intro-VIRUSESVirus 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: AVERAGEnmin = 23nmax = 178
Distances, Cα: AVERAGE
Distances, Cα: NSETtot # 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.