
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0316AL242_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL242_1-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    M     284      Q     292          4.883
LGA    S     285      V     293          3.681
LGA    T     286      H     294          3.849
LGA    S     287      F     295          2.546
LGA    L     288      T     296          4.568
LGA    E     289      -       -           -
LGA    A     290      R     297          1.598
LGA    S     291      -       -           -
LGA    Q     292      E     298          3.103
LGA    V     293      M     299          1.309
LGA    H     294      P     300          1.062
LGA    F     295      -       -           -
LGA    T     296      -       -           -
LGA    R     297      E     301          3.203
LGA    E     298      E     302           #
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      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    M     299      K     325          3.597
LGA    P     300      G     326          4.025
LGA    E     301      E     327           #
LGA    E     302      K     328          3.838
LGA    F     303      T     329          3.366
LGA    T     304      E     330          3.469
LGA    L     305      V     331          4.487
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    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    E     306      L     359           #
LGA    C     307      I     360           #
LGA    T     308      D     361           #
LGA    A     309      N     362          3.633
LGA    K     310      A     363          2.613
LGA    F     311      Y     364          0.936
LGA    R     312      R     365          3.848
LGA    Y     313      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    R     314      C     370          4.064
LGA    Q     315      Q     371          2.590
LGA    P     316      Y     372          4.306
LGA    D     317      I     373           -
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      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   90    5.0     23    3.42     8.70     14.419     0.653

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.396322 * X  +   0.918025 * Y  +  -0.012632 * Z  +  21.287622
  Y_new =  -0.363882 * X  +   0.144431 * Y  +  -0.920179 * Z  + -14.131688
  Z_new =  -0.842923 * X  +   0.369283 * Y  +   0.391293 * Z  + -38.790451 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.756468   -2.385125  [ DEG:    43.3424   -136.6576 ]
  Theta =   1.002693    2.138900  [ DEG:    57.4501    122.5499 ]
  Phi   =  -0.742751    2.398841  [ DEG:   -42.5565    137.4435 ]
 
# 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: T0316AL242_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL242_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   90   5.0   23   3.42    8.70  14.419
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL242_1-D3
REMARK Aligment from pdb entry: 1xng_B
ATOM    797  N   MET   284      30.105  12.835   7.296  1.00  0.00              
ATOM    798  CA  MET   284      30.842  13.016   8.541  1.00  0.00              
ATOM    799  C   MET   284      30.491  11.845   9.446  1.00  0.00              
ATOM    800  O   MET   284      29.386  11.783   9.984  1.00  0.00              
ATOM    801  N   SER   285      31.431  10.922   9.607  1.00  0.00              
ATOM    802  CA  SER   285      31.212   9.738  10.427  1.00  0.00              
ATOM    803  C   SER   285      31.005  10.045  11.900  1.00  0.00              
ATOM    804  O   SER   285      30.420   9.245  12.621  1.00  0.00              
ATOM    805  N   THR   286      31.490  11.199  12.345  1.00  0.00              
ATOM    806  CA  THR   286      31.335  11.588  13.741  1.00  0.00              
ATOM    807  C   THR   286      29.883  11.978  13.996  1.00  0.00              
ATOM    808  O   THR   286      29.313  11.652  15.036  1.00  0.00              
ATOM    809  N   SER   287      29.286  12.673  13.033  1.00  0.00              
ATOM    810  CA  SER   287      27.894  13.090  13.139  1.00  0.00              
ATOM    811  C   SER   287      26.993  11.859  13.172  1.00  0.00              
ATOM    812  O   SER   287      26.042  11.787  13.952  1.00  0.00              
ATOM    813  N   LEU   288      27.299  10.882  12.322  1.00  0.00              
