Protein structure

Helices

Type	310	α	π
Residues per turn	3.0	3.6	4.4
Atoms in H-bonded ring	10	13	16
Hydrogen bonding	n-n+3	n-n+4	n-n+5
Angle between neighboring residues	120	100	82
Helical rise per amino acid residue (Å)	2.0	1.5	1.15
Φ (°)	-49	-60	-57
Ψ (°)	-26	-45	-70

• π-helix – methan monooxygenase from Methylococcus capsulatus (1MTY), chain E, residues 306-317
  • sele chain E and resi 306-317
  • zoom to selection (A button (=action) → zoom)
  • show (S button) selection as cartoon and sticks
  • A → find → polar contacts → just intra-main chain
• 3₁₀ helix – Aplysia limacina myoglobine (1MBA), residues 35-43
  • sele resi 35-43
  • zoom to selection
  • show selection as cartoon and sticks
  • hide waters (H button)
  • A → find → polar contacts → just intra-main chain
• α-helix – haloalkane dehalogenase DhaA (1CQW), residues 230-239
  • sele resi 230-239
  • hide everything
  • show selection as cartoon and sticks
  • zoom to selection
  • A → find → polar contacts → just intra-main chain
  • measure dihedral angles Φ (C²³³-N²³⁴-C_α²³⁴-C²³⁴) and Ψ (N²³⁴-C_α²³⁴-C²³⁴-N²³⁵) of the GLU 234 residue

β-structures

• β-sheet – haloalkane dehalogenase DhaA (1CQW)
  • paralel, residues 111-116 and 134-140
    • hide everything
    • sele resi 111-116 or resi 134-140
    • show selection as cartoon and sticks
    • A → find → polar contacts → just intra-main chain
  • antiparalel, residues 24-28 and 31-38
    • sele resi 24-28 or resi 31-38
    • show selection as cartoon and sticks
    • A → find → polar contacts → just intra-main chain
    • measure dihedral angles Φ (C²⁴-N²⁵-C_α²⁵-C²⁵) and Ψ (N²⁵-C_α²⁵-C²⁵-N²⁶) of the TYR 25 residue
• β-turn – haloalkane dehalogenase DhaA (1CQW), residues 28-31
  • show structure as cartoon
  • sele resi 28-31
  • show sticks for selection
  • label (L button) with residue identifier
  • color (C button) selection a different color (by element)
  • A → find → polar contacts → within selection
• polyproline helix – colagen (1Q7D)
  • show as sticks
  • color by chains
  • find polar contacts of the backbone

Folds

• α-protein
  • up-and-down bundle – coat protein of tobacco mozaic virus (2TMV)
    • color carbon atoms as spectrum
  • globin-like – Aplysia limacina myoglobine (1MBA)
    • color by secondary structure
    • show protein surface
• β-protein
  • jellyroll – coat protein of satellite tobacco necrosis virus (2BUK)
    • color carbon atoms as spectrum
  • β-barrel – Escherichia coli porin Ompf (2OMF)
    • color carbon atoms as spectrum
    • show surface
  • β-propeller – G protein (1GOT), chain B,
    • sele chain B
    • invert selection: A → modify → invert → within any
    • remove selected atoms
    • color carbon atoms as spectrum
    • show surface
• α/β-protein
  • Rossmann –3α,20β-hydroxysteroid dehydrogenase (1HDC), chain A
    • sele chain A
    • extract selection to object
    • rename object to chainA
    • hide 1HDC
    • zoom on object chainA
    • color it as spectrum
  • TIM barell – triosephosphate isomerase (1YPI), chain A
    • sele chain A
    • extract selection to object
    • hide 1YPI
    • color object as spectrum
• α+β-protein
  • β-Grasp (ubiquitin-like) – ubiqitin (1UBQ)
    • color as spectrum

Nucleic acid structure

DNA

• A-DNA (440D)
• B-DNA (3BSE)
• Z-DNA (2DCG)
• For nucleic acid structures:
  • remove water molecules
  • show lines on top of cartoon
  • find polar contacts
  • show surface
• nucleosome (1KX3)
• color by chain

RNA

• A-RNA helix – 16S rRNA from Thermus thermophilus (1N32), chain A, nucleotides 656-682, 705-716 and 734-750
  • sele chain A and resi 656-682 or resi 705-716 or resi 734-750
  • hide everything
  • show selection as cartoon and lines
  • show surface for selection
• bulge loop – HIV-1 trans-activation response region, RNA stem (397D), nucleotides 23-25
  • sele resi 23-25
  • color selection red
  • find polar contacts within selection
  • label the selected residues
• hairpin loop (UNCG tetraloop) – ribosomal A site (1BYJ), nucleotides 12-15
  • show lines on top of cartoon
  • sele resi 12-15
  • show sticks for selection
  • color selection by elements
  • label the selected residues
  • find polar contacts within selection
• phenylalanine tRNA (1EIY), chain C
  • sele chain C
  • extract selection to object
  • hide everything and show object as cartoon
• hammerhead ribozyme (3ZD5)
  • show lines on top of cartoon
  • show surface