|
PENCE / CIHR-Group
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Funding for this software has been provided in part by the
Canadian Institutes of Health Research (CIHR Group)
and the
Protein Engineering Networks of
Centres of Excellence (PENCE).
|
|
PENCE / CIHR-Group
|
|
Funding for this software has been provided in part by the
Canadian Institutes of Health Research (CIHR Group)
and the
Protein Engineering Networks of
Centres of Excellence (PENCE).
VADAR uses the programs:
ANAREA - T. J. Richmond J. Mol. Biol. 178:63-89 (1984)
VOLUME - F. M. Richards J. Mol. Biol. 82:1-14 (1974)
Copyright (C) 1995 - No portion of this program may be incorporated into other programs or sold for profit without express written consent of the authors.
1. Lee, B. & Richards, F.M., J. Mol. Biol. 55:379-400 (1971).
2. Chothia, C., Nature 254:304-308 (1975).
3. Richards, F.M., Ann. Rev. Biophys. Bioeng. 6:151-176 (1977).
4. Eisenberg, D. & McLachlan, A.D., Nature 319:199-203 (1986).
5. Miller, S. Janin, J., Lesk, A. & Chothia, C. J., Mol. Biol.
196:641-656 (1987).
6. Chiche, L. Gregoret, L.M., Cohen, F.E. & Kollman, P.A. Proc. Natl.
Acad. Sci. (USA) 87:3240-3243 (1990).
7. Chothia, C., J. Mol. Biol. 105, 1-14 (1976).
8. Janin, J., Nature 277:491-493 (1979).
9. Shrake, A. & Rupley, J.A., J. Mol. Biol. 79, 351-371 (1973).
10. Richmond, T.J., J. Mol. Biol. 178, 63-89 (1984).
11. T. J. Richmond J. Mol. Biol. 178:63-89 (1984)
12. F. M. Richards J. Mol. Biol. 82:1-14 (1974)
13. F.Richards/C.Kundrot Proteins 3:71-84 (1988)
PC(Linux): vadar v1.4 (2.1 MB)
We have been unable to compile vadar under linux at this time, (there is
some pretty old fortran source code here).
Once you have downloaded the software, you then proceed by
uncompressing and untarring the files. For example:
While running, VADAR creates temporary files in the current directory.
If VADAR exits prematurely (either by a user stopping the program or
by an unexpected error within VADAR), it is possible that the temporary
files will be left in the current directory. The user is then
responsible for deleting them.
Different versions of VADAR usually have different versions of
the vadar.parms file. If you run VADAR with an incorrect
vadar.parms file, then it will most likely not run properly,
and may die mysteriously. Please make sure that all users
are aware that they need to update their vadar.parms files.
The following gives the parameter file (lines beginning with #)
followed by any explanation that is necessary.
HBOND_DIST = 3.5 Angs.
Accessible Surface Area is given in the RES. ASA column in the
Main Chain panel, and the SIDE SURF(ASA) column in the Side Chain
panel.
Accessible Surface Area is defined as the area (measured in square
angstroms) of the molecular surface which is contact with solvent.
It may also be described as the area over which the centre of a
molecule of radius 1.4 angstroms can move while maintaining
unobstructed contact with the van der Waals surface of the molecule.
The concept of accessible surface area provides a quantitative
definition of the exterior and interior of proteins and other
macromolecules.
The fractional surface ASA is calculated by comparing
the accessible surface area against a table listing average areas.
The residue areas (as well as the atomic areas and side chain areas)
were calculated from a peptide created using BIOSYM software with the
sequence Gly-Xaa-Gly in the extended (phi=180, psi=-180) position.
Each of the twenty amino acids was substituted in the Xaa postion.
The area of for each atom in each residue was calculated using
ANAREA using atomic radii and/or van der Waals radii from 1) Shrake,
2) Richards 3) some other fellows. These atomic areas and residue
areas will be slightly different than those published by Shrake,
Richards etc. b because these earlier authors used approximate
algorithms. The areas calculated with ANAREA are exact
(calculated analytically).
The values for the average areas vary depending on the vanderwaals
radius chosen in the Main Chain Info section of the parameter file.
