Trajectory SP790

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: P185 AP03746
Lipids: POPC
Heteromolecules:
Ions: CL
Water model: W

  Download all Compresed Files.


Sequence :
WKFGKKLERIGQNVFRAAEKVLPVATGYAQLPATL-
AGAKQG
Total charge (e): +5
Number of residues: 41
By amino acid:
  Basic: 7
  Acidic: 2
  Hydrophobic: 25
  Polar: 7
Electrostatic Dipolar Moment (e nm): 12.24
Longitudinal (e nm): 11.89
Transversal (e nm): 2.91
Hydrophobic Dipolar Moment (nm): 2.52
Longitudinal (nm): 0.27
Transversal (nm): 2.5
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): 0.64644500 ± 0.00090055
Upper leaflet (nm2): 0.64644500 ± 0.00090055
Lower leaflet (nm2): 0.64644500 ± 0.00090055
Average Z coordinate
Peptide (nm): 8.576680 ± 0.031629
First Residue (nm): 8.7392700 ± 0.0409911
Last Residue (nm): 8.8943000 ± 0.0535437
Membrane (nm): 6.78163000 ± 0.00923625
Upper leaflet Head Group (nm): 8.7393800 ± 0.0109919
Lower leaflet Head Group (nm): 4.82902000 ± 0.00735524
Bilayer Thickness (nm): 3.9103600 ± 0.0132258
Peptide insertion (nm): -0.1626970 ± 0.0334845
Contacts
Peptide - Water: 49.330000 ± 0.822437
Peptide - Head groups: 23.480000 ± 0.383253
Peptide - Tail groups: 22.170000 ± 0.335535
Tilt (°): 88.915700 ± 0.700622
PepDF:
5(ns):  CVS
Displacement (nm): 0.5704680 ± 0.0220828
Precession(°): 0.128495 ± 0.757251
50(ns)  CVS
Displacement (nm): 1.7665900 ± 0.0887185
Precession(°): -0.0188002 ± 2.5792800
100(ns)  CVS
Displacement(nm): 2.460930 ± 0.116037
Precession(°): -0.79428 ± 3.95572
200(ns)  CVS
Displacement(nm): 3.176100 ± 0.117277
Precession(°): -6.95164 ± 5.16981

  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.