The analysis of atomic contacts in proteins can be done in many ways in
WHAT IF.
If you take the trouble of digging through the undocumented SPECIAL menu
routines, you will find at least ten routines that look at contacts in
different ways. The menu activated with the ANACON command holds a set of
options to analyze contacts in one protein (and other molecules if wanted).
There are two ways to look at contacts. The first one simply lists, and
indicates with dashed lines at the screen, all atomic contacts. The other
way of looking at contacts is more complicated, and goes via a 2D-plot.
The main principle is that you create a two dimensional contact plot, and
that you can then analyze the local structures by picking the square in the
contact map that belongs with the contact you are interested in.
You will often be prompted for a "Maximal allowed Van der Waals radius limit"
or something related. This is the distance between the Van der Waals radii
that is maximally allowed between two atoms in order to be called in contact.
If you, for example, put this distance at 0.5 Angstrom, two carbons (Carbon
has a default Van der Waals radius of 1.8 Angstrom) are still called in
contact if they are 4.1 Angstrom away from each other (2*1.8+0.5=4.1).
The command CONATM does the same as the command CONRES (see above). However,
on top of that, it will fill the squares with little squares that are
indicative of the individual atomic contacts. For all pairs of inter range
atoms that are within contact distance a little square will be put in
the residue square. The same coloring rules as for the residue square
are used for the atomic squares.
The command CONHAN does roughly the same as the command CONRES. It draws
squares for contacting residues. The difference is that CONHAN gives the
whole square one color. This color is a function of the local chiralities
of the two contacting residues. Red means negative hand; Green positive; and
Blue means no noticeable hand. You will be prompted for the contact distance
and for the chirality cutoff. With this parameter you will have to experiment
a little. The suggested cutoff is 10.0.
As usual you will be prompted for the mol-object number and the mol-item name.
After typing go this plot is just as pickable as all other contact plots.
The command CONRES will make WHAT IF loop over both ranges. It will then
search for all inter range residue pairs that have at least one atom pair
within contact distance (you will be prompted for that distance). For
every pair it will draw a square at the PS300 in the matrix. The dimensions
of the square are either proportional with the number of atoms in the residues,
or homogeneous, depending on the program parameters.
The left and upper line of the square get the color of the alpha carbon
of the residue in the second, vertical, range. The right and bottom line
get the color of the alpha carbon of the residue in the first, horizontal,
range.
The CONRES command depends a bit on the side chain conformations.
If the sidechain gets another rotamer, different contacts will be found.
Sometimes this is not desirable. For such cases the options RSCACA and
RSCBCB exist.
The command RSCACA will make WHAT IF loop over two ranges you are
prompted for. It will then
search for all inter C-alpha - C-alpha distances that are shorter than
a cutoff you will be prompted for. Each such pair will be represented
by a square. The dimensions
of the square are either proportional with the number of atoms in the residues,
or homogeneous, depending on the program parameters.
The left and upper line of the square get the color of the alpha carbon
of the residue in the second, vertical, range. The right and bottom line
get the color of the alpha carbon of the residue in the first, horizontal,
range.
The command RSCBCB functions virtually identical as the RSCACA command.
The only difference is that C-beta - C-beta distances will be used
instead of C-alpha - C-alpha distances.
The command CNTRES will list all residues from the first range, and give
for all of them the number of residues in the second range that have at least
one atom within the given distance cutoff.
The command CNTATM will list all residues from the first range, and give
for each of them the number of atoms in the second range that are within
the given distance cutoff of at least one atom in the residue in the first
range.
The command CONTAC allows you to list all contacts between the two ranges set.
A contact is defined as two atoms who's Van der Waals surfaces come within
X Angstrom. You will be prompted for X. If the appropriate parameter
has been set (see chapter on parameters) then dotted lines will be drawn
at the PS300 between all contacting atoms.
The command CONTYP allows you to list all contacts between the two ranges set.
Rather then the CONTAC option, you will not get ALL contacts, but only those
between the residues and atoms you asked for. You will be prompted first for
the residues in the first range to be used, and then for the atoms in those
residues. If you only gave one residue type, you can specify individual
atoms. If you gave more residues, you can only answer `main chain` or
`side chain`, or take all atoms by just hitting return. Thereafter you will
be prompted the same way for the residues and atoms in the second range.
