Table 3.

Key amino acids for intra-, trans- or cis interaction of classic CLDNs

Amino acid positions counted by human CLDN-5 sequence	Key features	Ref
W30 and G48/L49/W50 and R81	The canonical CLDN signature to create its first ECL structure.	[138]
S69/Q78/R81 and E159	Cis-interaction by a stable hydrogen bond between S69 and E159.	[140, 150]
F139	It interacts with W30 and stabilizes the secondary structure. Only CLDN-5 has F at this position among classic CLDNs.	[146]
L73 and F147/Y148	Cis-interaction. F147/Y148 creates a hydrophobic pocket.	[140]
H61 to K65	The interface of cis-interaction for dimerization.	[229]
P135	It makes TJ strands more rigid by reducing the conformational flexibility of cis-/trans-interaction	[141]
F35, N39 to Q44	The interface of trans-interaction. The interaction of these hydrophobic residues may create a barrier against water molecules.	[148, 150]
F147 to Q156	The interface of trans-interaction. F147A, Y148A or Q156E mutant does not form trans-interaction.	[230, 231]
K65 and D68	The salt bridge (or hydrogen bond) between these positions limits the ion permeability.	[146, 232]
Q57	A polar but uncharged amino acid like Q and H is necessary for some CLDNs to form cis-interaction and to localize at the TJs.	[161, 162]
Q57 and H61 and Q63	Putative ion gate for extracellular ions is located here in channel-forming CLDNs. Barrier forming CLDNs have Q57 and Q61 (only CLDN-5 has H here) and Q63 and make multiple hydrogen bonds to close this gate.	[148]