Amino acid sequence motifs from phage clones isolated after 3 rounds of selection with either M-CLL or U-CLL mAbs
| CLL mAb no. . | Mutation status . | No. of sequences . | Motif/occurrence cutoff, % . | Amino acids comprising motifs* . | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 169 | M-CLL | 8 | 50 | N | Y | — | A | AL/ST | Ali | L | — | — | R | |||||||||
| 183 | M-CLL | 8 | 50 | F | ST | Y | ST | — | — | — | L | HR | — | L | LI | |||||||
| 255 | M-CLL | 16 | 50 | FW | — | — | P | — | — | — | — | W | — | — | Ali | — | Ali | T | ||||
| 412 | M-CLL | 13 | 50 | P | — | — | — | — | Y | H | H | — | FY | — | — | — | ST | |||||
| 014 | U-CLL | 4 | 66.7 | P | ||||||||||||||||||
| 068 | U-CLL | 6 | 50 | ST | — | VL | P | |||||||||||||||
| 114 | U-CLL | 4 | 66.7 | H | ||||||||||||||||||
| 270 | U-CLL | 15 | 50 | — | ||||||||||||||||||
| CLL mAb no. . | Mutation status . | No. of sequences . | Motif/occurrence cutoff, % . | Amino acids comprising motifs* . | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 169 | M-CLL | 8 | 50 | N | Y | — | A | AL/ST | Ali | L | — | — | R | |||||||||
| 183 | M-CLL | 8 | 50 | F | ST | Y | ST | — | — | — | L | HR | — | L | LI | |||||||
| 255 | M-CLL | 16 | 50 | FW | — | — | P | — | — | — | — | W | — | — | Ali | — | Ali | T | ||||
| 412 | M-CLL | 13 | 50 | P | — | — | — | — | Y | H | H | — | FY | — | — | — | ST | |||||
| 014 | U-CLL | 4 | 66.7 | P | ||||||||||||||||||
| 068 | U-CLL | 6 | 50 | ST | — | VL | P | |||||||||||||||
| 114 | U-CLL | 4 | 66.7 | H | ||||||||||||||||||
| 270 | U-CLL | 15 | 50 | — | ||||||||||||||||||
Multiple alignments were performed using the ClustalW2 multiple sequence alignment tool.32 Peptide motifs were identified by requiring 50% amino acid identity or chemical similarity for positions at which 6 or more residues were available; a score of 66.7% was required when fewer than 6 residues were present at a given alignment position. The following list of chemical similarities was used for these assignments: Ali(phatic): A, V, L, I; aliphatic with polar hydroxyl group: S, T; neutral with polar side chains: N, Q, C, M; cyclic imino: P; nonpolar: G; acidic: D, E; basic: H, K, R; aromatic: F, Y, W.