
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   49 (  196),  selected   49 , name T0289TS125_4u-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS125_4u-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.857
LGA    M     225      M     225          1.870
LGA    E     226      E     226          1.266
LGA    K     227      K     227          0.284
LGA    V     228      V     228          1.593
LGA    D     229      D     229          2.200
LGA    Y     230      Y     230          3.604
LGA    -       -      P     231           -
LGA    P     231      R     232          4.816
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    R     232      V     238          2.112
LGA    N     233      A     239          3.767
LGA    E     234      A     240          3.270
LGA    -       -      V     241           -
LGA    I     242      I     242          1.030
LGA    H     243      H     243          2.080
LGA    -       -      P     244           -
LGA    P     244      N     245          3.510
LGA    N     245      L     246          4.074
LGA    L     246      Q     247          2.808
LGA    Q     247      D     248          1.870
LGA    D     248      Q     249          1.062
LGA    Q     249      D     250          3.098
LGA    D     250      W     251          1.944
LGA    W     251      -       -           -
LGA    K     252      K     252          1.523
LGA    P     253      P     253          1.156
LGA    L     254      L     254          1.368
LGA    H     255      H     255          1.018
LGA    P     256      P     256          2.174
LGA    G     257      G     257          2.422
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    D     258      L     271          1.725
LGA    V     260      G     272           #
LGA    F     261      -       -           -
LGA    V     262      -       -           -
LGA    S     263      G     273          1.987
LGA    L     264      D     274          2.341
LGA    D     265      C     275          3.518
LGA    G     266      T     276          2.088
LGA    K     267      V     277          1.432
LGA    V     268      Y     278          1.593
LGA    I     269      P     279          0.622
LGA    P     270      V     280          1.273
LGA    F     281      F     281          1.958
LGA    V     282      V     282          1.152
LGA    N     283      N     283          1.967
LGA    K     290      E     284          5.035
LGA    K     291      A     285          3.646
LGA    E     292      A     286          4.286
LGA    A     293      Y     287           #
LGA    F     294      Y     288          3.339
LGA    A     295      E     289          2.839
LGA    K     296      K     290          1.095
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   74    5.0     44    2.53    43.18     38.621     1.675

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.519709 * X  +   0.677765 * Y  +  -0.520132 * Z  +  29.646646
  Y_new =   0.177354 * X  +   0.681135 * Y  +   0.710352 * Z  +  33.237701
  Z_new =   0.835732 * X  +   0.276929 * Y  +  -0.474196 * Z  +   6.385065 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.613024   -0.528569  [ DEG:   149.7152    -30.2848 ]
  Theta =  -0.989465   -2.152128  [ DEG:   -56.6922   -123.3078 ]
  Phi   =   2.812729   -0.328864  [ DEG:   161.1575    -18.8425 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0289TS125_4u-D2                              