Then the contacts will be listed, and drawn at the screen.
A contact is defined as two atoms who's Van der Waals surfaces come within
X Angstrom. You will be prompted for X. If the graphics screen is present,
dotted lines will be drawn
between all contacting atoms.
The command CONTPS allows you to list all contacts between the two ranges set.
Rather then the CONTAC option, you will not get ALL contacts, but only those
between the residues you asked for. You will be prompted first for
the residues in the first range to be used, thereafter you will
be prompted the same way for the residues in the second range.
Then the contacts will be listed, and drawn at the screen.
A contact is defined as two atoms who's Van der Waals surfaces come within
X Angstrom. You will be prompted for X. If the graphics screen is present,
dotted lines will be drawn
between all contacting atoms.
The command BUMPS allows you to list all bumps between the two ranges set.
A bump is defined as two atoms who's Van der Waals surfaces overlap more than
X Angstrom. You will be prompted for X. The default value for X is 0.25 A.
Several cases are treated special, for example, bumps within one residue
are not listed, and
bumps of a cysteine with the sidechain of its partner in a cys-cys bridge is
are based on statistically derived distances rather than on the sum
of the Van der Waals radii.
If a graphics screen is present, then dotted lines will be drawn
between all bumping atoms. I
The command TABBMP will cause WHAT IF to prompt you for a range
of residues, a table number and a table name. Thereafter you are asked
for a second range. The total 'bump' value for the residues in the
first range will be stored in the table. Only bumps with the second
range will be looked for. If the symmetry flag is switched on (see
USESYM in the chapter on symmetry) symmetry related copies of the
second range will also be used.
The command SHOSBR will cause WHAT IF to search for salt-bridges.
A salt-bridge is defined as a basic nitrogen
and an acidic oxygen being 'near' each other. 'Near' has a default of 4.5 A
Angstrom between their atom centers,
but can be changed because WHAT IF prompts you for it. You will also be
prompted for a decision on
histidines. They can either be considered as basic, or being left out of the
determination.
The command PARAMS brings you in the menu from which you can change the
parameters relevant for the ANACON option.
There are ten parameters that can be changed to influence what the pictures
at the screen will look like.
The user changes these parameters by name. They are called:
BOXTYP = Type of contact boxes used
FRMCOL = Colour of frame around plot
SEQCOL = Colour of sequence characters in frame
NEICOL = Colour of neighboring residues after picking
LABCOL = Colour of labels after picking
CACFLG = Flag for making Ca-crosses or not
1O3FLG = Flag for one or three letter code residues
HOFFLG = Flag to skip lower triangle
CACCOL = Colour of Ca-crosses in squares
CONLIN = Display lines in CONTAC, BUMPS, etc., or not
The contact boxes can be perfect aquares (BOXTYP=1) or have the
lengths of their axes as function of the number of atoms in the
residues that make the contact they represent (BOXTYP=0). In case
BOXTYP=0, the residues can no longer be shown on the diagonal.
This is the color of the frame around the plot.
(As usual blue=0, red=120, green=240, and 360 is blue again).
This is the color with which the sequence will be drawn in the frame
around the plot.
(As usual blue=0, red=120, green=240, and 360 is blue again).
After picking NEIM at the screen menu, you will see the two contacting
residues colored by atom type. The residues around this pair can get one
fixed color, determined by this parameter, or can be colored by atom type
too. To color by atom type this parameter should be set to -1. Otherwise
to 0-360.
The squares used to indicate the contacts are scaled by the number of atoms
in the residues. Especially if you use the CONATM option it might be nice
to know what are backbone and what are side chain atoms. The CACFLG parameter
can be used to draw lines between the main chain and side chain atoms in the
two residues. This then results of course in crosses being drawn in the squares.
This flag allows you to choose whether the sequence in the frame is
written in one- or in three-
letter code.
If this parameter is set to one, the CONRES results will only use the upper
half of the triangle, and the CONATM results the lower one.
This is the color of the crosses drawn if the CACFLG parameter is activated.
The command CONLIN determines whethet the contact calculation related
options like CONTAC, BUMPS, etc. will only list the contacts, or will
also display them at the screen.
The command SHOPAR will show the present value for all parameters relevant
for the ANACON option.