Figure 1. Levels of structural organization in proteins: from primary (i.e., the amino acid sequence) to secondary structure elements (an α‐helix and an antiparallel three β‐stranded β‐sheet are shown here) to tertiary and quaternary structure. Tertiary and quaternary structures are represented by the monomer and the dimer of the human Cu,Zn superoxide dismutase (PDB ID: 1L3N), respectively.

Figure 2.

1. Scheme of the backbone dihedral angles ω, ϕ, and ψ. The atoms C ^α–C–N′–C ^α′ and C ^α′–C′–N″–C ^α″ are confined to be in a plane (peptide plane). The atoms bound to C ^α and C ^α″ (H ^α and side‐chain) are not shown for clarity.
   
2. Ramachandran plot. The most favored, the allowed, and the generously allowed regions are shown in red, yellow, and beige, respectively. The sterically disallowed conformations (atoms come closer than the sum of the van der Waals radii) are in white. The graph has been generated with the PROCHECK program [ 46].
   

Figure 3. Side‐chain dihedral angles are named χ ₁ (defined by the atoms N–C ^α–C ^β–C ^γ), χ ₂ (defined by the atoms C ^α–C ^β–C ^γ–C ^δ), χ ₃ (defined by the atoms C ^β–C ^γ–C ^δ–Cɛ), and so on.

1. Side‐chain dihedral angles for a Lys residue. Schematic representation of the side‐chain dihedral angle χ ₁ for Val
   
2. and Ile
   
3. residues.
   

For Val the staggered conformation with χ ₁ = 180° is the sterically and energetically more favored because the two methyl groups bound to C ^β are both close to the small H ^α atom, while for Ile the most favored conformation is the one with χ ₁ = 300°.

Figure 4. Side view of a right‐handed α‐helix

1. In the top and bottom views of the same α‐helix, the four non‐hydrogen‐bonded carbonyl groups at the C‐terminus
   
2. and the four non‐hydrogen‐bonded nitrogen groups at the N‐terminus
   
3. are pointing upwards towards the viewer.
   

The side‐chain atoms are not shown for clarity. The residues are represented as balls and sticks, and the hydrogen bonds (i.e., O _i and N _{i + 4} ) are shown as dashed black lines.

Figure 5. Parallel

1. and antiparallel
   
2. three β‐stranded β‐sheets.
   

The side‐chain atoms are not shown for clarity. The residues are represented as balls and sticks, and the hydrogen bonds are shown as dashed black lines.

Figure 6.

1. Example of a classic β‐bulge. The side‐chains (green spheres) of the three residues forming the β‐bulge (in this example residues Ile15, Lys16, and Lys24 of the solution structure of staphylococcal nuclease, PDB ID: 2KHS) are all above the plane. The hydrogen bonds are shown as dashed black lines.
   
2. Type I and
   
3. type I′ β‐turns. The residues forming the β‐turns are shown as balls and sticks. PDB IDs 9PAP and 2ACT were used to generate type I and I′ β‐turns, respectively. The hydrogen bonds (i.e., O _i and N _{i + 3} ) are shown as dashed black lines.
   

Figure 7.

1. Topology diagram of a Greek key motif. Three antiparallel β‐strands are connected by two short β‐turns, followed by a long turn connecting the fourth β‐strand, which is hydrogen‐bonded in an antiparallel arrangement with the first β‐strand.
   
2. Up‐and‐down topological diagram of eight antiparallel β‐strands joined by hairpins. An up‐and‐down β‐barrel is formed when the first β‐strand is joined by hydrogen bonds to the last one.
   
3. Jelly roll topological diagram.
   

Figure 8. Example of coiled‐coil (a, PDB ID: 2XU6, MDV1 coiled‐coil domain), four‐helix bundle (b, PDB ID: 1QPU, cytochrome b ₅₆₂), and globin (c, PDB ID: 2HHB, human deoxyhemoglobin) types of fold. They represent the three major ways for α‐helices to pack together to generate domains of the α‐class. The heme porphyrin rings are shown as sticks in cytochrome b ₅₆₂ and human deoxyhemoglobin.

