Trajectory SP774

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: 19186
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P177 AP03488
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
LWENFKNAGKKFILNILDKIRCRVAGGCRT
Total charge (e): +5
Number of residues: 30
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 15
  Polar: 6
Electrostatic Dipolar Moment (e nm): 2.32
Longitudinal (e nm): 2.29
Transversal (e nm): 0.36
Hydrophobic Dipolar Moment (nm): 4.11
Longitudinal (nm): 3.89
Transversal (nm): 1.33
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
 
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Contacts per residue
(normalized by number of beads in the residue)
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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): 0.644905000 ± 0.000981474
Upper leaflet (nm2): 0.644905000 ± 0.000981474
Lower leaflet (nm2): 0.644905000 ± 0.000981474
Average Z coordinate
Peptide (nm): 4.951090 ± 0.031425
First Residue (nm): 4.958240 ± 0.046119
Last Residue (nm): 4.8168700 ± 0.0422525
Membrane (nm): 6.80370000 ± 0.00987007
Upper leaflet Head Group (nm): 8.7588500 ± 0.0116063
Lower leaflet Head Group (nm): 4.84463000 ± 0.00821791
Bilayer Thickness (nm): 3.9142200 ± 0.0142211
Peptide insertion (nm): -0.1064600 ± 0.0324817
Contacts
Peptide - Water: 40.430000 ± 0.937491
Peptide - Head groups: 18.580000 ± 0.329448
Peptide - Tail groups: 16.615000 ± 0.343583
Tilt (°): 90.643100 ± 0.756941
PepDF:
5(ns):  CVS
Displacement (nm): 0.6204520 ± 0.0276151
Precession(°): 1.33595 ± 1.09691
50(ns)  CVS
Displacement (nm): 1.9260600 ± 0.0890159
Precession(°): 12.84020 ± 3.60987
100(ns)  CVS
Displacement(nm): 2.565210 ± 0.104488
Precession(°): 25.40890 ± 5.07614
200(ns)  CVS
Displacement(nm): 3.09551 ± 0.13553
Precession(°): 51.6991 ± 6.2999

  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.