Table 1.

Summary of simulation systems used in this study. For systems 4–16 the bound peptide was modelled based on the peptide in system 3. For systems 4–15, the C-terminal amino acid of the bound peptide takes the equivalent position of C-terminal arginine of system number 3, while in system 16, the arginine of the peptide was at the equivalent position of the C-terminal arginine of system 3 and a C-terminal valine residue was added.

System	Name	PDB ID of NRP1 structure	Bound peptide/amino acid/amino acid analog
1	NRP1-VEGF-A	4DEQ	VEGF-A
2	NRP1-HRG	5IJR	Arginine analogue (HRG)
3	NRP1-S1	7JJC	NSPRRAR
4	NRP1-R	7JJC	R
5	NRP1-RRAR	7JJC	RRAR
6	NRP1-ARAR	7JJC	ARAR
7	NRP1-RRAA	7JJC	RRAA
8	NRP1-RAAR	7JJC	RAAR
9	NRP1-RRAK	7JJC	RRAK
10	NRP1-RRAH	7JJC	RRAH
11	NRP1-RRRR	7JJC	RRRR
12	NRP1-TKPR	7JJC	TKPR
13	NRP1-TKPPR	7JJC	TKPPR
14	NRP1-PPR	7JJC	PPR
15	NRP1-PPRV	7JJC	PPRV
16	NRP1-PPR(V)	7JJC	PPRV
17	NRP1-EG00229	3I97	EG00229 (inhibitor)