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Conformation-Dependent Library (CDL) for Omega, peptide bond dihedral angle

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The omega Conformation-Dependent Library Download

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
              

Article

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites.
Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL, Jr., and Karplus PA, Proc Natl Acad Sci U S A 2012, 109(2):449-53. Article

Figures

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