In-silico design and evaluation of an epitope-based serotype-independent promising vaccine candidate for highly cross-reactive regions of pneumococcal surface protein A

Table 4 Dimplot interaction plot analysis between PspA_1-5c+p residues and HLF molecule in the docked complex and control. a The interaction detail between PspA (clade2) residues and HLF A and B chains (as a docked control model). b The interatin detail between model 0 of PspA_1-5c+p residues (Family 2 Domain) and HLF A and B chains. And c The interaction detail between model 2 of PspA_1-5c+p residues (Family 1Domain) and HLF A and B chains

(a)
PspA(clade2)-HLF docked complex (2PMS)
Atom name	Res. No.	Res. name	H-bond distance (A°)	Atom name	Res. No.	Res. name	H-bond distance (A°)
PspA (clade2) (C chain)				HLF (A chain)
ND2	183	Asn	2.76	O	39	Lys	2.76
OE1	180	Glu	3.05	NZ	39	Lys	3.05
NE2	175	Gln	3.04	O	21	Phe	3.04
OE1	175	Gln	3.14	NH1	25	Arg	3.14
NH2	175	Gln	2.68	OE1	24	Gln	2.68
OD1	231	Asp	3.23	NE	5	Arg	3.23
OE2	182	Glu	2.45	NH1	40	Arg	2.45
OE1	279	Glu	2.97	NH2	28	Arg	2.97
OE2	279	Glu	3.07	NH1	28	Arg	3.07
OD2	237	Asp	2.77	NE	28	Arg	2.77
PspA (clade2) (C chain)				HLF (A chain)
ND2	183	Asn	2.81	O	39	Lys	2.81
OE1	180	Glu	2.92	N2	39	Lys	2.92
OE2	171	Glu	3.15	NE2	14	Gln	3.15
OD1	231	Asp	3.15	N	5	Arg	3.15
OD1	231	Asp	3.14	NE	5	Arg	3.14
OD2	231	Asp	2.91	NB2	5	Arg	2.91
NE2	175	Gln	2.53	OE1	24	Gln	2.53
NE2	175	Gln	3.25	O	21	Phe	3.25
OE2	279	Glu	3.02	NH1	28	Arg	3.02
OE1	175	Gln	3.06	NB1	25	Arg	3.06
OD2	237	Asp	2.76	NE	28	Arg	2.76
OE2	182	Glu	3.28	NB2	40	Arg	3.28
OE2	182	Glu	2.52	NB1	40	Arg	2.52

(b)
PspA_1-5c+p-HLF docked complex (Model 0)
Atom name	Res. No.	Res. name	H-bond distance (A°)	Atom name	Res. No.	Res. name	H-bond distance (A°)
PspA_1-5c+p (C chain)				HLF (A chain)
OD2	385	Asp	2.78	NB1	28	Arg	2.78
OD2	371	Asp	2.74	NB2	28	Arg	2.74
OE1	375	Glu	2.73	NB2	28	Arg	2.73
O	381	Ala	2.67	NB1	25	Arg	2.67
OE2	378	Glu	3.11	N	24	Gln	3.11
OE2	378	Glu	2.78	NB1	4	Arg	2.78
OE1	374	Glu	2.94	N	24	Gln	2.94
OE2	374	Glu	2.93	OC	6	Ser	2.93
O	374	Glu	2.83	N	24	Gln	2.83
N2	382	Lys	2.57	OE1	24	Gln	2.57
OE1	367	Glu	2.67	NB1	5	Arg	2.67
OE1	367	Glu	2.69	NB2	5	Arg	2.69
O	373	Asp	2.65	NB2	4	Arg	2.65
OD1	373	Asp	2.76	NE	4	Arg	2.76
OD2	373	Asp	2.67	NB2	4	Arg	2.67
OE1	495	Glu	2.9	NE	310	Arg	2.9
OE1	491	Glu	2.83	NB1	310	Arg	2.83
OE2	488	Glu	2.78	NB1	273	Arg	2.78
OE1	488	Glu	2.72	NB2	273	Arg	2.72
OE2	491	Glu	2.7	NE	273	Arg	2.7
OE2	491	Glu	2.88	NE1	273	Arg	2.88
OE2	491	Glu	2.87	NB1	269	Trp	2.87
PspA_1-5c+p (C chain)				HLF (B chain)
O	549	Leu	2.62	NZ	181	Lys	2.62
O	548	Asp	2.47	NZ	181	Lys	2.47
O	550	Lys	3.24	N	178	Gly	3.24
OE2	608	Glu	2.69	NB1	172	Arg	2.69
OE1	608	Glu	2.78	NB2	172	Arg	2.78

(c)
PspA_1-5c+p -HLF docked complex (Model 2)
Atom name	Res. no	Res. name	H-bond distance (A°)	Atom name	Res. No.	Res. name	H-bond distance (A°)
PspA_1-5c+p (C chain)				HLF (A chain)
–	–	–	–	–	–	–	–
PspA_1-5c+p (C chain)				HLF (B chain)
OE2	27	Glu	2.93	OC1	91	Thr	2.93
OE1	27	Glu	2.91	OD1	309	Ser	2.91
OC	21	Ser	2.77	O	89	Pro	2.77
OE1	18	Glu	3.28	NE2	88	Gln	3.28
O	231	Glu	2.62	NB1	31	Arg	2.62
O	297	Leu	2.72	NB1	28	Arg	2.72
O	292	Lys	2.79	NB2	28	Arg	2.79
O	292	Lys	3.33	NB1	28	Arg	3.3
OE2	303	Glu	2.77	NB2	28	Arg	2.77
O	296	Glu	2.67	NB1	28	Arg	2.67
OD2	298	Asp	2.71	NB2	25	Arg	2.71
OD1	307	Asp	2.66	NB2	5	Arg	2.66
OD2	307	Asp	2.64	NB2	5	Arg	2.64
OE2	300	Glu	2.75	NB2	4	Arg	2.75
OE1	300	Glu	2.77	NB1	4	Arg	2.77
OD2	17	Asp	2.81	NB2	90	Arg	2.81
O	55	Asp	2.63	NB2	314	Arg	2.63
OD1	55	Asp	3.03	NE	314	Arg	3.03
OE1	36	Glu	2.73	NB2	273	Arg	2.73
OD1	17	Asp	2.75	NB1	250	Arg	2.75
O	72	Lys	2.66	NB2	250	Arg	2.66

ISSN: 1479-5876