Side chain stereo view

Fig. 37.—(a) Stereo view of one turn of the 3-fold double helix of welan (43). The two chains are drawn in open and filled bonds for distinction. The vertical line represents the helix axis. Both intra-and inter-chain hydrogen bonds and side chains, hydrogen bonded to carboxylate groups, stabilize the double helix. Calcium ions (crossed circles) are present near the carboxylate groups, but outside the helix to make inter double-helical connections. 

Fig. 38.—Stereo view of three turns of the 2-fold galactomannan (45) helix containing galactose side-chains on alternate mannose residues. In this conformation, the side chains are turned up toward the non-reducing end, and the backbone is stabilized by intrachain hydrogen bonds. The helix axis is represented by the vertical line.

Fig. 39.—fa) Stereo view of two turns of the left-handed. 2-fold helix of E. coli capsular polysaccharide (46) stabilized by hydrogen bonds involving both main and side chains. The vertical line represents the helix axis. 

FIGURE 2.6 The procarcinogen benzo[a]pyrene oriented in the CYPlAl active site (stereo view) via n- n stacking between aromatic rings on the substrate and those of the complementary amino acid side chains, such that 7,8-epoxidation can occur. The substrate is shown with pale lines in the upper structures. The position of metabolism is indicated by an arrow in the lower structure (after Lewis 1996). 

Fig. 2.12 The j8-peptide 3,4-helical structure. (A) Stereo-view along the helix axis of the left-handed 3,4-helix formed by, 8 -peptide 66 in solution as determined by NMR in CD3OH (adapted from [103, 154]). Side-chains have been omitted for clarity. (B) Top view.

Fig. 2.30 Comparison of antiparallel hairpin structures in / -peptides 120-122. (A) / -Pep-tides 120, 121 with a 12-membered R/S dini-pecotic (Nip or/ -HPro) turn segment (gray color). Summary of backbone-backbone and side-chain-side-chain NOEs collected in CD2CI2 and X-ray crystal structure of 121 (stereo-view) [154, 193], The intramolecular H-bond N" 0 distances are shown. The angles (N-H -O) are 170.8° (inner H-bond) and 1 72.3 ° (outer H-bond). (B) jS-Peptide 122 with...

Fig. 2.36 The y-peptide 2.614-helical fold. (A) Stereo-view along the helix axis of the (P)-2.6i4-helical structure adopted by y -hexapep-tide 141 in pyridine. This low energy confor-mer was obtained by simulated annealing calculations under NMR restraints. Side-chains have been partially omitted for clarity.

Fig. 103. Basic pancreatic trypsin inhibitor as an example of a small disulfide-rich structure, (a) a-Carbon stereo (b) backbone schematic, viewed as in a, with disulfides shown as zig-zags. Figure 2 shows an all-atom stereo of this protein with side chains.

Fig. 4 Stereo views (in transparent, space-filling models) of selected hydrophobic interactions in the Fab-peptide and -pentasaccharide complexes. A Trp P3 buried in the hydrophobic cavity formed by CDR L3, His H58 and Trp H47. B Interactions of the side chain of Met P5 with Trp H33. C and D Interactions of the peptide and pentasaccharide, respectively, with His L27D and Tyr L32 (the pocket which accommodates the GlcNAc D methyl group). In (C) the hydrogen bond between the Asp P2 side chain and His L27D NE2 is also shown. A corresponding hydrogen bond between Rha Al 3-OH and His L27D NE2, shown in (D), represents an element of structural mimicry. Reproduced from [80]. 2003 by The National Academy of Sciences of the USA...

Stereo view of the peptidomimetic inhibitor Ro 31-8959 (saquinavir) bound to the active site of HIV PR. The distribution of the specificity subsites S and S is identical to that shown in Figure 2. Note the stacking interaction between the quinoline moiety and the PI side chain of phenylalanine. 

Stereo view of the sixty propane minima (thick lines) obtained with the modified force field (see text) on the surface of the A peptide chain (medium lines) of the GCN4 leucine zipper (PDB code 2ZTA). Although the peptide chain was removed during the MCSS procedure, its backbone and hydrophobic side chains are also drawn (thin lines) to show how the propane minima match the aliphatic groups of chain B. Hydrophobic residues are labeled at their Ca atom.Five clusters of propane minima that do not match the hydrophobic side chain of the helix involved in the interhelical interactions are labeled from A (top right) to E (bottom center) and discussed in the text. 

Figure 24 Stereo views of (A) computed39 179 and (B) X-ray180 structures of gramicidin S, showing (among other things) a hydrogen bond between the ornithine side chain and the phenylalanine backbone carbonyl group.

Fig. 19.11. Stereo view showing two of the situations given in Fig. 19.10b. In myoglobin, the side-chain of Ser3 at the N-terminus of helix A hydrogen bonds with the free NH of residue 6, (n) to NH(n+3), and the carboxylate of Glu6 interacts with NH of residue 3, (n) to NH(n-3). Ca atoms drawn hatched, all side-chains (except those mentioned) indicated only with their Cp atoms [596]...

