Trajectory SP935

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: 45482
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P257 AP00476
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: PW

  Download all Compresed Files.


Sequence :
LNALKKVFQGIHEAIKLINNHVQ
Total charge (e): +2
Number of residues: 23
By amino acid:
  Basic: 9
  Acidic: 1
  Hydrophobic: 12
  Polar: 5
Electrostatic Dipolar Moment (e nm): 5.98
Longitudinal (e nm): 5.87
Transversal (e nm): 1.15
Hydrophobic Dipolar Moment (nm): 2.72
Longitudinal (nm): 1.43
Transversal (nm): 2.31
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): 0.650202000 ± 0.000946741
Upper leaflet (nm2): 0.650202000 ± 0.000946741
Lower leaflet (nm2): 0.650202000 ± 0.000946741
Average Z coordinate
Peptide (nm): 8.3615300 ± 0.0333781
First Residue (nm): 8.2593100 ± 0.0423838
Last Residue (nm): 8.5504900 ± 0.0407207
Membrane (nm): 6.56034000 ± 0.00917351
Upper leaflet Head Group (nm): 8.5293900 ± 0.0109528
Lower leaflet Head Group (nm): 4.59412000 ± 0.00744309
Bilayer Thickness (nm): 3.9352700 ± 0.0132425
Peptide insertion (nm): -0.1678540 ± 0.0351292
Contacts
Peptide - Water: 0.0 ± 0.0
Peptide - Head groups: 14.787500 ± 0.279003
Peptide - Tail groups: 13.505000 ± 0.280394
Tilt (°): 84.807300 ± 0.986458
PepDF:
5(ns):  CVS
Displacement (nm): 0.5981650 ± 0.0255077
Precession(°): -1.56584 ± 1.14889
50(ns)  CVS
Displacement (nm): 1.9327400 ± 0.0984623
Precession(°): -18.27150 ± 3.81228
100(ns)  CVS
Displacement(nm): 2.701690 ± 0.114206
Precession(°): -39.50580 ± 5.06269
200(ns)  CVS
Displacement(nm): 3.438160 ± 0.175006
Precession(°): -81.83690 ± 6.19869

  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.