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        -57.8      -47.0        i+4
  pi-helix                        -57.1      -69.7        i+5
  3-10 helix                      -74.0       -4.0        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)
  
  or (n parentheses) values given by the PPS course 
  (http://broccoli.mfn.ki.se/pps_course_96/ss_960723_6.html).
  
                                phi(deg)   psi(deg)  H-bond pattern
  ------------------------------------------------------------------
  right-handed alpha-helix        -57 (-64)  -47 (-41)    i+4
  pi-helix                        -57        -70          i+5
  3-10 helix                      -49 (-71)  -26 (-18)    i+3
  ------------------------------------------------------------------
  
  

  • All three right-handed 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
  • Definition 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  
  -----------------------------------------------------------------
  

enlarge image

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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