
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0316TS349_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS349_2-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    S     285      T     308           #
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    T     286      Y     349          2.976
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    S     287      E     352          2.094
LGA    L     288      E     353          2.369
LGA    E     289      C     354          1.139
LGA    A     290      L     355          0.739
LGA    S     291      G     356          4.074
LGA    Q     292      G     357          2.068
LGA    V     293      G     358          3.510
LGA    H     294      L     359          1.947
LGA    F     295      I     360          1.914
LGA    T     296      D     361          1.666
LGA    R     297      N     362          1.433
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    E     298      V     369          4.169
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   90    5.0     13    2.54     0.00     11.809     0.493

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.099956 * X  +  -0.961270 * Y  +   0.256845 * Z  +  22.482880
  Y_new =  -0.514101 * X  +  -0.270907 * Y  +  -0.813824 * Z  +  43.226391
  Z_new =   0.851886 * X  +  -0.050698 * Y  +  -0.521268 * Z  + -23.642000 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.044639    0.096953  [ DEG:  -174.4450      5.5550 ]
  Theta =  -1.019575   -2.122017  [ DEG:   -58.4174   -121.5826 ]
  Phi   =  -1.378763    1.762829  [ DEG:   -78.9973    101.0027 ]
 
# 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: T0316TS349_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS349_2-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   90   5.0   13   2.54    0.00  11.809
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS349_2-D3
PFRMAT TS
TARGET T0316
MODEL  2  REFINED
PARENT 1VL2_A
ATOM   2184  N   MET   284      12.261  12.596   9.964  1.00  0.00
ATOM   2185  CA  MET   284      13.010  12.598  11.237  1.00  0.00
ATOM   2186  C   MET   284      14.554  12.694  10.921  1.00  0.00
ATOM   2187  O   MET   284      15.207  13.457  11.636  1.00  0.00
ATOM   2188  CB  MET   284      12.630  11.379  12.055  1.00  0.00
ATOM   2189  CG  MET   284      11.233  11.286  12.611  1.00  0.00
ATOM   2190  SD  MET   284      10.773  12.638  13.730  1.00  0.00
ATOM   2191  CE  MET   284      11.782  12.145  15.067  1.00  0.00
ATOM   2192  N   SER   285      15.140  11.897   9.984  1.00  0.00
ATOM   2193  CA  SER   285      16.551  11.999   9.560  1.00  0.00
ATOM   2194  C   SER   285      16.877  13.445   8.990  1.00  0.00
ATOM   2195  O   SER   285      18.069  13.758   8.981  1.00  0.00
ATOM   2196  CB  SER   285      16.823  10.904   8.520  1.00  0.00
ATOM   2197  OG  SER   285      17.024   9.574   9.010  1.00  0.00
ATOM   2198  N   THR   286      16.003  14.105   8.181  1.00  0.00
ATOM   2199  CA  THR   286      16.151  15.492   7.647  1.00  0.00
ATOM   2200  C   THR   286      16.124  16.521   8.810  1.00  0.00
ATOM   2201  O   THR   286      16.967  17.431   8.783  1.00  0.00
ATOM   2202  CB  THR   286      15.110  15.828   6.522  1.00  0.00
ATOM   2203  OG1 THR   286      13.796  16.176   7.086  1.00  0.00
ATOM   2204  CG2 THR   286      14.903  14.620   5.548  1.00  0.00
