# PropKa configuration file version version_A # Model pKa values model_pkas C- 3.20 model_pkas ASP 3.80 model_pkas GLU 4.50 model_pkas HIS 6.50 model_pkas CYS 9.00 model_pkas TYR 10.00 model_pkas LYS 10.50 model_pkas ARG 12.50 #model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London model_pkas N+ 8.00 model_pkas CG 11.50 model_pkas C2N 11.50 model_pkas N30 10.00 model_pkas N31 10.00 model_pkas N32 10.00 model_pkas N33 10.00 model_pkas NAR 5.00 model_pkas OCO 4.50 model_pkas SH 10.00 model_pkas OP 6.00 # Custom ligand pKa values # P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya: # Measurement of Nucleobase pKa Values in Model Mononucleotides # Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes # Journal of the American Chemical Society 2004 126 (9), 2862-2869 # custom_model_pkas DA-N1 3.82 custom_model_pkas DA-N3 3.82 custom_model_pkas DA-N7 3.82 custom_model_pkas DA-OP1 1.00 custom_model_pkas DA-OP2 1.00 custom_model_pkas DG-N1 9.59 custom_model_pkas DG-N3 9.59 custom_model_pkas DG-N7 9.59 custom_model_pkas DG-OP1 1.00 custom_model_pkas DG-OP2 1.00 custom_model_pkas DC-N3 4.34 custom_model_pkas DC-OP1 1.00 custom_model_pkas DC-OP2 1.00 custom_model_pkas DT-N3 10.12 custom_model_pkas DT-OP1 1.00 custom_model_pkas DT-OP2 1.00 # protein group mapping protein_group_mapping ASP-CG COO protein_group_mapping GLU-CD COO protein_group_mapping HIS-CG HIS protein_group_mapping CYS-SG CYS protein_group_mapping TYR-OH TYR protein_group_mapping LYS-NZ LYS protein_group_mapping ARG-CZ ARG #protein_group_mapping SER-OG SER protein_group_mapping THR-OG1 ROH protein_group_mapping SER-OG ROH# protein_group_mapping ASN-CG AMD protein_group_mapping GLN-CD AMD protein_group_mapping TRP-NE1 TRP # matrix for propka interactions # 'N' non-iterative interaction # 'I' iterative interaction # '-' no interaction #CYS interaction_matrix CYS I#N+ interaction_matrix N+ N I#HIS interaction_matrix HIS I N I#LYS interaction_matrix LYS N N N I#AMD interaction_matrix AMD N - N - -#COO interaction_matrix COO I N I N N I#ARG interaction_matrix ARG N N N N - N I#TRP interaction_matrix TRP N - - - - N - -#ROH interaction_matrix ROH N - - - - N - - -#TYR interaction_matrix TYR N I I I N N N N N I#SER interaction_matrix SER N N N N N N I N N N I #CG interaction_matrix CG N N N N - N I - - N I I#C2N interaction_matrix C2N N N N N - N I - - N I I I#N30 interaction_matrix N30 N I N N - N N - - I N I I I#N31 interaction_matrix N31 N I N N - N N - - I N I I I I#N32 interaction_matrix N32 N I N N - N N - - I N I I I I I#N33 interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1 interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH interaction_matrix OH N - - - - N - - - N N - - - - - - - N - -#O3 interaction_matrix O3 N - N - - N - - - N N - - - - - - N N - - -#CL interaction_matrix CL N - N - - N - - - N N - - - - - - N N - - - -#F interaction_matrix F N - N - - N - - - N N - - - - - - N N - - - - -#NAM interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1 interaction_matrix N1 N - N - - N - - - N N - - - - - - N N - - - - - - -#O2 interaction_matrix O2 N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP interaction_matrix OP I N I N N I N N N N N N N N N N N I I N N N N N N N N I#SH interaction_matrix SH I N N N N N N N N N N I I I I I I N N N N N N N N N N N I # Cutoff values for side chain interactions # default value sidechain_cutoffs default 3.0 4.0 # COO sidechain_cutoffs COO COO 2.5 3.5 Sidechain_cutoffs COO SER 2.65 3.65 sidechain_cutoffs COO ARG 1.85 2.85 sidechain_cutoffs COO LYS 2.85 3.85 sidechain_cutoffs COO HIS 2.0 3.0 sidechain_cutoffs COO AMD 2.0 3.0 sidechain_cutoffs COO TRP 2.0 3.0 sidechain_cutoffs COO ROH 2.65 3.65 