Trajectory SP764

Force field: martini_v2.2
Simulation length (ns): 5000
Electric field (kJ mol-1 nm-1 e-1): 0
Temperature (K): 300 (v-rescale)
Pressure (bar): 1 (Parrinello-rahman semiisotropic)
Number of particles: 19190
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P172 AP03324
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
VITDTLKGVAKTVAAELLRKAHCKLTNSC
Total charge (e): +3
Number of residues: 29
By amino acid:
  Basic: 8
  Acidic: 2
  Hydrophobic: 13
  Polar: 8
Electrostatic Dipolar Moment (e nm): 3.51
Longitudinal (e nm): 3.4
Transversal (e nm): 0.85
Hydrophobic Dipolar Moment (nm): 2.53
Longitudinal (nm): 2.51
Transversal (nm): 0.3
Secondary structure: Helix
Activity:

Download Files
  ITP file.
  JSON file.
  PDB file.

Click on any component to highlight it from the plot.
Upper leaflet
Lower leaflet

Lipids


Membrane model for: POPC (Healthy mammal)

POPC
2-oleoyl-sn-glycero-3-phosphocholine
Total charge (e): 0

  See POPC lipid
  Download ITP File.
  Download PDB File.
Last snapshot
  Download PDB File.
Total contacts per residue
 
  Download PDB File.
Contacts per residue
(normalized by number of beads in the residue)
  Download PDB File.

Molecular Dynamics based descriptors
Average and standard deviation, calculated using the autocorrelation function (for time series) or the width of the distribution, for the last microsecond of the trajectory

Area per lipid
Membrane (nm2): 0.645194000 ± 0.000954674
Upper leaflet (nm2): 0.645194000 ± 0.000954674
Lower leaflet (nm2): 0.645194000 ± 0.000954674
Average Z coordinate
Peptide (nm): 4.9601400 ± 0.0249284
First Residue (nm): 4.9845300 ± 0.0396359
Last Residue (nm): 4.8480800 ± 0.0349521
Membrane (nm): 6.80251000 ± 0.00982771
Upper leaflet Head Group (nm): 8.7578500 ± 0.0116598
Lower leaflet Head Group (nm): 4.84519000 ± 0.00792144
Bilayer Thickness (nm): 3.9126500 ± 0.0140961
Peptide insertion (nm): -0.1149490 ± 0.0261567
Contacts
Peptide - Water: 36.045000 ± 0.755193
Peptide - Head groups: 17.275000 ± 0.260454
Peptide - Tail groups: 15.182500 ± 0.321288
Tilt (°): 86.103700 ± 0.732178
PepDF:
5(ns):  CVS
Displacement (nm): 0.6344810 ± 0.0256507
Precession(°): 1.22836 ± 1.10808
50(ns)  CVS
Displacement (nm): 1.975470 ± 0.093905
Precession(°): 12.46980 ± 3.07223
100(ns)  CVS
Displacement(nm): 3.141090 ± 0.148428
Precession(°): 25.63420 ± 3.76313
200(ns)  CVS
Displacement(nm): 4.66179 ± 0.22006
Precession(°): 52.84740 ± 4.61392

  Download JSON File.

Peptide Analyses

Peptide Displacement Fingerprint (PepDF)
Lateral displacement vs Rotational Displacement along the trajectory, for different time windows .

Density maps:
2D-density maps of lipids around the peptide along XY and YZ axis, calculated for each lipid type along the last microsecond.

Lipid-Peptide Analyses:

z-Position
Z-coordinate, averaged for differetn parts of the the system: peptide, membrane, first and last backbone (BB) residues and upper of lower leaflet lipids’ headgroups (HGs).
Minimum distance
Minimum distance (nm) between the peptide backbone and the lipids (headgroups and tailgroups).
Number of contacts
Number of contacts between the peptide backbone and the water or the lipids separated by lipid headgroups (HG) or lipid tails, using a cut-off of 0.6 nm.
Lateral density
Lateral density for the different components of the system: headgroups, tail groups, peptide and water.