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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.
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BMC Bioinformatics

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