ATOM   2205  N   SER   287      15.067  16.605   9.637  1.00  0.00
ATOM   2206  CA  SER   287      14.986  17.480  10.840  1.00  0.00
ATOM   2207  C   SER   287      16.331  17.483  11.619  1.00  0.00
ATOM   2208  O   SER   287      16.783  18.585  11.971  1.00  0.00
ATOM   2209  CB  SER   287      13.788  17.050  11.711  1.00  0.00
ATOM   2210  OG  SER   287      12.492  17.437  11.280  1.00  0.00
ATOM   2211  N   LEU   288      16.803  16.316  12.070  1.00  0.00
ATOM   2212  CA  LEU   288      18.045  16.094  12.758  1.00  0.00
ATOM   2213  C   LEU   288      18.988  15.681  11.655  1.00  0.00
ATOM   2214  O   LEU   288      18.972  14.491  11.313  1.00  0.00
ATOM   2215  CB  LEU   288      17.797  14.839  13.652  1.00  0.00
ATOM   2216  CG  LEU   288      17.103  15.099  14.989  1.00  0.00
ATOM   2217  CD1 LEU   288      17.191  13.802  15.770  1.00  0.00
ATOM   2218  CD2 LEU   288      17.732  16.202  15.813  1.00  0.00
ATOM   2219  N   GLU   289      20.062  16.460  11.325  1.00  0.00
ATOM   2220  CA  GLU   289      20.859  16.016  10.139  1.00  0.00
ATOM   2221  C   GLU   289      21.683  14.791  10.461  1.00  0.00
ATOM   2222  O   GLU   289      22.614  14.857  11.287  1.00  0.00
ATOM   2223  CB  GLU   289      21.834  17.064   9.625  1.00  0.00
ATOM   2224  CG  GLU   289      22.686  16.745   8.402  1.00  0.00
ATOM   2225  CD  GLU   289      24.085  16.357   8.826  1.00  0.00
ATOM   2226  OE1 GLU   289      24.837  17.044   9.545  1.00  0.00
ATOM   2227  OE2 GLU   289      24.365  15.255   8.307  1.00  0.00
ATOM   2228  N   ALA   290      21.275  13.667   9.859  1.00  0.00
ATOM   2229  CA  ALA   290      21.989  12.410   9.998  1.00  0.00
ATOM   2230  C   ALA   290      22.675  11.843   8.682  1.00  0.00
ATOM   2231  O   ALA   290      23.674  11.133   8.861  1.00  0.00
ATOM   2232  CB  ALA   290      20.926  11.406  10.467  1.00  0.00
ATOM   2233  N   SER   291      22.371  12.336   7.453  1.00  0.00
ATOM   2234  CA  SER   291      22.931  11.751   6.237  1.00  0.00
ATOM   2235  C   SER   291      23.552  12.826   5.306  1.00  0.00
ATOM   2236  O   SER   291      22.862  13.436   4.471  1.00  0.00
ATOM   2237  CB  SER   291      21.820  10.951   5.537  1.00  0.00
ATOM   2238  OG  SER   291      20.665  11.695   5.161  1.00  0.00
ATOM   2239  N   GLN   292      24.877  12.891   5.346  1.00  0.00
ATOM   2240  CA  GLN   292      25.742  13.751   4.529  1.00  0.00
ATOM   2241  C   GLN   292      26.839  12.900   3.836  1.00  0.00
ATOM   2242  O   GLN   292      27.675  12.297   4.540  1.00  0.00
ATOM   2243  CB  GLN   292      26.452  14.704   5.488  1.00  0.00
ATOM   2244  CG  GLN   292      25.763  15.898   6.085  1.00  0.00
ATOM   2245  CD  GLN   292      25.220  16.895   5.077  1.00  0.00
ATOM   2246  OE1 GLN   292      24.362  16.573   4.247  1.00  0.00
ATOM   2247  NE2 GLN   292      25.734  18.124   5.080  1.00  0.00
ATOM   2248  N   VAL   293      26.730  12.622   2.526  1.00  0.00
ATOM   2249  CA  VAL   293      27.757  11.873   1.798  1.00  0.00
ATOM   2250  C   VAL   293      28.513  12.843   0.879  1.00  0.00
ATOM   2251  O   VAL   293      28.020  13.164  -0.213  1.00  0.00
ATOM   2252  CB  VAL   293      27.139  10.725   1.008  1.00  0.00
ATOM   2253  CG1 VAL   293      28.185   9.963   0.160  1.00  0.00