Figure 9. Example of β‐barrel

1. PDB ID: 1PRN, membrane channel porin), β‐sandwich
   
2. PDB ID: 1F6L, variable light chain dimer of antiferritin antibody) and six β‐propeller types of fold
   
3. In the β‐propeller the six motifs formed by four up‐and‐down antiparallel β‐strands are shown with different colors.
   
4. γB crystallin protein (PDB ID: 4GCR). The protein is composed of two domains. Each domain is built from an eight‐stranded antiparallel β‐sandwich structure composed of two Greek key motifs shown in red and green, respectively, for the N‐terminal domain. The C‐terminal domain is shown as a white ribbon for clarity.
   
5. Greek key β‐barrel fold adopted by the N‐terminal domain of Fusarium oxysporum trypsin protein (PDB ID: 1FN8).
   

The Greek key motif is shown in red. The four β‐strands forming the Greek key motif are numbered as in Figure 7a.

Figure 10.

1. α/β‐barrel/TIM fold present in the N‐terminal domain of Ala racemase (PDB ID: 1EPV).
   
2. α/β‐twist/Rossman fold in lactate dehydrogenase enzyme (PDB ID: 1A5Z).
   
3. α/β‐horseshoe fold in porcine ribonuclease inhibitor (PDB ID: 2BNH).
   

Figure 11.

1. Chemical structures of nucleobases adenine (A), guanine (G), thymine (T), uridine (U), and cytosine (C).
   
2. Nucleotide structure and definition of torsion angles. The 2′‐OH group present only in RNA is indicated in blue.
   
3. Watson–Crick base pairs.
   
4. Left: structure of two most populated sugar conformations C3′‐endo and C2′‐endo. Right: presentation of the sugar pucker mode described by the pseudorotation phase P and puckering maximum amplitude ν _max.
   

Figure 12. Ribosomal RNA torsion angle distribution extracted from the crystal structure (PDB ID: 1JJ2, 2736 residues). The one‐dimensional torsion angle distributions show two sets of residues that have been separated by residues with C3′‐endo (black) and C2′‐endo (blue) sugar conformation. The two‐dimensional plot shows the correlation of torsion angles ζ _i and α _i+1 for all residues.

Figure 13. Structures of B‐DNA, Z‐DNA, A‐DNA, and A‐RNA.

Figure 14.

1. Crystal structure of the triplex DNA (PDB ID: 1D3R).
   
2. NMR structure of the human telomeric i‐motif d(CCCTAA ^5meCCCTAACCCUAACCCT) (PDB ID: 1EL2).
   
3. Guanine quartet showing the Hoogsteen hydrogen bonds.
   
4. Various G‐quadruplex strand stoichiometries.
   
5. Crystal structure of the unimolecular d(AG ₃(TTAG ₃) ₃) G‐quadruplex in K ⁺ ions (PDB ID: 1KF1).
   
6. NMR structure of the bimolecular d(G ₃T ₄G ₄) G‐quadruplex in Na ⁺ ions (PDB ID: 1U64).
   
7. Crystal structure of the quadrimolecular d(TG ₄T) G‐quadruplex (PDB ID: 352D).
   

Figure 15.

1. Some examples of RNA structure elements. The nucleic acid backbone is indicated by a thick line and the bases by thin lines. The size of the stems, loops, connections and bulges are variable.
   
2. G·U wobble base pair.
   
3. Reverse Hoogsteen A·U base pair.
   
4. cis‐Watson–Crick–Hoogsteen G·A base pair.
   
5. C·G·CH ⁺ base triplet.
   

Figure 16.

1. U‐turn RNA motif of the crystal structure of the 58 nucleotide ribosomal RNA fragment (PDB ID: 1HC8).
   
2. K‐turn RNA motif of the Haloarcula marismortui large ribosomal subunit (PDB ID: 1JJ2).
   
3. C‐loop RNA motif of the Escherichia coli threonyl‐tRNA synthetase mRNA (PDB ID: 1KOG).
   
4. Kissing loop RNA motif of the Vibrio vulnificus A‐riboswitch with U34·A65·C61–G37 and A33·A66·C60–G38 tetrads (PDB ID: 1Y26).
   
5. The UUCG tetraloop RNA motif and NMR restraints statistics of the 14mer cUUCGg tetraloop RNA structure (PDB ID: 2KOC).