ATOM    814  CA  LEU   288      26.507   9.662  12.278  1.00  0.00              
ATOM    815  C   LEU   288      26.690   8.870  13.572  1.00  0.00              
ATOM    816  O   LEU   288      25.772   8.185  14.024  1.00  0.00              
ATOM    817  N   GLU   289      27.875   8.968  14.166  1.00  0.00              
ATOM    818  CA  GLU   289      28.162   8.277  15.416  1.00  0.00              
ATOM    819  C   GLU   289      27.339   8.918  16.530  1.00  0.00              
ATOM    820  O   GLU   289      26.850   8.234  17.424  1.00  0.00              
ATOM    821  N   ALA   290      27.187  10.238  16.475  1.00  0.00              
ATOM    822  CA  ALA   290      26.412  10.942  17.493  1.00  0.00              
ATOM    823  C   ALA   290      24.940  10.563  17.438  1.00  0.00              
ATOM    824  O   ALA   290      24.223  10.653  18.440  1.00  0.00              
ATOM    825  N   SER   291      24.484  10.149  16.262  1.00  0.00              
ATOM    826  CA  SER   291      23.093   9.750  16.092  1.00  0.00              
ATOM    827  C   SER   291      22.798   8.398  16.721  1.00  0.00              
ATOM    828  O   SER   291      21.649   8.086  17.027  1.00  0.00              
ATOM    829  N   GLN   292      23.834   7.588  16.904  1.00  0.00              
ATOM    830  CA  GLN   292      23.632   6.289  17.512  1.00  0.00              
ATOM    831  C   GLN   292      23.922   5.108  16.610  1.00  0.00              
ATOM    832  O   GLN   292      23.818   3.964  17.050  1.00  0.00              
ATOM    833  N   VAL   293      24.277   5.368  15.356  1.00  0.00              
ATOM    834  CA  VAL   293      24.582   4.282  14.432  1.00  0.00              
ATOM    835  C   VAL   293      25.855   3.546  14.828  1.00  0.00              
ATOM    836  O   VAL   293      26.801   4.149  15.337  1.00  0.00              
ATOM    837  N   HIS   294      25.866   2.241  14.584  1.00  0.00              
ATOM    838  CA  HIS   294      27.014   1.403  14.902  1.00  0.00              
ATOM    839  C   HIS   294      28.208   1.782  14.039  1.00  0.00              
ATOM    840  O   HIS   294      28.072   2.017  12.835  1.00  0.00              
ATOM    841  N   PHE   295      29.379   1.812  14.667  1.00  0.00              
ATOM    842  CA  PHE   295      30.627   2.180  14.009  1.00  0.00              
ATOM    843  C   PHE   295      30.940   1.372  12.747  1.00  0.00              
ATOM    844  O   PHE   295      31.380   1.933  11.745  1.00  0.00              
ATOM    845  N   THR   296      30.708   0.065  12.782  1.00  0.00              
ATOM    846  CA  THR   296      31.004  -0.766  11.615  1.00  0.00              
ATOM    847  C   THR   296      30.036  -0.490  10.466  1.00  0.00              
ATOM    848  O   THR   296      30.441  -0.424   9.298  1.00  0.00              
ATOM    849  N   ARG   297      28.763  -0.330  10.797  1.00  0.00              
ATOM    850  CA  ARG   297      27.751  -0.039   9.791  1.00  0.00              
ATOM    851  C   ARG   297      28.115   1.267   9.091  1.00  0.00              
ATOM    852  O   ARG   297      28.119   1.346   7.864  1.00  0.00              
ATOM    853  N   GLU   298      28.419   2.300   9.876  1.00  0.00              
ATOM    854  CA  GLU   298      28.785   3.590   9.301  1.00  0.00              
ATOM    855  C   GLU   298      30.011   3.477   8.390  1.00  0.00              
ATOM    856  O   GLU   298      30.010   3.985   7.267  1.00  0.00              
ATOM    857  N   MET   299      31.054   2.802   8.863  1.00  0.00              
ATOM    858  CA  MET   299      32.262   2.644   8.063  1.00  0.00              
ATOM    859  C   MET   299      31.967   1.910   6.756  1.00  0.00              
ATOM    860  O   MET   299      32.402   2.332   5.681  1.00  0.00              
ATOM    861  N   PRO   300      31.220   0.819   6.860  1.00  0.00              
ATOM    862  CA  PRO   300      30.867  -0.002   5.707  1.00  0.00              
ATOM    863  C   PRO   300      30.095   0.792   4.654  1.00  0.00              
ATOM    864  O   PRO   300      30.515   0.893   3.497  1.00  0.00              
ATOM    865  N   GLU   301      28.977   1.367   5.069  1.00  0.00              
ATOM    866  CA  GLU   301      28.109   2.120   4.172  1.00  0.00              
ATOM    867  C   GLU   301      28.747   3.387   3.613  1.00  0.00              
ATOM    868  O   GLU   301      28.621   3.682   2.424  1.00  0.00              