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS125_4u-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   74   5.0   44   2.53   43.18  38.621
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS125_4u-D2
PFRMAT   TS
TARGET   T0289
MODEL    4  UNREFINED
PARENT   1yw4a   
ATOM   1966  N   ILE   224      26.012  27.689  20.483    1.00  0.50
ATOM   1967  CA  ILE   224      25.357  28.614  21.393    1.00  0.50
ATOM   1968  C   ILE   224      24.941  27.852  22.646    1.00  0.50
ATOM   1969  O   ILE   224      24.475  26.717  22.565    1.00  0.50
ATOM   1971  N   MET   225      25.126  28.474  23.804    1.00  0.50
ATOM   1972  CA  MET   225      24.741  27.858  25.066    1.00  0.50
ATOM   1973  C   MET   225      23.409  28.480  25.482    1.00  0.50
ATOM   1974  O   MET   225      22.464  27.773  25.822    1.00  0.50
ATOM   1980  N   GLU   226      23.349  29.808  25.442    1.00  0.50
ATOM   1981  CA  GLU   226      22.142  30.556  25.789    1.00  0.50
ATOM   1982  C   GLU   226      22.296  32.019  25.365    1.00  0.50
ATOM   1983  O   GLU   226      23.416  32.518  25.231    1.00  0.50
ATOM   1992  N   LYS   227      21.174  32.702  25.156    1.00  0.50
ATOM   1993  CA  LYS   227      21.212  34.103  24.752    1.00  0.50
ATOM   1994  C   LYS   227      21.054  35.023  25.954    1.00  0.50
ATOM   1995  O   LYS   227      20.403  34.674  26.942    1.00  0.50
ATOM   2000  N   VAL   228      21.659  36.202  25.865    1.00  0.50
ATOM   2001  CA  VAL   228      21.577  37.190  26.934    1.00  0.50
ATOM   2002  C   VAL   228      20.341  38.046  26.704    1.00  0.50
ATOM   2003  O   VAL   228      20.425  39.110  26.095    1.00  0.50
ATOM   2008  N   ASP   229      19.195  37.571  27.185    1.00  0.50
ATOM   2009  CA  ASP   229      17.938  38.293  27.028    1.00  0.50
ATOM   2010  C   ASP   229      17.995  39.623  27.776    1.00  0.50
ATOM   2011  O   ASP   229      18.280  39.661  28.971    1.00  0.50
ATOM   2015  N   TYR   230      17.729  40.716  27.070    1.00  0.50
ATOM   2016  CA  TYR   230      17.757  42.030  27.696    1.00  0.50
ATOM   2017  C   TYR   230      16.373  42.614  27.970    1.00  0.50
ATOM   2018  O   TYR   230      15.466  42.537  27.139    1.00  0.50
ATOM   2024  N   PRO   231      16.230  43.193  29.158    1.00  0.50
ATOM   2025  CA  PRO   231      14.992  43.823  29.590    1.00  0.50
ATOM   2026  C   PRO   231      15.317  44.952  30.569    1.00  0.50
ATOM   2027  O   PRO   231      16.238  44.836  31.381    1.00  0.50
ATOM   2034  N   ARG   232      14.561  46.042  30.470    1.00  0.50
ATOM   2035  CA  ARG   232      14.741  47.222  31.317    1.00  0.50
ATOM   2036  C   ARG   232      16.114  47.847  31.089    1.00  0.50
ATOM   2037  O   ARG   232      16.382  48.418  30.032    1.00  0.50
ATOM   2040  N   ASN   233      19.892  46.864  33.574    1.00  0.50
ATOM   2041  CA  ASN   233      20.618  46.364  32.413    1.00  0.50
ATOM   2042  C   ASN   233      22.001  46.992  32.292    1.00  0.50
ATOM   2043  O   ASN   233      22.135  48.214  32.208    1.00  0.50
ATOM   2051  N   GLU   234      23.023  46.139  32.275    1.00  0.50
ATOM   2052  CA  GLU   234      24.414  46.576  32.167    1.00  0.50
ATOM   2053  C   GLU   234      25.286  45.463  31.597    1.00  0.50
ATOM   2054  O   GLU   234      25.291  44.342  32.108    1.00  0.50
ATOM   2060  N   ILE   242      26.025  45.787  30.540    1.00  0.50
ATOM   2061  CA  ILE   242      26.916  44.832  29.884    1.00  0.50