The tables may be found in the lib directory under tables/area*
This is calculated for both the side chain and main chain ASA.
Van der Waals Surface Area
Van der Waals surface area is the actual exposed or visible area of
a molecule assuming the atomic surface is defined by the van der
Waals radius of each component atom in the molecule. It may also
be described as the area over which the centre of an infinitely
small point (of radius 0.0 angstroms) can move while maintaining
unobstructed contact with the van der Waals surface. The van der
Waals surface area is sometimes known as the atomic or molecular
surface area. It is nearly equal to the sum of the "contact" and
"reentrant" surface areas described by Richards (1977). Note that
the van der Waals surface area is always smaller than the ASA and
that it is measured in square angstroms.
The main chain info panel gives the total ASA for each residue.
The side chain info panel gives only the total ASA for the
side chain (everything except the N, C, and O). In addition,
the file OUTPUT.area.atom (where OUTPUT is the name of the
output file) contains the ASA broken down by individual atom.
The file OUTPUT.area.atom is optional and can be turned off
in the vadar.parms file (see the help page on vadar.parms).
Stats Section on ASA
Once these conditions are met then the bturn type is assigned
according to the rules:
disulfide bonds
The disulfide bond information is taken directly from the pdb file, from the
SSBOND header.
S-S DISTANCE (disulfide bond distance) is measured as the distance from
SG to SG, and should be less than 3 Angstroms.
hbonds
VADAR uses a heuristic method of calculating the presence or absence of
hydrogen bonds. Two of the better known procedures for determining
the presence of hydrogen bonds are those of Kabsch and Sander (1983)
which uses an energy-based calculation and that of Baker and Hubbard
(1984) which uses a simple distance cut-off. The Kabsch-Sander
approach is usually a little too generous on the allowed H-bond distances
but a little too strict on the allowed angles. On the other hand, the
Baker-Hubbard approach is a little too strict on the allowed distances
and probably too generous on the allowed H-N to C-O angles. We have
developed a compromise between these two methods which seems to reproduce
hydrogen bond patterns identified by crystallographers and NMR
spectroscopists. The algorithm proceeds as follows:
(these values are set in the vadar.parms file, and their defaults
are given here).
HBOND_DIST = 3.5 Angs.
This is used to account for the fact that H-bonds are
directional and that in-plane H-bonds can extend for upto HBOND_DIST Angs
while "bent" H-bonds require closer proximity to the donor/acceptor
pairs (HBOND_DIST2 Angstroms).
hbond angle
The hydrogen bond angle represents the angle between the
NH of the donor and the CO of the acceptor. It is referenced
so that a straight vector is considered to be at a 180
degree angle.
hbond energy
The variable rON here is used to repressent the distance from
the O of the acceptor to the N of the donor. Similarly, rCH,
rOH, and rCN are defined. Hbond energy is then defined as:
hbond stats
These statistics should all be self explanatory:
Expected hbond stats
Torsion
The phi and psi angles are compared to a set of standards, using the
Ramachandran Plot, and assigned a number based on the likelihood of that
phi/psi combination.
The Ramachandran table may be found in the library directory in
the file called rama.table. (The library directory may be installed
in a number of places and you may need to check with the system
administrator but typically it is called /usr/local/lib/VADAR/tables).
Omega
The omega angles is looked at, and a quality number is assigned
as follows:
VDW
This statistic is based on the fractional volume for each
residue. The quality number is assigned as:
ENV
This statistic is based on the environment class (of the side chain).
It is calculated by looking at a table of environment values /
residues, with scores from 0-9. This table
The environment table may be found in the library directory in
the file called env.table. (The library directory may be installed
in a number of places and you may need to check with the system
administrator but typically it is called /usr/local/lib/VADAR/tables).
Statistics
The resolution and rvalue are taken from the input (PDB) file.
They have no expected values.
The definitions of phipsi core, allowed, generous, and outside are
defined above in the ``Torsion'' section.
96% of the values are expected to be in the core,
3% are expected to be in the allowed,
0 % are expected to be in the generous, and
1% are expected to be in the outside.
Packing defects are considered to be residues whos fractional
volume is > 1.195 or < .795. 7% of your residues are expected
to fall into this region.
