Structural Elements of Proteins

Peptide group

• Bond distances in the peptide group (GIF, VRML)
• The bond angles are approximately 120 deg.

Helices

• Right-handed alpha helix
  • solid ribbon, lines, atomic numbering (GIF: mono, stereo; VRML)
  • dihedral angles (GIF: mono, stereo; VRML)
  • hydrogen bonding pattern C=Oi ... H-Ni+4 (VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• Left-handed alpha helix
  • solid ribbon, lines (GIF: mono, stereo; VRML)
  • line ribbon, lines (GIF: mono, stereo)
  • spacefill (mono, stereo)
  • hydrogen bonding pattern C=Oi ... H-Ni+4 (VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• Pi helix
  • solid ribbon, lines (GIF: mono, stereo; VRML)
  • line ribbon, lines (GIF: mono, stereo; VRML)
  • hydrogen bonding pattern C=Oi ... H-Ni+5 (VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• 3-10 helix
  • solid ribbon, lines (GIF: mono, stereo)
  • line ribbon, lines (GIF: mono, stereo; VRML)
  • hydrogen bonding pattern C=Oi ... H-Ni+3 (VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• Comparing the helices
  • dihedral angles

                                phi(deg)   psi(deg)  H-bond pattern
  ------------------------------------------------------------------
  right-handed alpha-helix        -65        -40          i+4
  left-handed alpha-helix         +65        +40          i+4
  pi-helix                        -30        -90          i+5
  3-10 helix                      -60        -30          i+3
  
  (omega is 180 deg in all cases)
  -----------------------------------------------------------------
  
  These are the values of the ideal structures shown. A more realistic 
  description from an analysis of experimental structures gives,
  for example 
  (Creighton, Proteins, 2nd ed., W.H. Freeman, 1993, Table 5.2)
  
                                phi(deg)   psi(deg)  H-bond pattern
  ------------------------------------------------------------------
  right-handed alpha-helix        -57        -47          i+4
  pi-helix                        -57        -70          i+5
  3-10 helix                      -49        -26          i+3
  ------------------------------------------------------------------
  
  A left-handed helix was never observed in protein structures.
  

  • all three helix types on one image

Beta strand and Extended conformation

• Beta strand
  • lines (GIF: mono, stereo; VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• Extended Conformation
  • Defintion of Torsional Angles (GIF, VRML)
  • Bond Distances (VRML)
  • Through Space Distances (VRML)
  • Bond Angles (VRML)
  • The coordinates of this model structure were generated with InsightII (Molecular Simulations, Inc.).
• Comparing the conformations

                                phi(deg)   psi(deg)   omega (deg)
  ------------------------------------------------------------------
  extended conformation           180        180         180       
  beta strand                    -120        120         180  
  -----------------------------------------------------------------
  

phi    -      dihedral angle about the N-Calpha bond
psi    -      dihedral angle about the Calpha-C bond
omega  -      dihedral angle about the C-N (peptide) bond

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