From: The role of hydrophobic interactions in positioning of peripheral proteins in membranes
 |  | Experimenta | Calculationb | ||||
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Protein name | PDB id | Residues buried from water or important for membrane binding | Method | References | Δ G calc (kcal/mol) | D (Å) | Residues penetrating the hydrocarbon membrane core |
Lipid clamps (specific binding of lipid ligands) | |||||||
C2 domain of phospholipase A2 | 1rlw | A34, F35, G36, M38, L39, Y96, V97, M98 | Bn, SL | [6, 84, 85] | -7.1 | 5.3 | A34, F35, G36, M38, L39, Y96, V97, M98 |
C2A domain of synaptotagmin I | 1byn | M173, G174, F234 | Bn, SL | [7, 86] | -4.4 | 3.7 | M173, G174, F234 |
C2 domain of protein knase Cα | 1dsy | N189, R249, R252 | SL | [8] | -2.0 | 1.5 | P188, N189, T250 |
C2B domain of synaptotagmin I | 1uov | G305, I367 | SL | [9] | -4.3 | 2.4 | V304, G305, I367, G368 |
C2 domain of protein kinase Cε | 1gmi | I89, Y91 | Bn | [87] | -5.1 | 2.4 | V29, P31, I89 |
PX domain (p40phox) | 1h6h | F35, Y94, V95 | Bn | [39] | -4.5 | 3.2 | F35, Y94, V95 |
PX domain (p47phox) | 1o7k | W80 | Bn | [39] | -1.9 | 1.4 | W80 |
FYVE domain of EEA1 | 1hyi | V21, T22 | NMR | [40] | -2.9 | 2.5 | V21, T22 |
FYVE domain of Vps27p | 1vfy | L185, L186 | Bn | [88] | -4.0 | 2.9 | L185, L186 |
C1 domain of protein kinase Cδ | 1ptr | W252, L254, V255 | Bn | [89] | -5.7 | 6.8 | M239, P241, L250, W252, G253, L254, V255 |
Epsin ENTH domain | 1h0a | L6, M10 | Bn | [77] | -5.2 | 2.9 | L6, M10, I13, V14 |
Discoidin domain of factor V | 1czs | W26, W27 | Bn | [90] | -3.0 | 4.2 | W26, W27, L79, and S80 |
Discoidin domain of factor Va | 1sdd | Y1956, L1957, W2063, W2064 | Bn | [91] | -5.6 | 3.3 | Y1956, L1957, W2063, W2064 |
Discoidin domain of factor VIII | 1d7p | M2199, F2200, L2251, L2252 | Bn | [92] | -8.1 | 3.9 | M2199, F2200, L2251, L2252 |
Annexin V | 1a8a | T72, S144 , W185, S228, S303 | SL | [93] | -6.3 | 2.5 | L29, T72, A101, W185, A260 |
Annexin XII | 1dm5 | E142, S144, G145 | SL | [94] | -8.3 | 3.1 | I29, L101, I185 |
Equinatoxin II | 1iaz | W112 | NMR | [95] | -2.2 | 3.1 | P81, V82, W112 |
Other proteins | |||||||
Prostaglandin H2 synthase 1 | 1q4g | I74, W75, W77, L78, F88, F91, L92, W98, L99, F102 | Bn, Fn | [96] | -37.8 | 7.2 | I74, W75, W77, L78, T81, L82, F88, F91, L92, W98, L99, F102, V103, T106, F107, I108 |
Antimicrobial peptide kalata B1 | 1nb1 | W19-V21, L27-V29 | NMR | [97] | -5.4 | 5.2 | W19-V21, L27-V29 |
Pancreatic phospholipase A2, group IB | 4p2p | W3 | Flq | [11] | -8.7 | 3.5 | W3, H17, L19, M20, L64, V65 |
Bee venom phospholipase A2 | 1poc | I2, K14, I78 | SL* | [42] | -10.3 | 5.7 | I1, I2, Y3, P4, G5,I78, F82, M86, L90 |
Human secretory phospholipase A2, group IIa | 1n28 | V3, K10, L19, F23, F63 | SL* | [43] | -6.6 | 4.8 | V3, L19, F23, F63 |
Snake venom phospholipase A2, group I | 1poa | W61, F64, Y110 | Bn | [98] | -5.4 | 4.5 | Y3, W18, W19, W61, F64 |
Snake venom phospholipase A2, group II | 1vap | W20, W30, W109 | FL | [99] | -10.2 | 4.3 | F3, M13, L19, W30, M61, W109 |
Snake venom phospholipase A2, group IIB | 1jia | Y120, P121, I124, L125 | Bn | [100]d | -8.7 | 3.1 | V20, F24, A119, P121, I124 |
Phospholipase C | 2ptd | I43, W47, W242 | Bn | [101] | -6.0 | 3.9 | P42, I43, W47, T240, A241, W242 |
α-toxin (bacterial phospholipase C) | 1ca1 | Y331, F334 | Fn | [102] | -4.5 | 2.2 | V143, A146, M210, W214, Y331, F334 |
15-lipoxygenase | 1lox | Y15, F70, L71, W181c, L195 | Bn | [103] | -7.4 | 6.3 | L71, I194, L195, L291, Y292, F412 |
8R-lipoxygenase | 1zq4 | W413, W449 | FL, Fn | [104] | -5.0 | 5.9 | W413, F414, Y448, W449, V560, M570 |
Cholesterol oxidase | 1coy | M81 | FLq | [105] | -4.1 | 5.3 | M81, M332, W333, L369, Y372 |
Signal peptidase | 1kn9 | W300 | Fn | [106] | -4.5 | 4.5 | W300, M301, F303, L314, L316 |
Synapsin I | 1auv | Regions 166–192, 233–258, 278–327 | CL | [107] | -4.4 | 2.5 | L168, V172, L297 |
α-synuclein | 1xq8 | T59, V63, G67, V70, V74, V77, T81, A85, A89 | SL | [108] | -22.8 | 17.9 | T59, V63, V66, G67, V70, V74, V77, A78, T81, A85, I88, A89 |
Perfringolysin | 1pfo | W466 | Bn | [109] | -5.5 | 3.4 | L462, W466, L491, Y492 |
Daptomycin | 1t5n | Kyn14 | FL | [110] | -9.8 | 4.9 | Dka1, W2, Kyn14 |
Lactoferricin B | 1lfc | W6, W8 | FL | [111] | -4.6 | 5.3 | W6, W8, L13-P16, I18 |
Hanatoxin | 1d1h | W30 | FLq | [112] | -2.5 | 3.9 | Y4, L5, F6, W30 |
Subtilosin | 1pxq | W34 | FL | [113] | -6.7 | 5.1 | F22, F31, W34 |