ATOM   2062  C   ILE   242      28.325  45.007  30.455    1.00  0.50
ATOM   2063  O   ILE   242      28.997  45.999  30.176    1.00  0.50
ATOM   2068  N   HIS   243      28.766  44.034  31.247    1.00  0.50
ATOM   2069  CA  HIS   243      30.074  44.093  31.892    1.00  0.50
ATOM   2070  C   HIS   243      31.286  43.835  30.997    1.00  0.50
ATOM   2071  O   HIS   243      32.259  43.208  31.419    1.00  0.50
ATOM   2076  N   PRO   244      31.223  44.322  29.763    1.00  0.50
ATOM   2077  CA  PRO   244      32.323  44.175  28.817    1.00  0.50
ATOM   2078  C   PRO   244      32.454  45.456  28.008    1.00  0.50
ATOM   2079  O   PRO   244      31.455  46.110  27.703    1.00  0.50
ATOM   2084  N   ASN   245      33.690  45.810  27.670    1.00  0.50
ATOM   2085  CA  ASN   245      33.963  47.010  26.884    1.00  0.50
ATOM   2086  C   ASN   245      33.127  46.993  25.609    1.00  0.50
ATOM   2087  O   ASN   245      32.884  45.935  25.028    1.00  0.50
ATOM   2089  N   LEU   246      32.695  48.172  25.172    1.00  0.50
ATOM   2090  CA  LEU   246      31.872  48.288  23.973    1.00  0.50
ATOM   2091  C   LEU   246      32.557  47.682  22.753    1.00  0.50
ATOM   2092  O   LEU   246      31.897  47.280  21.797    1.00  0.50
ATOM   2097  N   GLN   247      33.884  47.619  22.793    1.00  0.50
ATOM   2098  CA  GLN   247      34.659  47.068  21.688    1.00  0.50
ATOM   2099  C   GLN   247      35.143  45.645  21.955    1.00  0.50
ATOM   2100  O   GLN   247      36.070  45.174  21.296    1.00  0.50
ATOM   2103  N   ASP   248      34.536  44.960  22.920    1.00  0.50
ATOM   2104  CA  ASP   248      34.945  43.590  23.236    1.00  0.50
ATOM   2105  C   ASP   248      34.940  42.717  21.978    1.00  0.50
ATOM   2106  O   ASP   248      33.983  42.737  21.203    1.00  0.50
ATOM   2110  N   GLN   249      36.011  41.956  21.776    1.00  0.50
ATOM   2111  CA  GLN   249      36.125  41.087  20.603    1.00  0.50
ATOM   2112  C   GLN   249      35.231  39.857  20.696    1.00  0.50
ATOM   2113  O   GLN   249      34.909  39.391  21.790    1.00  0.50
ATOM   2119  N   ASP   250      34.833  39.331  19.540    1.00  0.50
ATOM   2120  CA  ASP   250      34.004  38.137  19.514    1.00  0.50
ATOM   2121  C   ASP   250      34.835  36.958  20.007    1.00  0.50
ATOM   2122  O   ASP   250      36.053  36.915  19.805    1.00  0.50
ATOM   2127  N   TRP   251      34.156  36.009  20.642    1.00  0.50
ATOM   2128  CA  TRP   251      34.768  34.802  21.189    1.00  0.50
ATOM   2129  C   TRP   251      35.639  35.091  22.401    1.00  0.50
ATOM   2130  O   TRP   251      36.496  34.288  22.765    1.00  0.50
ATOM   2138  N   LYS   252      35.422  36.244  23.028    1.00  0.50
ATOM   2139  CA  LYS   252      36.187  36.589  24.221    1.00  0.50
ATOM   2140  C   LYS   252      35.813  35.601  25.324    1.00  0.50
ATOM   2141  O   LYS   252      34.634  35.427  25.628    1.00  0.50
ATOM   2145  N   PRO   253      36.823  34.964  25.912    1.00  0.50
ATOM   2146  CA  PRO   253      36.635  33.982  26.978    1.00  0.50
ATOM   2147  C   PRO   253      36.085  34.603  28.264    1.00  0.50
ATOM   2148  O   PRO   253      36.580  35.633  28.727    1.00  0.50
ATOM   2153  N   LEU   254      35.063  33.971  28.836    1.00  0.50
ATOM   2154  CA  LEU   254      34.454  34.452  30.073    1.00  0.50
ATOM   2155  C   LEU   254      34.930  33.593  31.249    1.00  0.50
ATOM   2156  O   LEU   254      34.550  32.437  31.378    1.00  0.50