Free energy of folding is calculated from the difference of
the actual asa's compared to the expected.
The expectd is 16.02 - .99*number of residues.
Numburied is the number of residues whos fractional asa is
less than or equal to 0.05. The expected is
(cubedroot(number of residues) - 2) ** 3
# buried charges is calculated as the number of residues with
the ASA = 0. The expected value is 2% of the number of residues.
The fraction buried side asa for a residue is calculated
(call this buried). Then:
Mean Residue Volume
Mean residue volume is the average volume of space that a residue
of a particular type occupies when buried in an average protein.
Mean residue volume is measured in cubic angstroms.
CONSENSUS calculates three secondary structures then merges them
into one consensus secondary structure. It also places helix N-caps
and assigns short beta bridges.
DEFINE1
is a distance matrix approach to secondary structure, using masks.
DEFINE2 is based on phi/psi angles
DEFINE3 is based on hydrogen bonds (also uses phi/psi angles)
The first set of tables contains surface area broken down by
amino acid for each residue. The second set of tables contain total
surface area per residue. The third set of tables contain
total surface area of the side chains only.
There are different tables of each type, and that one that is
used for a VADAR run depends on the vanderwaals radius chosen
in the Main Chain Info section of the parameter file. These
tables may be found in the LIB_PATH/tables directory (this
location will vary depending on where you system administrator
has chosen to install it). The residue areas (as well as
the atomic areas and side chain areas) were calculated
from a peptide created using BIOSYM software with the sequence
Gly-Xaa-Gly in the extended (phi=180, psi=-180) position. Each of
the twenty amino acids was substituted in the Xaa postion. The area
of for each atom in each residue was calculated using ANAREA using
atomic radii and/or van der Waals radii from 1) Shrake, 2) Richards
3) some other fellows. These atomic areas and residue areas will be
slightly different than those published by Shrake, Richards etc.
because these earlier authors used approximate algorithms. The
areas calculated with ANAREA are exact (calculated analytically).
NOTE: the volume tables in
SEQSEE are
identical to the volume (shrake) definitions of VADAR.
Residue Volume Ratio
The residue volume ratio is the ratio of the actual residue volume to
the mean residue volume. In cases of perfect packing this ratio
should be exactly 1.0. If this ratio ranges from between 0.9
to 1.1 it indicates that packing defects are present in the
molecule. If this ratio exceeds this range then one can assume
that gross structural problems exist within the model.
Statistics
Expected Statistics
This file last updated:
Questions to:
bionmrwebmaster@biochem.ualberta.ca
Download
Select the version of vadar corresponding to your operating system.
Solaris: vadar v1.4 (1.07 MB)
SGI(Irix6.5): vadar v1.4 (0.69 MB)
Installation
> uncompress vadar-v1.4-sgi6.tar.Z
> tar xvf vadar-v1.4-sgi6.tar
> cd vadar-v1.4-sgi6
Look at the README file for details on installation.
> more README
It is pretty simple, all you have to do is know where you want to
put the executables and where to put the documentation, library and
example files. The installation script prompts you for
the names of these directories.
> ./Install
Finally you can test the program by going to the directory where the
program is installed and type the name. The README file also explains
how to set your path environment variable to include the location
of the executable.
Input
VADAR expects as input a standard pdb (Protein Databank) file.
As an example we have enclosed the pdb2lz2.ent file in the
lib/SAMPLE directory. Part of that file is printed here to show
the input format.