sidechain_cutoffs COO TYR 2.65 3.65 sidechain_cutoffs COO N+ 2.85 3.85 sidechain_cutoffs COO CG 1.85 2.85 sidechain_cutoffs COO C2N 1.85 2.85 sidechain_cutoffs COO N30 2.85 3.85 sidechain_cutoffs COO N31 2.85 3.85 sidechain_cutoffs COO N32 2.85 3.85 sidechain_cutoffs COO N33 2.85 3.85 sidechain_cutoffs COO NAR 2.0 3.0 sidechain_cutoffs COO OCO 2.5 3.5 sidechain_cutoffs COO OH 2.65 3.65 sidechain_cutoffs COO NAM 2.0 3.0 # SER sidechain_cutoffs SER SER 3.5 4.5 sidechain_cutoffs SER ARG 2.5 4.0 sidechain_cutoffs SER HIS 2.0 3.0 sidechain_cutoffs SER AMD 2.5 3.5 sidechain_cutoffs SER CYS 3.5 4.5 sidechain_cutoffs SER TRP 2.5 3.5 sidechain_cutoffs SER ROH 3.5 4.5 sidechain_cutoffs SER CG 2.5 4.0 sidechain_cutoffs SER C2N 2.5 4.0 sidechain_cutoffs SER NAR 2.0 3.0 sidechain_cutoffs SER OH 3.5 4.5 sidechain_cutoffs SER SH 3.5 4.5 sidechain_cutoffs SER TYR 3.5 4.5 sidechain_cutoffs SER N+ 3.0 4.5 sidechain_cutoffs SER NAM 2.5 3.5 # ARG sidechain_cutoffs ARG CYS 2.5 4.0 sidechain_cutoffs ARG TYR 2.5 4.0 sidechain_cutoffs ARG OCO 1.85 2.85 sidechain_cutoffs ARG SH 2.5 4.0 # HIS sidechain_cutoffs HIS AMD 2.0 3.0 sidechain_cutoffs HIS TYR 2.0 3.0 sidechain_cutoffs HIS OCO 2.0 3.0 # CYS sidechain_cutoffs CYS CYS 3.0 5.0 sidechain_cutoffs CYS TRP 2.5 3.5 sidechain_cutoffs CYS ROH 3.5 4.5 sidechain_cutoffs CYS AMD 2.5 3.5 sidechain_cutoffs CYS TYR 3.5 4.5 sidechain_cutoffs CYS N+ 3.0 4.5 sidechain_cutoffs CYS CG 2.5 4.0 sidechain_cutoffs CYS C2N 2.5 4.0 sidechain_cutoffs CYS N30 3.0 4.5 sidechain_cutoffs CYS N31 3.0 4.5 sidechain_cutoffs CYS N32 3.0 4.5 sidechain_cutoffs CYS N33 3.0 4.5 sidechain_cutoffs CYS OH 3.5 4.5 sidechain_cutoffs CYS NAM 2.5 3.5 sidechain_cutoffs CYS SH 3.0 5.0 # TYR sidechain_cutoffs TYR TYR 3.5 4.5 sidechain_cutoffs TYR N+ 3.0 4.5 sidechain_cutoffs TYR AMD 2.5 3.5 sidechain_cutoffs TYR TRP 2.5 3.5 sidechain_cutoffs TYR ROH 3.5 4.5 sidechain_cutoffs TYR CG 2.5 4.0 sidechain_cutoffs TYR C2N 2.5 4.0 sidechain_cutoffs TYR OCO 2.65 3.65 sidechain_cutoffs TYR NAR 2.0 3.0 sidechain_cutoffs TYR OH 3.5 4.5 sidechain_cutoffs TYR NAM 2.5 3.5 sidechain_cutoffs TYR SH 3.5 4.5 # N+ sidechain_cutoffs N+ OCO 2.85 3.85 sidechain_cutoffs N+ SH 3.0 4.5 # LYS sidechain_cutoffs LYS OCO 2.85 3.85 # OCO sidechain_cutoffs OCO OCO 2.5 3.5 sidechain_cutoffs OCO TRP 2.0 3.0 sidechain_cutoffs OCO ROH 2.65 3.65 sidechain_cutoffs OCO AMD 2.0 3.0 sidechain_cutoffs OCO CG 1.85 2.85 sidechain_cutoffs OCO C2N 1.85 2.85 sidechain_cutoffs OCO N30 2.85 3.85 sidechain_cutoffs OCO N31 2.85 3.85 sidechain_cutoffs OCO N32 2.85 3.85 sidechain_cutoffs OCO N33 2.85 3.85 sidechain_cutoffs OCO NAR 2.0 3.0 sidechain_cutoffs OCO OH 2.65 3.65 sidechain_cutoffs OCO NAM 2.0 3.0 # NAR sidechain_cutoffs NAR AMD 2.0 3.0 # SH sidechain_cutoffs SH ROH 3.5 4.5 sidechain_cutoffs SH TRP 2.5 3.5 sidechain_cutoffs SH AMD 2.5 3.5 sidechain_cutoffs SH NAM 2.5 3.5 sidechain_cutoffs SH CG 2.5 4.0 sidechain_cutoffs SH C2N 2.5 4.0 sidechain_cutoffs SH OH 3.5 4.5 sidechain_cutoffs SH SH 3.0 5.0 # Maximal interaction energies for side chains sidechain_interaction 0.85 # Angular dependent sidechain interactions angular_dependent_sidechain_interactions HIS angular_dependent_sidechain_interactions ARG angular_dependent_sidechain_interactions AMD angular_dependent_sidechain_interactions TRP # exception interaction values COO_HIS_exception 1.60 OCO_HIS_exception 1.60 CYS_HIS_exception 1.60 CYS_CYS_exception 3.60 # Coulomb interaction parameters coulomb_cutoff1 4.0 coulomb_cutoff2 10.0 coulomb_diel 80.0 # Backbone hydrogen bond parameters backbone_NH_hydrogen_bond COO -0.85 2.00 3.00 #backbone_NH_hydrogen_bond C- -0.85 2.00 3.00 backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00 backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20 backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50 backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50 backbone_CO_hydrogen_bond HIS 0.85 2.00 3.00 backbone_CO_hydrogen_bond OCO 0.85 3.00 4.00 backbone_CO_hydrogen_bond CG 0.85 2.00 4.00 backbone_CO_hydrogen_bond C2N 0.85 2.00 4.00 backbone_CO_hydrogen_bond N30 0.85 2.00 4.00 backbone_CO_hydrogen_bond N31 0.85 2.00 4.00 backbone_CO_hydrogen_bond N32 0.85 2.00 4.00 backbone_CO_hydrogen_bond N33 0.85 2.00 4.00 backbone_CO_hydrogen_bond NAR 0.85 2.00 3.50 # Group charges charge COO -1 charge HIS +1 charge CYS -1 charge TYR -1 charge LYS +1 charge ARG +1 charge N+ +1 charge C- -1 charge OCO -1 charge SER -1 charge CG +1 charge C2N +1 charge N30 +1 charge N31 +1 charge N32 +1 charge N33 +1 charge NAR +1 charge SH -1 charge OP -1 # list of acids acid_list ASP acid_list GLU acid_list CYS acid_list TYR acid_list SER acid_list C- acid_list OCO acid_list OP acid_list SH # list of bases base_list ARG base_list LYS base_list HIS base_list N+ base_list CG base_list C2N base_list N30 base_list N31 base_list N32 base_list N33 base_list NAR # list of groups used in backbone reorganisation calculations backbone_reorganisation_list ASP backbone_reorganisation_list GLU # Residues that should be ignored ignore_residues HOH ignore_residues H2O ignore_residues HOH ignore_residues SO4 ignore_residues PO4 ignore_residues PEG ignore_residues EPE #ignore_residues NAG ignore_residues TRS # Relative Van der Waals volume parameters for the radial volume model # Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51 VanDerWaalsVolume C 1.40 # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms VanDerWaalsVolume C4 2.64 # 38.79 hydrodphobic carbon atoms + unidentified atoms VanDerWaalsVolume N 1.06 # radius: 1.55, volume: 15.60 all nitrogen atoms VanDerWaalsVolume O 1.00 # radius: 1.52, volume: 14.71 all oxygen atoms VanDerWaalsVolume S 1.66 # radius: 1.80, volume: 24.43 all sulphur atoms VanDerWaalsVolume F 0.90 # raidus: 1.47, volume: 13.30 for fluorine VanDerWaalsVolume Cl 1.53 # radius: 1.75, volume: 22.44 for chlorine VanDerWaalsVolume P 1.66 # radius: 1.80, volume: 24.42 for phosphorus # Other desolvation parameters desolvationSurfaceScalingFactor 0.25 desolvationPrefactor -13.0 desolvationAllowance 0.0 desolv_cutoff 20.0 buried_cutoff 15.0 Nmin 280 Nmax 560 # Ligand groups ligand_typing groups min_bond_distance_for_hydrogen_bonds 4 # covalent coupling coupling_max_number_of_bonds 3 shared_determinants 0 common_charge_centre 0 remove_penalised_group 1 # non-covalent coupling max_intrinsic_pKa_diff 2.0 min_interaction_energy 0.5 max_free_energy_diff 1.0 min_swap_pka_shift 1.0 min_pka 0.0 max_pka 10.0 pH variable reference neutral # ions ions 1P 1 # generic charged atoms ions 2P 2 ions 1N -1 ions 2N -2 ions MG 2 #Magnesium Ion ions CA 2 #Calcium Ion ions ZN 2 #Zinc Ion ions NA 1 #Sodium Ion ions CL -1 #Chloride Ion ions MN 2 #Manganese (ii) Ion ions K 1 #Potassium Ion ions CD 2 #Cadmium Ion ions FE 3 #Fe (iii) Ion ions SR 2 #Strontium Ion ions CU 2 #Copper (ii) Ion ions IOD -1 #Iodide Ion ions HG 2 #Mercury (ii) Ion ions BR -1 #Bromide Ion ions CO 2 #Cobalt (ii) Ion ions NI 2 #Nickel (ii) Ion ions FE2 2 #Fe (ii) Ion # write out order of residues write_out_order ASP write_out_order GLU write_out_order C- write_out_order HIS write_out_order CYS write_out_order TYR write_out_order LYS write_out_order ARG write_out_order SER write_out_order N+ write_out_order CG write_out_order C2N write_out_order N30 write_out_order N31 write_out_order N32 write_out_order N33 write_out_order NAR write_out_order OCO write_out_order SH write_out_order OP