Fig. 14. X-ray crystal structure of full-length yeast CCS [pdb code Iqup (Lamb et al., 1999)]. (a) One monomer of yCCS is in light gray and the other is in dark gray. The cysteine residues of the MXCXXC motif in domain 1 are labeled and form a disulfide bond in each subunit. Amino acid side chains that are important in the formation of the positive patch at the dimer interface (Arg-188 and Arg-217) and the solvent-exposed Trp-183 residues of loop 6 at the center of this patch are shown in ball-and-stick representation. Domain 3 is not visible in the crystal structure (see text), (b) Stereo view of the image in (a) rotated 90° in the horizontal plane of the page and then 90° counterclockwise around an axis perpendicular to the page. The side chains that form the putative ySODl interaction surface are represented as ball-and-stick. The cysteine residues of the domain 1 MXCXXC motif are also represented in ball-and-stick.

Fig. 11. A stereodiagram of the Ca trace of apo- and holo-ALBP. The small stereo diagram at the bottom shows the Ca models of both the apo and the holo forms of crystalline ALBP. Every tenth residue is numbered, and because of the close similarity in the conformation of the two proteins much of the diagram appears as one solid line. At the top of the molecule (shown in the enlargement) Phe-57 appears twice. This is due to the fact that this side chain has two different conformations in the structures of the apo and holo forms. With Phe-57 swung to the left, the holo-form is viewed. When located in the rightmost position, Phe-57 is as appears in the apo form, seemingly closing the portal to the ligand-binding cavity.

Fig. 7. Stereo view of human serum albumin illustrating the overall topology and secondary structure. The positions of the 17 disulfides and the side chain of Cys-34 are shown in red. Structurally, HSA consists of 28 helices, which range in size from 5 to 31 amino acids in length and which can be grouped into 10 principal helices within each domain. The positions of the two major binding sites of HSA, located within subdomains IIA and IIIA, are illustrated with the ligand 2,3,5-triiodobenzoic acid, shown in white. Figure drawn using program RIBBONS (Carson, 1987).

Fig. 13. Stereo view showing the homology between the triiodobenzoic acid-binding sites within subdomain IIA (A) and subdomain IIIA (B) the subdomains have been superimposed by the method of least squares. The protein components are shown in orange and green for ESA and HSA, re.spectively, and the positions of bound triiodobenzoic acid are shown in red and yellow for ESA and HSA, respectively. It should be noted that many of the side-chain conformations illustrated in Fig. 6 can be determined with confidence only at higher resolution. In addition, the complex has not been refined. Reproduced with permission from Ho et al. (1993). 

Figure 13 shows stereo views of the a-carbon skeletons of the three CDR of the four light chains, and Fig. 14 shows the three CDR of the two heavy chains. Even without the side chains the differences in orientation are striking. The differences in secondary structure clearly reveal the nature of immunological specificity in that no two backbones are alike in secondary structure addition of different side... 

FIGURE 18.10 The two central CP binding sites in a mutant CIC Cl /H+exchanger (PDB code lOTU). Stereo view of the ion-binding sites. Selected residues in the vicinity of the bound chloride ions are shown. Hydrogen bonds between the protein and chloride ions (red spheres) as well as between the side chain of Glu " and the rest of the protein are shown as black dashed lines. (From Dutzler et al., 2003. Copyright2003 with permission from AAAS.)... 

Figure 9. Thermolysin-inhibitor complex - an example of inhibitors bound to zinc endoproteases with the long spacer consensus. A stereo view of the active site site of thermolysin showing details of enzyme-inhibitor 2 interactions (Brookhaven Databank Code 5TLN). Enzyme side chains involved in inhibitor recognition are shown in magenta. The color code is as given for Fig. 6.

Fig. 5. Stereograms of the LHC-il complex seen from the stromal side. (A) dashed chain indicates a tentative fit of residues 100-116. (B) a corresponding stereo view ofthe chlorophyll and lutein molecules only. Figure source KQhIbrandt, Wang and Fujiyoshi (1994) Atomic model of plant light-harvesting complex by electron crystallography. Nature 367 618.

Figure 8.51. Stereo representations of the 14 lowest-energy calculated structures of the hexameric P-peptide 8.23 based on distance restraints derived from ROESY spectra. Side and top views are shown in (a) and (b) respectively, with the side chains of the p-amino acids omitted for clarity (reproduced with permission from [74]).

Fig. 3. Stereo view of the all heavy-atom presentation of a single conformer of the globular domain in bPrP(121-230). Brown color is used for 20 amino side chains that form a hydrophobic core of the protein molecule (see text).

Figure 14 Stereo view of the newly ordered loops showing their relationship to the active site and enzyme surface. The inner loop (401 13) is colored in yellow while the outer loop (541-557) is colored in blue. Individual subunits in the El dimer are shown in red and green, respectively. The PLThDP and side chain for His407 are shown with a ball and stick representation.

Fig. 11. Stereo view of C2 jaws of the apo and Sm1 forms of PLC-51. The apo form is shown with dark backbone and light side chains, and the Sm3t form with light backbone and dark side chains. (Redrawn with permission from Grobler et al. 1996.)...

Fig. 7. Stereo pair a-carbon drawing of reduced tuna cytochrome c. Only those side chains which bond to the heme, and a few key lysines and aromatic groups, are shown. The heme is seen in vertical edge view at the center. Adapted from reference 7.

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