Transcript Residue 2 residue statistics

RESIDUE 2 RESIDUE
STATISTICS
(INTRAPROTEIN)
AND
SOLVENT ACCESSIBLE SURFACE
AREA
(SASA)
intro-VIRUSES
Virus Name
PDB ID
HUMAN PAPILLOMAVIRUS 16
1DZL
BACTERIOPHAGE GA
1GAV
L-A virus
1M1C
SATELLITE PANICUM MOSAIC VIRUS
1STM
SATELLITE TOBACCO NECROSIS
2BUK
CANINE PARVOVIRUS
2CAS
Human hepatitis B virus
2G34
RYEGRASS MOTTLE VIRUS
2IZW
BACTERIOPHAGE MS2
2MS2
CARNATION MOTTLE VIRUS
1OPO
BACTERIOPHAGE PP7
1DWN
LIST OF
RESIDUE
NAMES/NUMBER
#/Code
Name
Hydropathy
1
R+
ARG
Arginine
-4.5
2
K+
L YS
Lysine
-3.9
3
D-
ASP
Aspartic Acid
-3.5
4
E-
GLU
Glutamic Acid
-3.5
5
N
ASN
Asparagine
-3.5
6
Q
GLN
Glutamine
-3.5
7
H+
HIS
Histidine
-3.2
8
P
PRO
Proline
-1.6
9
Y
TYR
Tyrosine
-1.3
10 W
TRP
Trytophan
-0.9
11
S
SER
Serine
-0.8
12 T
THR
Threonine
-0.7
13
G
GLY
Glycine
-0.4
14 A
ALA
Alanine
1.8
15 M
MET
Methionine
1.9
16 C
CYS
Cysteine* (CYX*)
2.5
17
F
PHE
Phenylalanine
2.8
18 L
LEU
Leucine
3.8
19 V
VAL
Valine
4.2
20 I
ILE
Isoleucine
4.5
intro, R2R STATS
 11 viruses are used.
 Residue 2 residue statistics are collected if
any non-hydrogen atoms within each residue
are within 3.5 Å of each other.
 Statistics are ONLY collected for interactions
of residues within the same protein of the
viral capsid.
 All viruses used have icosahedral symmetry.
 A protein was used to collect statistics if it was a
protein within the “identity” subunit.
Distances, Cα
 If two residues are neighbors then the
distance between their Cα atoms was
calculated.
 These distances were tabulated by residue-
residue type and their average and standard
deviation were found.
Distances, Cα: AVERAGE
nmin = 23
nmax = 178
Distances, Cα: AVERAGE
Distances, Cα: NSET
tot # of data points =14827
Distance, Cα: STANDARD DEV
intro, SASA
 11 viruses are used.
 The SASA is calculated for every atom using the
LCPO method (J Comp Chem, 22, 2, 217-230,
1999).
 The LCPO method occasionally gives a negative
SASA, if this occurred the SASA for that atom was set
to zero.
 Each residue is then assigned a SASA value
based on the sum of the SASA’s of the atoms in
that residue.
 These values are then tabulated into averages,
and standard deviations for each residue type.
intro, SASA
 Side Note:
 When calculating the neighbor map for the LCPO
algorithm on atom i only atoms that were on the
same molecule of atom i were used as neighbors
of atoms i.
 This has the effect of finding not whether an atom
is buried inside a viral capsid but rather it is buried
within its own protein.
SASA: Average
SASA: # of amino acids
SASA: Standard Deviation
SASA: Histograms
SASA: Histograms
SASA: Histograms
SASA: Histograms
SASA: Conclusion
 The general trend of the average seems to
imply that the more hydrophilic an amino
acid is the higher its SASA is going to be.
 However, from the large standard deviations
and the evidence given by the histograms this
trend should probably not be taken as an
absolute.