ATOM 1 N LYS 1 -7.237 14.795 -10.161 1.00 58.48 2LZ2 81
ATOM 2 CA LYS 1 -6.682 13.509 -9.562 1.00 57.62 2LZ2 82
ATOM 3 C LYS 1 -6.904 13.768 -8.083 1.00 49.27 2LZ2 83
ATOM 4 O LYS 1 -6.436 14.842 -7.821 1.00 46.31 2LZ2 84
ATOM 5 CB LYS 1 -5.227 13.264 -9.843 1.00 47.34 2LZ2 85
ATOM 6 CG LYS 1 -4.509 11.995 -9.589 1.00 40.83 2LZ2 86
ATOM 7 CD LYS 1 -3.472 11.949 -8.511 1.00 42.51 2LZ2 87
ATOM 8 CE LYS 1 -3.142 10.659 -7.735 1.00 29.40 2LZ2 88
ATOM 9 NZ LYS 1 -1.611 10.563 -7.962 1.00 25.79 2LZ2 89
ATOM 10 N VAL 2 -7.541 12.966 -7.306 1.00 54.46 2LZ2 90
ATOM 11 CA VAL 2 -7.850 13.069 -5.873 1.00 40.18 2LZ2 91
ATOM 12 C VAL 2 -6.720 12.181 -5.326 1.00 59.96 2LZ2 92
ATOM 13 O VAL 2 -6.445 11.077 -5.823 1.00 66.21 2LZ2 93
ATOM 14 CB VAL 2 -9.281 12.930 -5.463 1.00 20.34 2LZ2 94
ATOM 15 CG1 VAL 2 -9.543 13.495 -4.025 1.00 17.82 2LZ2 95
ATOM 16 CG2 VAL 2 -10.213 13.750 -6.477 1.00 5.96 2LZ2 96
Only standard residue names are accepted in the input file, as well as
standard atom names. If you have a pdb file which does not have a
residue or atom name which the program recognizes, then your output
file will contain lines looking like:
-1 n/a CCC C 0.0 NaN 0.0 NaN 360.0 360.0 360.0
-1 n/a CCC C 0.0 NaN 0.0 NaN 360.0 -85.2 180.0
-1 n/a CCC C 0.0 NaN 0.0 NaN 360.0 360.0 360.0
-1 n/a CCC C 0.0 NaN 0.0 NaN 44.2 -96.2 -180.0
If this happens, then use the VADAR menu option which gives the
``Log of VADAR Run'', and in the log file it will document the
offending atom or residue name.
How to Run
molscript < myoutput.mol > myoutput.ps
which will produce the postscript file myoutput.ps. Then
look at your structure using the postscript previewer (also
not included with VADAR):
xpsview myoutput.ps
/usr/local/brookhaven/pdb6cts.ent
the fortran programs may core dump. You must copy the file
into your home directory and then re-run it.
Run interactively? (1=yes,0=batch).
Must be set to 0. Then VADAR is called as follows:
vadar -f pdb_filename [ -o out_filename ]
Parameters File
The file ``vadar.parms'' is a file containing all of the defaults
for running VADAR. If a user does not have their own vadar.parms
file, then the system default is used.
# **** Parameter List for VADAR ****
#
# Users should feel free to copy this file to their own directory
# and make any changes they feel appropriate. Parameter entries are
# preceded by 2 consecutive angle brackets, the order of the parameters
# must be maintained! Comments and blank lines can be placed anywhere.
#
# PARAMETER FILE VERSION:
# >> 1.4
#
# ****************************************************************
# Run interactively? (1=yes,0=batch).
# >> 1
If you choose to run in batch, then vadar will be started up
in the background. You must then invoke VADAR as:
vadar -f pdb_filename [ -o out_filename ]
# ****************************************************************
# *** Display Options: (for next 4 options, 0=off 1=on)
#
# Hydrogen Bond Info
# >> 1
#
# Main Chain Info
# >> 1
#
# Side Chain Info
# >> 1
#
# Stats Info
# >> 1
#
# Molscript/Ribbons Output (0=none, 1=molscript, 2=ribbons)
# >> 0
#
#
# Area and volume output broken down by atoms
# >> 0
#
# Some proteins have multiple chains. Setting 0 here
# means that only the very first chain is processed, 1 means
# that all chains will be read in.
# >> 0
#
# Setting 1 here means that the main output will be in one
# big file, 0 means that the output will be in separate files
# (.bond .main .side .stats .areaatom .volatom .mol .ss).
# >> 0
The output from VADAR is broken down into different sections.
Turning off different portions will limit the output.
# ****************************************************************
# *** BOND INFO
# Hydrogen Bonding Values
# (see the online Help under Hydrogen Bonds for more details)
# Hydrogen Bond Distance
# >> 3.5
# Hydrogen Bond Angle
# >> 90
# Second Distance Check
# >> 2.5
These values are used to determine what is a legal hydrogen bond.
