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Table 1 Distribution of the residues of the HEL epitopes in the clusters identified by PEPOP

From: PEPOP: Computational design of immunogenic peptides

PEPOP cluster PEPOP segment Position ([PDB: 1SFG] chain A) mAb1
    D1.3 D11.15 D44.1 HyHEL-5 HyHEL-10 HyHEL-63
Cluster1 Segment17 93–94   1/10 (103)    7/16 (93, 96, 97, 100, 101, 102, 103) 7/23 (93, 96, 97, 100, 101, 102, 103)
  Segment18 96–97       
  Segment19 100–103       
Cluster2 Segment2 10–16 10/10 (13, 14, 19, 21, 22, 24, 117, 119, 121, 125) 9/10 (21, 23, 106, 112, 113, 116, 117, 118, 119)    5/16 (15, 16, 19, 20, 21) 8/23 (13, 14, 15, 16, 18, 19, 20, 21)
  Segment20 106–109       
  Segment21 111–114       
  Segment22 116–119       
  Segment23 121–129       
  Segment3 18–24       
  Segment4 27–28       
Cluster3 Segment10 56–57    11/11 (41, 45, 46, 47, 49, 53, 67, 68, 70, 81, 84) 13/14 (41, 43, 44, 45, 46, 47, (63, 73, 75, 48, 49, 89) 53, 67, 68, 70, 84) 4/16(63, 73, 75, 89) 6/23 (62, 63, 73, 75, 77, 89)
  Segment11 59       
  Segment12 61–63       
  Segment13 65–68       
  Segment14 70–79       
  Segment15 81–82       
  Segment16 84–90       
  Segment8 41–49       
  Segment9 53       
Cluster4 Segment1 1–8       
  Segment5 33–35       
  Segment6 37       
  Segment7 39       
amino acids not accessible     1/14 (69)   2/23 (98, 99)
  1. 1 Ratio of the number of amino acids in the epitope included in the cluster to the total number of amino acids in the epitope. The epitopes were defined as in the original publication (D1.3 [54], D11.15 [55], D44.1 [56], HyHEL-5 [57], HyHEL-10 [58], HyHEL-63 [59]). Positions of the amino acids in the epitope included in the cluster are indicated in parentheses. The ratios are in bold for the major clusters.