ATOM   2161  N   HIS   255      35.765  34.157  32.132    1.00  0.50
ATOM   2162  CA  HIS   255      36.272  33.397  33.281    1.00  0.50
ATOM   2163  C   HIS   255      35.200  32.929  34.254    1.00  0.50
ATOM   2164  O   HIS   255      34.114  33.503  34.327    1.00  0.50
ATOM   2168  N   PRO   256      35.505  31.869  34.997    1.00  0.50
ATOM   2169  CA  PRO   256      34.564  31.336  35.971    1.00  0.50
ATOM   2170  C   PRO   256      34.356  32.382  37.061    1.00  0.50
ATOM   2171  O   PRO   256      35.300  32.765  37.751    1.00  0.50
ATOM   2176  N   GLY   257      33.116  32.839  37.200    1.00  0.50
ATOM   2177  CA  GLY   257      32.787  33.852  38.186    1.00  0.50
ATOM   2178  C   GLY   257      31.755  34.830  37.651    1.00  0.50
ATOM   2179  O   GLY   257      30.591  34.807  38.065    1.00  0.50
ATOM   2180  N   ASP   258      28.950  36.250  35.514    1.00  0.50
ATOM   2181  CA  ASP   258      27.887  35.630  34.727    1.00  0.50
ATOM   2182  C   ASP   258      26.698  36.584  34.645    1.00  0.50
ATOM   2183  O   ASP   258      26.811  37.758  35.007    1.00  0.50
ATOM   2188  N   VAL   260      25.562  36.101  34.165    1.00  0.50
ATOM   2189  CA  VAL   260      24.399  36.967  34.055    1.00  0.50
ATOM   2190  C   VAL   260      23.429  36.756  35.215    1.00  0.50
ATOM   2191  O   VAL   260      23.208  35.623  35.653    1.00  0.50
ATOM   2196  N   PHE   261      22.870  37.852  35.720    1.00  0.50
ATOM   2197  CA  PHE   261      21.918  37.803  36.826    1.00  0.50
ATOM   2198  C   PHE   261      21.070  39.075  36.840    1.00  0.50
ATOM   2199  O   PHE   261      19.866  39.023  37.105    1.00  0.50
ATOM   2201  N   VAL   262      26.336  26.995  33.374    1.00  0.50
ATOM   2202  CA  VAL   262      26.394  28.321  33.979    1.00  0.50
ATOM   2203  C   VAL   262      27.737  29.003  33.722    1.00  0.50
ATOM   2204  O   VAL   262      27.824  29.945  32.930    1.00  0.50
ATOM   2206  N   SER   263      28.781  28.526  34.393    1.00  0.50
ATOM   2207  CA  SER   263      30.116  29.095  34.239    1.00  0.50
ATOM   2208  C   SER   263      31.194  28.047  34.507    1.00  0.50
ATOM   2209  O   SER   263      31.019  27.168  35.349    1.00  0.50
ATOM   2213  N   LEU   264      32.303  28.145  33.782    1.00  0.50
ATOM   2214  CA  LEU   264      33.386  27.196  33.963    1.00  0.50
ATOM   2215  C   LEU   264      34.660  27.615  33.252    1.00  0.50
ATOM   2216  O   LEU   264      35.562  26.805  33.042    1.00  0.50
ATOM   2217  N   ASP   265      34.740  28.889  32.884    1.00  0.50
ATOM   2218  CA  ASP   265      35.918  29.377  32.194    1.00  0.50
ATOM   2219  C   ASP   265      36.036  28.830  30.783    1.00  0.50
ATOM   2220  O   ASP   265      37.092  28.932  30.152    1.00  0.50
ATOM   2221  N   GLY   266      34.955  28.245  30.286    1.00  0.50
ATOM   2222  CA  GLY   266      34.939  27.685  28.939    1.00  0.50
ATOM   2223  C   GLY   266      34.072  28.501  27.980    1.00  0.50
ATOM   2224  O   GLY   266      34.263  28.452  26.765    1.00  0.50
ATOM   2230  N   LYS   267      33.122  29.252  28.529    1.00  0.50
ATOM   2231  CA  LYS   267      32.231  30.047  27.702    1.00  0.50
ATOM   2232  C   LYS   267      32.901  31.291  27.109    1.00  0.50
ATOM   2233  O   LYS   267      33.904  31.778  27.623    1.00  0.50
ATOM   2239  N   VAL   268      32.344  31.784  26.008    1.00  0.50
ATOM   2240  CA  VAL   268      32.865  32.968  25.340    1.00  0.50