See the help page on bonds for more details.
# Salt Bridge Distance
# >> 3.6
The distance used to determine what is a valid salt bridge.
# ****************************************************************
# *** MAIN CHAIN INFO
#
# Values for vanderwaals radius
# (this should also be set in the AREA section below)
# (0=Chothia, 1=Eisenberg, 2=Richards, 3=Shrake)
# >> 3
There are different values
# masks for predicting secondary structure
# >> BETA 4.95 4.95 4.95
# >> HELIX 0 3.75 5.36 5.02 6.11
# rmsd values for predicting secondary structure
# >> BETA_RMSD 0.6
# >> HELIX_RMSD 0.22
****************************************************************
*** STATS INFO
Take definition of polar/nonpolar asa and charged asa from
(0=Chothia, 1=Eisenberg, 2=Shrake)
>> 2
****************************************************************
** AREA INFO (part of main chain)
>> AREA
Probe radius.
>> 1.4
Values for vanderwaals radius
(this should also be set in the MAIN CHAIN section above)
(0=Chothia, 1=Eisenberg, 2=Richards, 3=Shrake)
>> 3
****************************************************************
** VOLUME INFO (part of main chain)
>> VOLUME
Length of the edge of the shell lattice
>> 2.80
Type of volume calculation
(1=Standard Voronoi procedure, 2=Richards Method B, 3=Radical Plane procedure)
>> 1
Value of rdelta for surface volume adjustment
>> 0.0
These values are used to determine what makes a valid hydrogen bond.
Refer to the Hydrogen Bonds section to see how they are used.
HBOND_ANGLE = 90
HBOND_DIST2 = 2.5 Angs.
Angles
The phi, psi, and omega angles for a protein are given in
the main chain panel of VADAR.
Given a residue with:
N.0 -- CA.0 -- CO.0 -- N.1 -- CA.1 -- CO.1 -- N.2 -- CA.2
The phi angle is defined as the angle between
CO.0 -- N.1 and CA.1 -- CO.1
The psi angle is defined as the angle between
N.1 -- CA.1 and CO.1 -- N.2
And the omega angle is defined as the angle between
CA.1 -- CO.1 and N.2 -- CA.2
*******************
The chi1 angle is given in the side chain panel.
Ideally, values of chi1 should be 60, 180, and -60.
The chi1 angle is defined as the dihedral angle between the
N -- CA -- CB -- XG of the same residue (where XG is either CG or OG).
Specifically:
FOR: ARG, ASN, ASP, GLN, GLU, HIS, LEU, LYS, MET, PHE, PRO, TRP, TYR
HA - CA - CB - CG
FOR: ILE, VAL
HA - CA - CB - CG1
FOR: SER
HA - CA - CB - OG
FOR: THR
HA - CA - CB - OG1
FOR: CYS
HA - CA - CB - SG
(ALA and GLY have no CHI1 angles)
*******************
The stats panel of VADAR includes the following. The items with
no explanation are self-explanatory.
Mean Chi Gauche+ = mean omega guache+ angles (excluding PROLINE)
( -120 <= chi <= 0 )
Mean Chi Gauche- = mean omega gauche- angles (excluding PROLINE)
( 0 < chi <= 120 )
Mean Chi Trans = mean omega trans angles (excluding PROLINE)
( -180 <= chi < -120 ) and ( 120 < chi <= 180 )
# res with Gauche+ Chi
# res with Gauche- Chi
# res with Trans Chi
Mean Helix Phi = mean phi angle of residues in a helix
Mean Helix Psi = mean psi angle of residues in a helix
Mean Omega (|omega|>90)
# res with |omega|<90
omega pooled =
(# res with gauche+ angles * standard deviation of those residues) +
(# res with gauche- angles * standard deviation of those residues) +
(# res with trans angles * standard deviation of those residues) /
(# res with gauche+ angles + # res with gauche- angles +
# res with trans angles)
# res in phipsi core \ These all relate to the quality index
# res in phipsi allowed \ ``torsion'' which is explained in the
# res in phipsi generous / quality help page.
# res in phipsi outside /
*******************
EXPECTED values for stats:
Mean Chi Gauche+ \
Mean Chi Gauche- > These values are set according to the values
Mean Chi Trans / in ????