ATOM    869  N   GLU   302      29.452   4.131   4.458  1.00  0.00              
ATOM    870  CA  GLU   302      30.107   5.345   4.004  1.00  0.00              
ATOM    871  C   GLU   302      31.147   5.017   2.934  1.00  0.00              
ATOM    872  O   GLU   302      31.298   5.752   1.955  1.00  0.00              
ATOM    873  N   PHE   303      31.860   3.910   3.121  1.00  0.00              
ATOM    874  CA  PHE   303      32.882   3.511   2.158  1.00  0.00              
ATOM    875  C   PHE   303      32.271   3.152   0.809  1.00  0.00              
ATOM    876  O   PHE   303      32.772   3.574  -0.238  1.00  0.00              
ATOM    877  N   THR   304      31.201   2.366   0.838  1.00  0.00              
ATOM    878  CA  THR   304      30.528   1.960  -0.391  1.00  0.00              
ATOM    879  C   THR   304      30.062   3.179  -1.171  1.00  0.00              
ATOM    880  O   THR   304      30.246   3.260  -2.380  1.00  0.00              
ATOM    881  N   LEU   305      29.476   4.141  -0.473  1.00  0.00              
ATOM    882  CA  LEU   305      28.992   5.334  -1.143  1.00  0.00              
ATOM    883  C   LEU   305      30.106   6.157  -1.784  1.00  0.00              
ATOM    884  O   LEU   305      30.011   6.516  -2.953  1.00  0.00              
ATOM    885  N   GLU   306      31.164   6.453  -1.034  1.00  0.00              
ATOM    886  CA  GLU   306      32.252   7.264  -1.572  1.00  0.00              
ATOM    887  C   GLU   306      33.059   6.545  -2.646  1.00  0.00              
ATOM    888  O   GLU   306      33.474   7.146  -3.639  1.00  0.00              
ATOM    889  N   CYS   307      33.271   5.252  -2.449  1.00  0.00              
ATOM    890  CA  CYS   307      34.038   4.466  -3.401  1.00  0.00              
ATOM    891  C   CYS   307      33.318   4.263  -4.735  1.00  0.00              
ATOM    892  O   CYS   307      33.957   4.198  -5.788  1.00  0.00              
ATOM    893  N   THR   308      31.995   4.188  -4.700  1.00  0.00              
ATOM    894  CA  THR   308      31.248   3.934  -5.925  1.00  0.00              
ATOM    895  C   THR   308      30.440   5.084  -6.488  1.00  0.00              
ATOM    896  O   THR   308      29.594   4.885  -7.358  1.00  0.00              
ATOM    897  N   ALA   309      30.709   6.293  -6.008  1.00  0.00              
ATOM    898  CA  ALA   309      29.973   7.452  -6.488  1.00  0.00              
ATOM    899  C   ALA   309      30.174   7.624  -7.989  1.00  0.00              
ATOM    900  O   ALA   309      29.289   8.114  -8.691  1.00  0.00              
ATOM    901  N   LYS   310      31.337   7.215  -8.478  1.00  0.00              
ATOM    902  CA  LYS   310      31.642   7.339  -9.897  1.00  0.00              
ATOM    903  C   LYS   310      30.610   6.653 -10.799  1.00  0.00              
ATOM    904  O   LYS   310      30.430   7.070 -11.941  1.00  0.00              
ATOM    905  N   PHE   311      29.931   5.619 -10.299  1.00  0.00              
ATOM    906  CA  PHE   311      28.949   4.891 -11.112  1.00  0.00              
ATOM    907  C   PHE   311      27.731   5.729 -11.479  1.00  0.00              
ATOM    908  O   PHE   311      27.001   5.413 -12.420  1.00  0.00              
ATOM    909  N   ARG   312      27.510   6.808 -10.738  1.00  0.00              
ATOM    910  CA  ARG   312      26.360   7.664 -10.996  1.00  0.00              
ATOM    911  C   ARG   312      26.725   8.892 -11.816  1.00  0.00              
ATOM    912  O   ARG   312      25.903   9.793 -12.008  1.00  0.00              
ATOM    913  N   TYR   313      27.956   8.919 -12.310  1.00  0.00              
ATOM    914  CA  TYR   313      28.430  10.048 -13.092  1.00  0.00              
ATOM    915  C   TYR   313      28.923   9.635 -14.470  1.00  0.00              
ATOM    916  O   TYR   313      29.160   8.457 -14.734  1.00  0.00              
ATOM    917  N   ARG   314      29.058  10.614 -15.357  1.00  0.00              
ATOM    918  CA  ARG   314      29.561  10.338 -16.695  1.00  0.00              
ATOM    919  C   ARG   314      31.081  10.221 -16.587  1.00  0.00              
ATOM    920  O   ARG   314      31.669  10.553 -15.561  1.00  0.00              
ATOM    921  N   GLN   315      31.741   9.745 -17.650  1.00  0.00              
ATOM    922  CA  GLN   315      33.199   9.622 -17.581  1.00  0.00              
