Peptide chain structure parameters, bond angles and conformational angles from the Cambridge Structural Database

Ashida, Tamaichi; Tsunogae, Yasuo; Tanaka, I.; Yamane, Takashi

doi:10.1107/s0108768187098045

Cited by 127 publications

(50 citation statements)

References 2 publications

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“…In general, bond lengths and bond angles of the Acc5 residue agree well with those reported for the trans peptide unit (53,54) and the Aib (54-57) and A C C~ (21) residues. The average value for the N-Ca-C' (7) bond angle is higher than the regular tetrahedral value, but the known dependence of this angle on the +torsion angle is found also in this study: in particular, the Acc5 residue in the semi-extended conformation (compound 3) shows a value closer to 109.5" than the A C C~ residues in the helical conformation (compounds 1 , 2 , 4 , and 5).…”

Section: X-ray D~pactionsupporting

confidence: 77%

Linear oligopeptides. 188.Crystallographic characterization of the conformation of the 1-aminocyclopentane-1-carboxylic acid residue in simple derivatives

Valle¹,

Crisma²,

Toniolo³

1988

Can. J. Chem.

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GIOVANNI VALLE, MARCO CRISMA, and CLAUDIO TONIOLO. Can. J. Chem. 66, 2575Chem. 66, (1988. The crystal structures of six derivatives of the Cm."-dialkylated a-aminoacid residue 1-aminocyclopentane-1-carboxylic acid (Acc5) have been determined. These are Z-AccS-OH, Z-Acc5-OH acetone hemi-solvate, Fmoc-Acc5-OH, m C l~c -~c c~-O H , p~r~z -~c c 5 -O~, and the 5(4H)-oxazolone from p~r~z -~c c s -O~. The values determined for the torsion angles about the N-Ca (4) and Ca-CO ($1 bonds correspond to folded, potentially a/310-helical conformations for the AccS residue of Z-AccS-OH, Z-AccS-OH acetone hemi-solvate, mC1Ac-Acc -OH, and p~r~z -~c c 5 -~~. The structure of F~O C -A C C~-O H , however, is unusual in having a semi-extended conformation for the 4 , I) angles, accompanied by a cis arrangement of the amide group of the secondary urethane moiety. The dependence of the N-Cm-C' bond angle on the I) torsion angle and the asymmetry at the Ca atom are relevant features of the Acc5 residues. The position of the cyclopentyl ring relative to the peptide chain and its puckering parameters for the six compounds are also discussed.GIOVANNI VALLE, MARCO CRISMA et CLAUDIO TONIOLO. Can. J. Chem. 66,2575Chem. 66, (1988. On a dCterminC les structures cristallines de six dCrivCs Ca~a-dialkylCs du rCsidu d'acide a-aminC, amino-1 cyclopentanecarboxylique-1 (Acc5). I1 s'agit du Z-Acc5-OH, du Z-AccS-OH hCmisolvatC par 17acCtone, du ~moc-Acc5-OH, du mC1Ac-AccS-OH, du p~r~z -~c c S -O~ et de la (4H)-oxazolone-5 prkparte a partir du p~r~z-AccS-OH. Les valeurs qui ont Ct C obtenues pour les angles de torsion autour des liaisons N-Ca (4) et Ca-CO (I)) du rCsidu AccS du Z-AccS-OH, du Z-AccS-OH hCmisolvatC par l'acCtone, du mC1Ac-Acc5-OH et du pBrBz-Accs-OH correspondent a des conformations repliCes qui sont possiblement a/310-hClicoldales. Toutefois, la structure du Fmoc-Acc5-OH est inhabituelle; sur la base des angles 4 et I) elle posskde une conformation semi-Ctendue qui est accompagnte par un arrangement cis du groupement amide de la portion secondaire de l1urCthane. Le fait que l'angle de la liaison N-Ca-C' varie en fonction de I'angle de torsion I) et de I'asymCtrie du Ca et sont caractCristiques importantes des rCsidus Acc5. On discute aussi de la position du cyclopentane par rapport i la chahe peptidique ainsi que des paramktres de plissement des six composCs.[Traduit par la revue]

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Section: X-ray D~pactionsupporting

confidence: 77%

Linear oligopeptides. 188.Crystallographic characterization of the conformation of the 1-aminocyclopentane-1-carboxylic acid residue in simple derivatives

Valle¹,

Crisma²,

Toniolo³

1988

Can. J. Chem.

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“…The geometry observed for the urethane, the amide bonds and the Z moieties is in good agreement with literature data [43][44][45][46] for all the peptides. In each struc-ture all the peptide bonds are trans and the urethane moiety is characterized by a type b conformation, 43,44 with a trans arrangement of both 1 and 0 torsion angles [peptide a: 1 ϭ Ϫ175.6(7)°, 0 ϭ 178.3(7)°; peptide b: 1 ϭ 173.9(6)°, 0 ϭ Ϫ176.8(4)°; peptide c: 1 ϭ 178.8(11)°, 0 ϭ Ϫ165.4(9)°; peptide d:…”

Section: Terminal Groups and Backbone Structuresupporting

confidence: 88%

“…The geometry of the peptide bond is in agreement with that reported in literature for the peptide unit. 45,46 The angle has a value of 112.2°larger than the regular tetrahedral value, in agreement with that reported for folded structures 23 ; the value for the angle is 101.7°. The bond angles N-C …”

Section: Geometry Of the Afc Residuesupporting

confidence: 85%

“…The geometry of the peptide bond is in agreement with that reported in literature for the peptide unit. 45,46 The average value for the angle (107.5°) is slightly smaller than the regular tetrahedral value, 23 while the average value for the angle is 101.1°. The average values of the bond angles N-C ␣ -C ␤2 and CЈ-C ␣ -C ␤1 , which represent a measure of the inclination of the amino and the carbonyl functions, respectively, toward the ring plane, are 115.0°and 107.2°.…”

Section: Geometry Of the Afc Residuementioning

confidence: 92%

See 1 more Smart Citation

The crystal structure of Afc-containing peptides

Lombardi¹,

Simone²,

Galdiero³

et al. 2000

Biopolymers

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“…All the values are in the expected ranges (Sequeira et al, 1981;Ashida et al, 1987;Engh & Huber, 1991). The geometry of the carboxyl groups is typical of an ionized form (Parthasarathy et al, 1974): the asymmetry between the two CÐO distances and OÐCÐC angles can be ascribed to the different hydrogen-bonding patterns involving the two carboxylic O atoms (see Tables 2 and 4).…”

Section: Commentmentioning

confidence: 88%