# res with Gauche+ Chi
# res with Gauche- Chi
# res with Trans Chi
Mean Helix Phi
Mean Helix Psi
Mean Omega (|omega|>90)
# res with |omega|<90
omega pooled =
# res in phipsi core \
# res in phipsi allowed \
# res in phipsi generous /
# res in phipsi outside /
Accessible Surface Area
Total ASA = Total accessible surface area of the folded protein
ASA of backbone = Total accessible surface area of backbone atoms
(N,C & O)
ASA of sidechains = Total accessible surface area of side chain atoms
ASA of C = Total ASA of all carbon atoms in the protein
ASA of N = Total ASA of all uncharged nitrogen atoms
ASA of N+ = Total ASA of all charged nitrogen atoms
ASA of O = Total ASA of all uncharged oxygen atoms
ASA of O- = Total ASA of all charged oxygen atoms
ASA of S = Total ASA of all sulfur atoms
Mean residue ASA = Total ASA divided by the number of residues in the protein
Mean frac ASA = Average fractional accessible surface area of each
residue in the protein. Fractional ASA's are determined
by the measured residue ASA divided by the residue-
specific ASA's in the extended state. These vary
according the van der Waals radii chosen.
% side ASA hydrophobic = the percentage of total side ASA of
hydrophobic residues (ALA, VAL, LEU, ILE, PRO, MET, PHE, TRP)
to the total side ASA.
For all ASA calculations: If the first atom in the input file is an N,
then both that N and the last O will be considered charged.
For the following discussion, these definitions are used:
ASA of C (CASA) = sum of all ASA's for C, CA, CB, CG's, CD's, CE's, CH's, CZ's
ASA of N (NASA) = sum of all ASA's for N, ND2, NE, NE1, NH1, NE2
ASA of N+ (NPASA) = sum of all ASA's for NZ, NH2, ND1
ASA of O (OASA) = sum of all ASA's for O, OD1, OE1, OG, OG1, OH (- last O)
ASA of O- (OMASA) = sum of all ASA's for OD2, OE2, as well as any OXT atoms
(+ last O)
ASA of S (SASA) = sum of all ASA's for SG, SD
(TASA) = total ASA's
And for SHRAKE only these definitions are used:
shrake_polar = ASN: CG
+ GLN: CD
- GLU: OE1
- ASP: OD1
- HIS: ND1, HE2
- ARG: NE, NH1
shrake_charged = GLU: OE1, OE2, CD
+ ASP: CG, OD1, OD2
+ HIS: ND1, CE1, NE2
+ LYS: NZ
+ ARG: NE, CZ, NH1, NH2
+ ALL: OXT
(for the nonpolar definitions, the values that overlap with the total
ASA's from above are compensated for in the following SHRAKE definitions);
Exposed nonpolar ASA = Total nonpolar accessible surface area. This
value has different definitions for different
authors and/or choices of van der Waals radii
1) Eisenberg = casa + sasa
2) Chothia = casa
3) Shrake = tasa - charged - polar
Exposed polar ASA = Total polar accessible surface area. This value also
has different definitions for different authors and/
or choices of van der Waals radii
1) Eisenberg = nasa + oasa - firstN - lastO
2) Chothia = nasa + oasa + sasa - firstN - lastO
3) Shrake = shrake_polar + nasa + oasa + sasa
- firstN - lastO
Exposed charged ASA = Total charged accessible surface area. This value
has different definitions for different authors and/
or choices of van der Waals radii
1) Eisenberg = npasa + omasa + firstN + lastO
2) Chothia = npasa + omasa + firstN + lastO
3) Shrake = shrake_charged + firstN + lastO
Fraction nonpolar ASA = Total nonpolar accessible surface area divided by the
total accessible surface area
Fraction polar ASA = Total polar accessible surface area divided by the
total accessible surface area
Fraction charged ASA = Total charged accessible surface area divided by the
total accessible surface area
*******************
*** Expected Values for Stats ***
Expected total ASA = Expected total accssible surface area of the folded
protein based on its molecular weight (ASA=6.3*MW**.73)
Exposed nonpolar ASA = TASA * 0.55
Exposed polar ASA = TASA * 0.30
Exposed charged ASA = TASA * 0.15
Fraction nonpolar ASA \
Fraction polar ASA > value come from where?
