Trajectory SP898

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: 19187
Time step (fs) : 25
Software: GROMACS 2021.5
Supercomputer: Finisterrae III CESGA
Peptides: P239 NC03613
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

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Sequence :
ECTRSGGACNSHDQCCANFCRKATSTCM
Total charge (e): +1
Number of residues: 28
By amino acid:
  Basic: 6
  Acidic: 2
  Hydrophobic: 7
  Polar: 15
Electrostatic Dipolar Moment (e nm): 2.73
Longitudinal (e nm): 2.12
Transversal (e nm): 1.71
Hydrophobic Dipolar Moment (nm): 6.43
Longitudinal (nm): 6.19
Transversal (nm): 1.74
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): 0.64359900 ± 0.00109955
Upper leaflet (nm2): 0.64359900 ± 0.00109955
Lower leaflet (nm2): 0.64359900 ± 0.00109955
Average Z coordinate
Peptide (nm): 8.8671200 ± 0.0355609
First Residue (nm): 9.0840100 ± 0.0743555
Last Residue (nm): 8.7199300 ± 0.0449488
Membrane (nm): 6.8182700 ± 0.0114663
Upper leaflet Head Group (nm): 8.7770100 ± 0.0137037
Lower leaflet Head Group (nm): 4.85998000 ± 0.00936874
Bilayer Thickness (nm): 3.9170400 ± 0.0166001
Peptide insertion (nm): 0.0901056 ± 0.0381099
Contacts
Peptide - Water: 44.18500 ± 1.16347
Peptide - Head groups: 16.185000 ± 0.355485
Peptide - Tail groups: 12.28000 ± 0.23995
Tilt (°): 97.77240 ± 1.07192
PepDF:
5(ns):  CVS
Displacement (nm): 0.6153270 ± 0.0242347
Precession(°): 2.03276 ± 1.35797
50(ns)  CVS
Displacement (nm): 1.913010 ± 0.081349
Precession(°): 20.75330 ± 4.01835
100(ns)  CVS
Displacement(nm): 2.916670 ± 0.124599
Precession(°): 43.57770 ± 5.54416
200(ns)  CVS
Displacement(nm): 4.254600 ± 0.188079
Precession(°): 92.7228 ± 5.7331

  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.