ATOM   2241  C   VAL   268      31.673  33.789  24.859    1.00  0.50
ATOM   2242  O   VAL   268      30.600  33.246  24.600    1.00  0.50
ATOM   2250  N   ILE   269      31.864  35.094  24.746    1.00  0.50
ATOM   2251  CA  ILE   269      30.798  35.977  24.298    1.00  0.50
ATOM   2252  C   ILE   269      30.896  36.098  22.777    1.00  0.50
ATOM   2253  O   ILE   269      31.992  36.117  22.212    1.00  0.50
ATOM   2258  N   PRO   270      29.754  36.162  22.109    1.00  0.50
ATOM   2259  CA  PRO   270      29.756  36.277  20.659    1.00  0.50
ATOM   2260  C   PRO   270      28.670  37.247  20.208    1.00  0.50
ATOM   2261  O   PRO   270      27.550  37.209  20.712    1.00  0.50
ATOM   2266  N   PHE   281      29.024  38.128  19.277    1.00  0.50
ATOM   2267  CA  PHE   281      28.100  39.122  18.733    1.00  0.50
ATOM   2268  C   PHE   281      27.375  39.964  19.787    1.00  0.50
ATOM   2269  O   PHE   281      26.155  40.101  19.752    1.00  0.50
ATOM   2277  N   VAL   282      28.119  40.550  20.736    1.00  0.50
ATOM   2278  CA  VAL   282      27.490  41.375  21.774    1.00  0.50
ATOM   2279  C   VAL   282      26.863  42.650  21.196    1.00  0.50
ATOM   2280  O   VAL   282      27.465  43.315  20.354    1.00  0.50
ATOM   2284  N   ASN   283      25.661  42.989  21.651    1.00  0.50
ATOM   2285  CA  ASN   283      24.977  44.187  21.172    1.00  0.50
ATOM   2286  C   ASN   283      24.008  44.688  22.239    1.00  0.50
ATOM   2287  O   ASN   283      22.798  44.470  22.147    1.00  0.50
ATOM   2292  N   LYS   290      24.532  45.367  23.269    1.00  0.50
ATOM   2293  CA  LYS   290      23.726  45.905  24.368    1.00  0.50
ATOM   2294  C   LYS   290      22.872  47.119  23.991    1.00  0.50
ATOM   2295  O   LYS   290      22.093  47.615  24.806    1.00  0.50
ATOM   2299  N   LYS   291      23.017  47.587  22.755    1.00  0.50
ATOM   2300  CA  LYS   291      22.271  48.747  22.278    1.00  0.50
ATOM   2301  C   LYS   291      20.801  48.439  22.012    1.00  0.50
ATOM   2302  O   LYS   291      19.939  49.295  22.201    1.00  0.50
ATOM   2304  N   GLU   292      20.512  47.218  21.573    1.00  0.50
ATOM   2305  CA  GLU   292      19.137  46.829  21.276    1.00  0.50
ATOM   2306  C   GLU   292      18.194  47.046  22.454    1.00  0.50
ATOM   2307  O   GLU   292      17.121  47.631  22.297    1.00  0.50
ATOM   2311  N   ALA   293      18.594  46.561  23.627    1.00  0.50
ATOM   2312  CA  ALA   293      17.809  46.683  24.857    1.00  0.50
ATOM   2313  C   ALA   293      16.284  46.694  24.674    1.00  0.50
ATOM   2314  O   ALA   293      15.598  47.574  25.205    1.00  0.50
ATOM   2320  N   PHE   294      15.731  45.723  23.928    1.00  0.50
ATOM   2321  CA  PHE   294      14.279  45.718  23.749    1.00  0.50
ATOM   2322  C   PHE   294      13.647  44.618  24.603    1.00  0.50
ATOM   2323  O   PHE   294      13.366  44.809  25.786    1.00  0.50
ATOM   2327  N   ALA   295      13.432  43.468  23.979    1.00  0.50
ATOM   2328  CA  ALA   295      12.870  42.315  24.650    1.00  0.50
ATOM   2329  C   ALA   295      13.566  41.134  24.007    1.00  0.50
ATOM   2330  O   ALA   295      13.258  39.972  24.272    1.00  0.50
ATOM   2331  N   LYS   296      14.520  41.463  23.141    1.00  0.50
ATOM   2332  CA  LYS   296      15.311  40.482  22.411    1.00  0.50
ATOM   2333  C   LYS   296      16.624  40.243  23.146    1.00  0.50
ATOM   2334  O   LYS   296      16.789  40.658  24.294    1.00  0.50
TER
END
