Trajectory SP1139

Force field: martini_v2.2P
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: 45506
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P359 NC02053
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
STNITVTLKKFPL
Total charge (e): +2
Number of residues: 13
By amino acid:
  Basic: 2
  Acidic: 0
  Hydrophobic: 6
  Polar: 5
Electrostatic Dipolar Moment (e nm): 1.55
Longitudinal (e nm): 1.4
Transversal (e nm): 0.67
Hydrophobic Dipolar Moment (nm): 1.97
Longitudinal (nm): 1.74
Transversal (nm): 0.92
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): 0.648494000 ± 0.000984603
Upper leaflet (nm2): 0.648494000 ± 0.000984603
Lower leaflet (nm2): 0.648494000 ± 0.000984603
Average Z coordinate
Peptide (nm): 8.4367400 ± 0.0364841
First Residue (nm): 8.5320300 ± 0.0381227
Last Residue (nm): 8.3340600 ± 0.0504893
Membrane (nm): 6.57992000 ± 0.00967062
Upper leaflet Head Group (nm): 8.5515200 ± 0.0113506
Lower leaflet Head Group (nm): 4.61006000 ± 0.00802072
Bilayer Thickness (nm): 3.9414500 ± 0.0138985
Peptide insertion (nm): -0.114772 ± 0.038209
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 9.710000 ± 0.239329
Peptide - Tail groups: 8.687500 ± 0.250924
Tilt (°): 101.07500 ± 1.35672
PepDF:
5(ns):  CVS
Displacement (nm): 0.721993 ± 0.033358
Precession(°): 2.03916 ± 2.08630
50(ns)  CVS
Displacement (nm): 2.266150 ± 0.111364
Precession(°): 18.37920 ± 6.69712
100(ns)  CVS
Displacement(nm): 3.517430 ± 0.166506
Precession(°): 35.9543 ± 10.4589
200(ns)  CVS
Displacement(nm): 5.15514 ± 0.21768
Precession(°): 89.3904 ± 14.8241

  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.