Fraction charged ASA /
B-Turns
A residue can only be a bturn if:
if phi(i+1) = -60 +- 30 AND
psi(i+1) = -30 +- 30 AND
phi(i+2) = -90 +- 30 AND
psi(i+2) = 0 +- 30
then residues i to i+3 are assigned to type I
if phi(i+1) = 60 +- 30 AND
psi(i+1) = 30 +- 30 AND
phi(i+2) = 90 +- 30 AND
psi(i+2) = 0 +- 30
then residues i to i+3 are assigned to type I'
if phi(i+1) = -60 +- 30 AND
psi(i+1) = 120 +- 30 AND
phi(i+2) = 80 +- 30 AND
psi(i+2) = 0 +- 30
then residues i to i+3 are assigned to type II
if phi(i+1) = 60 +- 30 AND
psi(i+1) = -120 +- 30 AND
phi(i+2) = -80 +- 30 AND
psi(i+2) = 0 +- 30
then residues i to i+3 are assigned to type II'
if phi(i+1) = -60 +- 30 AND
psi(i+1) = -30 +- 30 AND
phi(i+2) = -60 +- 30 AND
psi(i+2) = -30 +- 30
then residues i to i+3 are assigned to type III
if phi(i+1) = 60 +- 30 AND
psi(i+1) = 30 +- 30 AND
phi(i+2) = 60 +- 30 AND
psi(i+2) = 30 +- 30
then residues i to i+3 are assigned to type III'
if phi(i+1) = -60 +- 30 AND
psi(i+1) = 120 +- 30 AND
phi(i+2) = -90 +- 30 AND
psi(i+2) = 0 +- 30 AND
omega(i+1) = 0 +- 30
then residues i to i+3 are assigned to type VIa
if phi(i+1) = -120 +- 30 AND
psi(i+1) = 120 +- 30 AND
phi(i+2) = -60 +- 30 AND
psi(i+2) = 0 +- 30 AND
omega(i+1) = 0 +- 30
then residues i to i+3 are assigned to type VIb
H-Bonds
HBOND_ANGLE = 90
HBOND_DIST2 = 2.5 Angs.
332 * 0.42 * 0.20 * (1/rON + 1/rCH - 1/rOH - 1/rCN)
Mean hbond distance
Mean hbond energy
# res with hbonds
Mean hbond distance \ These were calculated from doing many
Mean hbond energy > VADAR runs on different proteain,
# res with hbonds / and taking the average values.
Quality Index
The quality index is broken into three sections.
The first assigns a rating from 0 to 3 for each residue.
A score of 0 is the lowest, with 3 being the best score.
The section section assign a rating from 0 to 9 for each residue.
A score of 0 is the lowest, with 9 being the best score.
The third section contains statistics giving the quality
of the structure.
170 < oemga <= 180 score 3
165 < oemga <= 170 score 2
160 < oemga <= 165 score 1
160 < oemga <= 160 score 0
0.80 <= fracvol <= 1.2 score 3
1.20 < fracvol <= 1.25 score 2
0.75 <= fracvol < 0.80 score 2
1.25 < fracvol <= 1.30 score 1
0.70 <= fracvol < 0.75 score 1
everything else score 0
Side Panel
The environment class is calculated based on the fractional
buried asa (accessible surface area) of the sidechain, and
as well the fractional asa of the residue.
if buried < 40
environment class = E0
if 40 < buried < 118
if the fractional asa (entire residue) < .45
environment class = P1
else environment class = P2
if buried > 118
if the fractional asa (entire residue) < .25
environment class = B1
if the fractional asa (entire residue) > .25 AND < .30
environment class = B2
else environment class = B3
Statistics
(Values for some of these data are dependent upon the choice of van der Waals
radii that are set in the vadar.parms file. The default values are for Shrake)
%HELIX = Percentage of helix as found in the consensus secondary structure.
%BETA = Percentage of beta strand.