ATOM    923  C   GLN   315      33.892  10.987 -17.520  1.00  0.00              
ATOM    924  O   GLN   315      33.311  12.000 -17.908  1.00  0.00              
ATOM    925  N   PRO   316      35.122  11.009 -17.020  1.00  0.00              
ATOM    926  CA  PRO   316      35.890  12.249 -16.939  1.00  0.00              
ATOM    927  C   PRO   316      36.527  12.479 -18.308  1.00  0.00              
ATOM    928  O   PRO   316      37.332  11.668 -18.769  1.00  0.00              
ATOM    929  N   ASP   317      36.161  13.584 -18.948  1.00  0.00              
ATOM    930  CA  ASP   317      36.660  13.926 -20.279  1.00  0.00              
ATOM    931  C   ASP   317      37.555  15.158 -20.184  1.00  0.00              
ATOM    932  O   ASP   317      37.165  16.147 -19.574  1.00  0.00              
ATOM    933  N   SER   318      38.743  15.115 -20.784  1.00  0.00              
ATOM    934  CA  SER   318      39.632  16.274 -20.718  1.00  0.00              
ATOM    935  C   SER   318      39.028  17.443 -21.482  1.00  0.00              
ATOM    936  O   SER   318      38.661  17.317 -22.648  1.00  0.00              
ATOM    937  N   LYS   319      38.914  18.584 -20.811  1.00  0.00              
ATOM    938  CA  LYS   319      38.355  19.768 -21.440  1.00  0.00              
ATOM    939  C   LYS   319      39.297  20.301 -22.508  1.00  0.00              
ATOM    940  O   LYS   319      40.475  19.932 -22.559  1.00  0.00              
ATOM    941  N   VAL   320      38.758  21.159 -23.364  1.00  0.00              
ATOM    942  CA  VAL   320      39.542  21.778 -24.417  1.00  0.00              
ATOM    943  C   VAL   320      40.714  22.470 -23.741  1.00  0.00              
ATOM    944  O   VAL   320      40.574  23.029 -22.648  1.00  0.00              
ATOM    945  N   THR   321      41.871  22.417 -24.387  1.00  0.00              
ATOM    946  CA  THR   321      43.067  23.041 -23.851  1.00  0.00              
ATOM    947  C   THR   321      43.072  24.529 -24.195  1.00  0.00              
ATOM    948  O   THR   321      42.948  24.902 -25.361  1.00  0.00              
ATOM    949  N   VAL   322      43.188  25.367 -23.169  1.00  0.00              
ATOM    950  CA  VAL   322      43.244  26.816 -23.342  1.00  0.00              
ATOM    951  C   VAL   322      44.592  27.263 -22.803  1.00  0.00              
ATOM    952  O   VAL   322      44.771  27.424 -21.598  1.00  0.00              
ATOM    953  N   HIS   323      45.565  27.465 -23.701  1.00  0.00              
ATOM    954  CA  HIS   323      46.908  27.891 -23.305  1.00  0.00              
ATOM    955  C   HIS   323      46.968  29.269 -22.656  1.00  0.00              
ATOM    956  O   HIS   323      46.198  30.170 -23.000  1.00  0.00              
ATOM    957  N   VAL   324      47.871  29.409 -21.689  1.00  0.00              
ATOM    958  CA  VAL   324      48.073  30.676 -21.002  1.00  0.00              
ATOM    959  C   VAL   324      49.065  31.438 -21.874  1.00  0.00              
ATOM    960  O   VAL   324      50.248  31.090 -21.935  1.00  0.00              
ATOM    961  N   LYS   325      48.572  32.464 -22.562  1.00  0.00              
ATOM    962  CA  LYS   325      49.401  33.260 -23.457  1.00  0.00              
ATOM    963  C   LYS   325      50.442  34.088 -22.707  1.00  0.00              
ATOM    964  O   LYS   325      50.308  34.337 -21.511  1.00  0.00              
ATOM    965  N   GLY   326      51.477  34.516 -23.422  1.00  0.00              
ATOM    966  CA  GLY   326      52.565  35.279 -22.821  1.00  0.00              
ATOM    967  C   GLY   326      52.137  36.548 -22.097  1.00  0.00              
ATOM    968  O   GLY   326      52.695  36.892 -21.055  1.00  0.00              
ATOM    969  N   GLU   327      51.143  37.239 -22.639  1.00  0.00              
ATOM    970  CA  GLU   327      50.690  38.481 -22.031  1.00  0.00              
ATOM    971  C   GLU   327      49.606  38.301 -20.977  1.00  0.00              
ATOM    972  O   GLU   327      49.119  39.283 -20.416  1.00  0.00              
ATOM    973  N   LYS   328      49.223  37.057 -20.713  1.00  0.00              
ATOM    974  CA  LYS   328      48.200  36.781 -19.707  1.00  0.00              
ATOM    975  C   LYS   328      48.759  37.025 -18.307  1.00  0.00              
ATOM    976  O   LYS   328      49.838  36.535 -17.969  1.00  0.00              
END
