bCIPA : bZIP Coiled-coil Interaction Prediction Algorithm


The bCIPA program is designed to estimate Tm values for bZIP pairs. The program is based on the method described in the following paper: For more information about coiled coils and our work please visit the Arndt lab home page.

Please cite the above publications if you use this program. For questions about the method or the program mail to: katja@biologie.uni-freiburg.de


Input form:

IMPORTANT: This is the latest version implementing data from Hagemann et al. For the first version described in the PNAS publication, please refer to this page.

Please enter the two sequences in one-letter amino acid code starting at the same helical position (a-g) and select the starting position (a-g).

 
 
  ← starting position of the heptad register
 
     

Only 'ACDEFGHIKLMNPQRSTVWY' are allowed for the sequences, whitespaces are ok. Sequences do not have to be named.

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Overview of dimeric, parallel coiled coil

Dimeric parallel coiled coil. (A) Helical wheel diagram looking down the helix axis from the N- to the C-terminus. Heptad positions are labeled a to g and a’ to g’ respectively. Positions a, d, e and g are color coded. (B) Side view. The helical backbones are represented by cylinders, the side-chains by knobs. The path of the polypeptide chain is indicated by a line wrapped around the cylinders. For simplicity, the supercoiling of the helices is not shown. While residues at positions a (purple) and d (blue) make up the hydrophobic interface, residues at positions e (orange) and g (red) pack against the hydrophobic core. They can participate in interhelical electrostatic interactions between residue i (g position) of one helix and residue i’+5 of the other helix (e’ position, belonging to the next heptad), as indicated by the hatched bars. Indicated is also the core-a position (green) which is often occupied by polar residues mediating specificity. (C) and (D) Coiled coil domain of the yeast transcription factor GCN4 as ribbon plot (PDB code: 1ZTA) to indicate supercoiling and g/e’ interactions. The plot was made using Pymol.

Properties of amino acids

Abbrev.
 Full Name Side chain type Mass pI pK1
(α-COOH)		 pK2
(α-+NH3)		 pKr (R)*
A
 Ala Alanine hydrophobic 89.09 6.01 2.35 9.87
C
 Cys Cysteine hydrophobic (Nagano, 1999) 121.16 5.05 1.92 10.70 8.18
D
 Asp Aspartic acid acidic 133.10 2.85 1.99 9.90 3.90
E
 Glu Glutamic acid acidic 147.13 3.15 2.10 9.47 4.07
F
 Phe Phenylalanine hydrophobic 165.19 5.49 2.20 9.31
G
 Gly Glycine hydrophobic 75.07 6.06 2.35 9.78
H
 His Histidine basic 155.16 7.60 1.80 9.33 6.04
I
 Ile Isoleucine hydrophobic 131.17 6.05 2.32 9.76
K
 Lys Lysine basic 146.19 9.60 2.16 9.06 10.54
L
 Leu Leucine hydrophobic 131.17 6.01 2.33 9.74
M
 Met Methionine hydrophobic 149.21 5.74 2.13 9.28
N
 Asn Asparagine hydrophilic 132.12 5.41 2.14 8.72
P
 Pro Proline hydrophobic 115.13 6.30 1.95 10.64
Q
 Gln Glutamine hydrophilic 146.15 5.65 2.17 9.13
R
 Arg Arginine basic 174.20 10.76 1.82 8.99 12.48
S
 Ser Serine hydrophilic 105.09 5.68 2.19 9.21
T
 Thr Threonine hydrophilic 119.12 5.60 2.09 9.10
V
 Val Valine hydrophobic 117.15 6.00 2.39 9.74
W
 Trp Tryptophan hydrophobic 204.23 5.89 2.46 9.41
Y
 Tyr Tyrosine hydrophobic 181.19 5.64 2.20 9.21 10.46

 

Amino acid Abbrev. Side chain Hydrophobic Polar Charged Small Tiny Aromatic or Aliphatic van der Waals volume*
Alanine Ala, A -CH3 X - - X X - 67
Cysteine Cys, C -CH2SH X - - X - - 86
Aspartate Asp, D -CH2COOH - X negative X - - 91
Glutamate Glu, E -CH2CH2COOH - X negative - - - 109
Phenylalanine Phe, F -CH2C6H5 X - - - - Aromatic 135
Glycine Gly, G -H X - - X X - 48
Histidine His, H -CH2-C3H3N2 - X positive - - Aromatic 118
Isoleucine Ile, I -CH(CH3)CH2CH3 X - - - - Aliphatic 124
Lysine Lys, K -(CH2)4NH2 - X positive - - - 135
Leucine Leu, L -CH2CH(CH3)2 X - - - - Aliphatic 124
Methionine Met, M -CH2CH2SCH3 X - - - - - 124
Asparagine Asn, N -CH2CONH2 - X - X - - 96
Proline Pro, P -CH2CH2CH2- X - - X - - 90
Glutamine Gln, Q -CH2CH2CONH2 - X - - - - 114
Arginine Arg, R -(CH2)3NH-C(NH)NH2 - X positive - - - 148
Serine Ser, S -CH2OH - X - X X - 73
Threonine Thr, T -CH(OH)CH3 X X - X - - 93
Valine Val, V -CH(CH3)2 X - - X - Aliphatic 105
Tryptophan Trp, W -CH2C8H6N X - - - - Aromatic 163
Tyrosine Tyr, Y -CH2-C6H4OH X X - - - Aromatic 141

*Source for the two tables: wikipedia

This page was last modified: 02. Mar. 2010 - 10h 21min