ATOM   2254  CG2 VAL   293      26.410   9.703   1.952  1.00  0.00
ATOM   2255  N   HIS   294      29.691  13.233   1.246  1.00  0.00
ATOM   2256  CA  HIS   294      30.514  14.126   0.416  1.00  0.00
ATOM   2257  C   HIS   294      31.821  13.367   0.179  1.00  0.00
ATOM   2258  O   HIS   294      32.732  13.375   1.033  1.00  0.00
ATOM   2259  CB  HIS   294      30.690  15.496   1.085  1.00  0.00
ATOM   2260  CG  HIS   294      31.523  16.445   0.281  1.00  0.00
ATOM   2261  ND1 HIS   294      32.844  16.739   0.560  1.00  0.00
ATOM   2262  CD2 HIS   294      31.201  17.183  -0.811  1.00  0.00
ATOM   2263  CE1 HIS   294      33.302  17.608  -0.322  1.00  0.00
ATOM   2264  NE2 HIS   294      32.324  17.893  -1.163  1.00  0.00
ATOM   2265  N   PHE   295      31.954  12.758  -0.999  1.00  0.00
ATOM   2266  CA  PHE   295      33.179  11.999  -1.361  1.00  0.00
ATOM   2267  C   PHE   295      33.217  11.768  -2.896  1.00  0.00
ATOM   2268  O   PHE   295      32.170  11.473  -3.504  1.00  0.00
ATOM   2269  CB  PHE   295      33.340  10.722  -0.567  1.00  0.00
ATOM   2270  CG  PHE   295      32.575   9.502  -0.861  1.00  0.00
ATOM   2271  CD1 PHE   295      31.458   9.222  -0.042  1.00  0.00
ATOM   2272  CD2 PHE   295      32.885   8.630  -1.871  1.00  0.00
ATOM   2273  CE1 PHE   295      30.689   8.082  -0.222  1.00  0.00
ATOM   2274  CE2 PHE   295      32.085   7.492  -2.113  1.00  0.00
ATOM   2275  CZ  PHE   295      30.983   7.223  -1.275  1.00  0.00
ATOM   2276  N   THR   296      34.430  11.514  -3.388  1.00  0.00
ATOM   2277  CA  THR   296      34.560  11.389  -4.830  1.00  0.00
ATOM   2278  C   THR   296      34.714   9.888  -5.300  1.00  0.00
ATOM   2279  O   THR   296      35.670   9.190  -4.946  1.00  0.00
ATOM   2280  CB  THR   296      35.695  12.362  -5.284  1.00  0.00
ATOM   2281  OG1 THR   296      35.342  13.761  -4.992  1.00  0.00
ATOM   2282  CG2 THR   296      35.935  12.260  -6.843  1.00  0.00
ATOM   2283  N   ARG   297      33.561   9.405  -5.810  1.00  0.00
ATOM   2284  CA  ARG   297      33.349   8.073  -6.421  1.00  0.00
ATOM   2285  C   ARG   297      34.249   7.847  -7.682  1.00  0.00
ATOM   2286  O   ARG   297      34.360   8.753  -8.526  1.00  0.00
ATOM   2287  CB  ARG   297      31.907   8.024  -6.898  1.00  0.00
ATOM   2288  CG  ARG   297      31.010   7.048  -6.246  1.00  0.00
ATOM   2289  CD  ARG   297      30.702   5.813  -6.985  1.00  0.00
ATOM   2290  NE  ARG   297      29.944   6.288  -8.089  1.00  0.00
ATOM   2291  CZ  ARG   297      29.537   5.533  -9.113  1.00  0.00
ATOM   2292  NH1 ARG   297      29.466   4.198  -9.116  1.00  0.00
ATOM   2293  NH2 ARG   297      29.087   6.219 -10.154  1.00  0.00
ATOM   2294  N   GLU   298      34.602   6.575  -7.907  1.00  0.00
ATOM   2295  CA  GLU   298      35.380   6.126  -9.051  1.00  0.00
ATOM   2296  C   GLU   298      34.541   6.346 -10.332  1.00  0.00
ATOM   2297  O   GLU   298      34.910   7.130 -11.198  1.00  0.00
ATOM   2298  CB  GLU   298      35.718   4.645  -8.879  1.00  0.00
ATOM   2299  CG  GLU   298      36.767   4.388  -7.820  1.00  0.00
ATOM   2300  CD  GLU   298      37.293   3.012  -7.562  1.00  0.00
ATOM   2301  OE1 GLU   298      38.301   2.890  -6.856  1.00  0.00
ATOM   2302  OE2 GLU   298      36.678   2.066  -8.082  1.00  0.00
ATOM   2303  OXT GLU   298      33.543   5.644 -10.456  1.00  0.00
TER
END