%COIL = Percentage of coil (not random coil) found. This value includes
both "%TURN" and all other structures that are neither helical
nor extended beta strands.
%TURN = Percentage of BTURNS found.
For statistics related to the following, please see the specific
help page dealing with that topic:
NUM. RESIDUES 95% BURIED = Number of residues with a fractional ASA of less
than 0.0501. 95% is a good criteria to identify
completely buried residues.
FREE ENERGY OF FOLDING = Hydrophobic free energy contribution to folding
based on the formulae given by Eisenberg (1986)
EXPECTED FREE ENERGY = Expected free energy of folding based on the number
of residues in the protein (SFE = 15.3-1.13*numres)
NUMBER OF PACKING DEFECTS= Number of residues with fractional volumes greater
than 1.205 or less than 0.795
# buried charges = number of residues that have either:
- NZ, NH2, or ND1 with the area equal to 0.
- frac. area of OD1 + frac. area of OD2 < 0.03
- frac. area of OE1 + frac. area of OE2 < 0.03
(where the frac. area is the area of the atom
divided by the standard area defined in the
area tables LIB_DIR/tables/area_aa.* )
Secondary Structure
For all of the secondary structure routines, if there is a type
I turn (for i..i+3), then residues i+1 and i+2 become C's, UNLESS
they are double bonded, in which case they do not change.
All algorithms are ``smoothed'' after calculating. There
must be at least 3 HELIX's in a row otherwise they are turned
to COILS. There must be at least 3 BETA's in a row otherwise
they are turned to COIL's.
***HELIX***
if -120 < phi < -34) AND -80 < psi < 6
it is a HELIX
if this residue is a HELIX but the previous residue is not,
AND the residue before that was not,
AND for the previous phi, -90 < phi < -55
then the previous residue is a HELIX
***BETA***
if ( -180 < phi < -40 OR 160 < phi <= 180 ) AND
( 70 < psi < 180 OR -180 < psi < -170 )
it is a HELIX
if this residue is a BETA but the previous residue is not,
AND the residue before that was not,
AND for the previous phi, phi < -100
then the previous residue is a BETA
***COIL***
everything else
***HELIX***
if:
a) there are two hydrogen bonds
b) one hydrogen bond is of distance 3 or 4
c) the other hydrogen bond is of distance > 1
d) psi < 100
then res(i) = HELIX
If there is HCHH or HHCH, and the phi and the psi angle of the
Coil are < 100, then turn the C to a H.
***BETA***
if:
a) it has a hydrogen bond distance > 2
b) -45 > phi > -180 AND ( 180 > psi > 95 OR -170 > psi > -180 )
then res(i) = BETA
if:
a) res(i-1) != BETA AND res(i-2) != BETA
b) phi(i-1) < -100
then res(i-1) = BETA
if:
a) if there is a bond of distance >= 6
b) phi < -95
res(i) = BETA
***COIL***
everything else is coil
Tables
TABLES:
Volume
Residue volume is the volume of space enclosed by the van der Waals
surface of a given residue. It is measured through the
construction of voronoi polyhedra as described by Richards (1977).
Residue volume is measured in cubic angstroms.
TOTAL VOLUME (PACKING) = Sum of volumes for all residues in protein.
EXPECTED TOTAL VOLUME = if (molWeight <= 3000)
then expvol = molWeight*1.01;
else expvol = molWeight*1.227 - 645.8;
MEAN RESIDUE VOLUME = This is calculated as the total volume divided by
the number of residues in the protein.
MEAN FRAC VOLUME = Average fractional volume of each residue in the
protein. Fractional volumes are determined by the
measured residue volume divided by the residue-
specific volumes quoted by Richards (1977). Note
that these values vary according the van der Waals
radii chosen.
TOTAL VOLUME (PACKING) = if the molecular weight is <= 3000,
then this is the molecular weight * 1.01,
otherwise this is the molecular weight * 1.227 - 645.8.
The molecular weight is calculated by adding up the
standard molecular weight for each amino acid, where the
standard molecular weights are given in the
lib/mol.weights table.
MEAN RESIDUE VOLUME \ these values are set from ???
MEAN FRAC VOLUME /
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