TABLE 4.
φ and ψ torsion angles for CDR H2 residues as part of the motif Xaa-Xaa-Gly-Gly-(Ser/Thr/Gly)
Angles are averaged in cases with multiple molecules in the asymmetric unit. Numbers 52–56 refer to the Kabat numbering scheme of CDR H2 residues, and italicized numerals refer to the position of the residue in a β-turn.
CDR H2 residue dihedral angles (°) |
Antibody | Primary sequence | Resolution | Turn type | PDB code | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
52 or 52A, 0 | 52A or 53, +1 | 53 or 54, +2 | 54 or 55, +3 | 55 or 56 | ||||||||||
Å | ||||||||||||||
φ | ψ | φ | ψ | φ | ψ | φ | ψ | φ | ψ | |||||
−71.9 | 163.0 | −32.5 | −63.4 | −93.4 | 2.31 | 86.5 | 10.5 | −67.8 | −31.0 | S55-3 | SNGGS | 1.95 | IVa | 4DQ9 |
−71.0 | 167.2 | −54.2 | −36.4 | −100.4 | −7.86 | 91.7 | 1.64 | −80.6 | −12.2 | S55-5 | SRGGS | 1.94 | I | 5DQD |
−72.5 | 168.6 | −60.7 | −36.3 | −88.2 | −10.0 | 78.6 | −1.78 | −68.0 | −37.7 | LPT-3 | GGGSS | 2.69 | I | 4C83 |
−79.7 | 172.0 | −57.6 | −39.4 | −79.1 | −4.48 | 95.5 | −8.60 | −65.9 | 155.7 | S25-26 | WSGGS | 1.95 | I | 4M7J |
−62.4 | 155.8 | −62.4 | −41.1 | −60.6 | −47.1 | 111.7 | −19.0 | −73.6 | −10.3 | A10F9 Fab | SSGGS | 3.20 | III | 3VRL |
−64.5 | 155.3 | −61.3 | −28.0 | −98.4 | −5.47 | 90.7 | −26.7 | −62.2 | −41.6 | 17/9 Fab | SNGGG | 2.90 | I | 1HIM |
−71.5 | 151.3 | −51.5 | −32.3 | −90.2 | −8.04 | 82.2 | 8.61 | −96.8 | −5.02 | mAb8 Fab | SSGGS | 2.85 | I | 4HZL |
−67.8 | 169.3 | −55.9 | −42.3 | −91.2 | 0.99 | 83.2 | −0.04 | −67.9 | −28.6 | Anti-parathyroid hormone-related protein | SSGGS | 2.00 | I | 3FFD |
−72.1 | 168.1 | −53.2 | −32.9 | −118.0 | 16.7 | 71.8 | 15.6 | −65.8 | −33.3 | Thr(P)-231/Ser(P)-235 | TSRGGb | 1.90 | I | 4GLR |
−76.6 | 168.0 | −53.5 | −35.3 | −80.6 | −13.0 | 80.5 | 12.9 | −103.3 | −40.5 | pSAb | ATGGH(T)c | 1.75 | I | 4JFZ |
−79.7 | 151.3 | −62.4 | −63.4 | −118.0 | −47.1 | 71.8 | −26.7 | −100.3 | −41.6 | Minimum | ||||
−62.4 | 172.0 | −32.5 | −28.0 | −60.6 | 16.7 | 111.7 | 15.6 | −62.2 | 155.7 | Maximum | ||||
17.3 | 20.7 | 29.9 | 35.4 | 57.4 | 63.8 | 39.9 | 42.3 | 38.1 | 65.9 | Difference |
a Turns that do not fall into any known classes are grouped under the miscellaneous type IV class.
b Outlier in terms of the motif sequence involved in binding to negative charge.
c The β-turn starts at the alanine residue, but this residue is not involved in recognition of the anion.