
216
GLY C 250
TRP C 252
NE2
N
N
N
N
N
NE1
TRP
TRP
TRP
SER
GLY
GLY
SER
Acceptor
C 252
OXT
C 252
O
C 252
O
214
O
C 250
O
216
O
217
O
Distance
3.13
3.03
2.69
3.00
3.15
2.92
3.12
b. Hydrophobic contacts file, .nnb
------------------------------The table below shows the LIGPLOT file format for the .nnb file
containing
the listing of hydrophobic contacts to be plotted.
Line 1: 'ligplot.nnb'
Line 2: (blank)
Line 3: '
Atom 1
Atom 2
Distance'
Lines 4 to end:-------------------------------------------------------------------------Field |
Column
| FORTRAN |
No. |
range
| format | Description
-------------------------------------------------------------------------1. |
1 - 3
|
A3
| Atom 1: standard 3 letter code
- |
4 - 4
|
1X
| Blank
2. |
5 - 5
|
A1
| Atom 1: chain identifier
- |
6 - 6
|
1X
| Blank
3. |
7 - 11
|
A5
| Atom 1: residue sequence number
- |
12 - 13
|
2X
| Blank
4. |
14 - 16
|
A3
| Atom 1: residue atom name (eg CA or ND1)
- |
17 - 21
|
5X
| Blank
5. |
22 - 24
|
A3
| Atom 2: residue standard 3 letter code
- |
25 - 25
|
1X
| Blank
6. |
26 - 26
|
A1
| Atom 2: chain identifier
- |
27 - 27
|
1X
| Blank
7. |
28 - 32
|
A5
| Atom 2: residue sequence number
- |
33 - 34
|
2X
| Blank
8. |
35 - 37
|
A3
| Atom 2: residue atom name (eg CA or ND1)
- |
38 - 41
|
4X
| Blank
9. |
42 - 45
| F4.2
| Contact distance
-------------------------------------------------------------------------Example of .nnb file
A sample ligplot.nnb file is given below:1
2
3
4
123456789012345678901234567890123456789012345
--------------------------------------------ligplot.nnb output
Atom 1
ALA C 251
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
GLY C 250
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
TRP C 252
CB
CE3
CZ3
CG
CD1
C
C
CD2
CE3
CZ3
C
CE2
CZ2
CH2
CZ2
CZ3
CH2
HIS
SER
SER
CYS
CYS
SER
SER
TRP
TRP
TRP
TRP
GLY
GLY
GLY
GLY
GLY
GLY
Atom 2
57
190
190
191
191
195
195
215
215
215
215
216
216
216
216
226
226
CD2
CB
CB
C
C
CA
CB
C
C
C
CB
CA
CA
CA
C
CA
CA
Distance
3.67
3.52
3.58
3.83
3.77
3.79
2.86
3.62
3.54
3.81
3.89
3.65
3.29
3.48
3.60
3.38
3.43
R E F E R E N C E S
------------------Bernstein F C, Koetzle T F, Williams G J B, Meyer E F Jr, Brice M D,
Rogers
J R, Kennard O, Shimanouchi T & Tasumi M (1977). The Protein Data Bank: a
computer-based archival file for macromolecular structures. J. Mol.
Biol.,
112, 535-542.
McDonald I K & Thornton J M (1994). Satisfying hydrogen bonding potential
in proteins. J. Mol. Biol., 238, 777-793.
Wallace A C, Laskowski R A & Thornton J M (1995). LIGPLOT: A program to
generate schematic diagrams of protein-ligand interactions. Prot. Eng.,
8,
127-134.