Conformation-Dependent Library (CDL) for Omega, peptide bond dihedral angle
Please cite us:
Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL, Jr., and Karplus PA
Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.
Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23
Library Format
omegaCDL_OmegaBetweenAsPhi1Psi0_KernRegr_v1.3.1_Aug12-2011.txt # Conformation-dependent library for omega, a torsion angle of the peptide bond # August 12, 2011 # # Copyright (c) 2011 Donald S. Berkholz, Camden M. Driggers, Maxim V. Shapovalov, Roland L. Dunbrack, Jr., and P. Andrew Karplus # Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS, Corvallis, OR 97331, USA # Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA # # Library instructions and comments start with "# " on every line. # A few parameters of interest to an end user are provided on the lines starting with "@ " for easier parsing. # The data lines do not have any special symbol or keyword in the beginning of each data line. # @ Version 1.3.1 @ Format 1.0 # # Method: non-adaptive kernel regression # kappa = 50 # approximate bandwidth = 16 deg # # =================== # Column descriptions # =================== # # Phi(+1) - phi backbone torsion angle of the following residue, +1 # Psi( 0) - psi backbone torsion angle of the current residue, 0 # Remarks: Traditionally a torsion angle of the peptide bond precedes a residue not follows. # The omega(+1) dependence on a backbone conformation is presented here as a function of the adjacent, enclosing psi(0) and phi(+1). See a diaram below: # # omega(0) phi(0) psi(0) omega(+1) phi(+1) psi(+1) omega(+2) # - N( 0) - Ca( 0) - C( 0) - N(+1) - Ca(+1) - C(+1) - # current residue following residue # # S - method source (B or I) # B = backbone-dependent (when a number of local data points >= 3) # I = backbone-independent (when a number of local data points < 3) # # Num - number of data points used to calculate a local value # # --------------------------- # SHORT LONG NAME # --------------------------- # W(+1) omega(+1), i.e. Ca(0) - C(0) - N(+1) - Ca(+1) # # Prefix "m" - mean value # Prefix "s" - standard deviation value # # Caution: The number of the locally available data points can be low. # Please use standard error of mean to estimate uncertainty of mean, i.e. # SEM = StandardDeviation / sqrt(Num) # # Please do not use the fixed-width field format instructions in your parser. The fixed-width format # in the current version of the library is made for simplicity of reading and understanding it by a user. # At the programming level please use the not-fixed width field formatting like, "... %i%f%f ..." # # # ------------------------------------------------------------------- # The following classes of residue types are enlisted in the library: # ------------------------------------------------------------------- # All [data # 28917] - 20 standard aa - i.e. Ala, Arg, Asn, Asp, Cys, Gly, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val # All_nonxpro [data # 27683] - 20 standard aa NOT preceding Pro - i.e. Ala, Arg, Asn, Asp, Cys, Gly, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val NOT before Pro # All_xpro [data # 1234 ] - 20 standard aa preceding Pro - i.e. Ala, Arg, Asn, Asp, Cys, Gly, Gln, Glu, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr or Val before Pro # # NonPGIV_nonxpro [data # 20342] - 16 general aa NOT preceding Pro - i.e. Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Leu, Lys, Met, Phe, Ser, Thr, Trp or Tyr NOT before Pro # IleVal_nonxpro [data # 3528 ] - Ile and Val NOT preceding Pro - i.e. Ile or Val NOT before Pro # Gly_nonxpro [data # 2599 ] - Gly NOT preceding Pro - i.e. Gly NOT before Pro # Pro_nonxpro [data # 1214 ] - Pro NOT preceding Pro - i.e. Pro NOT before Pro # # NonPGIV_xpro [data # 928 ] - 16 general aa preceding Pro - i.e. Ala, Arg, Asn, Asp, Cys, Gln, Glu, His, Leu, Lys, Met, Phe, Ser, Thr, Trp or Tyr before Pro # IleVal_xpro [data # 177 ] - Ile and Val preceding Pro - i.e. Ile or Val before Pro # Gly_xpro [data # 100 ] - Gly preceding Pro - i.e. Gly before Pro # Pro_xpro [data # 29 ] - Pro preceding Pro - i.e. Pro before Pro # # For additional information please visit: # ======================================== # # http://dunbrack.fccc.edu/omega # http://proteingeometry.sourceforge.net # # and for the publication itself: # =============================== # # Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL, Jr., and Karplus PA # "Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites" # Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):449-53. doi: 10.1073/pnas.1107115108. Epub 2011 Dec 23 # # http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258596/ # # @ ResTypeGroup Phi(+1) Psi(0) S Num mW(+1) sW(+1) All -180 -180 B 9 177.39 4.57 All -180 -170 B 3 179.05 5.10 All -180 -160 I 28917 179.07 6.33 All -180 -150 I 28917 179.07 6.33 ... All 90 -20 B 31 182.77 5.26 All 90 -10 B 66 180.88 5.21 All 90 0 B 81 178.81 4.96 All 90 10 B 66 176.71 5.13 All 90 20 B 27 175.23 5.66 ... IleVal_nonxpro -130 90 I 3528 178.64 6.31 IleVal_nonxpro -130 100 I 3528 178.64 6.31 IleVal_nonxpro -130 110 B 18 184.13 6.37 IleVal_nonxpro -130 120 B 80 181.05 5.96 IleVal_nonxpro -130 130 B 177 178.59 6.21 IleVal_nonxpro -130 140 B 142 176.69 6.92 IleVal_nonxpro -130 150 B 53 175.66 7.51 IleVal_nonxpro -130 160 B 33 175.50 6.93 IleVal_nonxpro -130 170 B 18 175.38 6.13 IleVal_nonxpro -120 -180 I 3528 178.64 6.31 IleVal_nonxpro -120 -170 I 3528 178.64 6.31 ... Pro_xpro 170 140 I 29 178.55 6.54 Pro_xpro 170 150 I 29 178.55 6.54 Pro_xpro 170 160 I 29 178.55 6.54 Pro_xpro 170 170 I 29 178.55 6.54
Figures
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