
#######################################################
#                                                     #
#                        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   35 (  170),  selected   35 , name T0316TS102_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS102_4-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      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    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    A     334      H     294          3.467
LGA    E     335      F     295          4.450
LGA    P     336      T     296           -
LGA    Q     337      R     297           #
LGA    R     338      E     298          2.418
LGA    A     339      M     299          2.426
LGA    A     345      P     300          2.711
LGA    V     346      E     301          3.165
LGA    V     347      E     302          4.299
LGA    F     348      F     303          1.456
LGA    Y     349      T     304          1.673
LGA    D     350      L     305          4.171
LGA    G     351      -       -           -
LGA    E     352      E     306          4.040
LGA    E     353      C     307          2.700
LGA    C     354      -       -           -
LGA    L     355      -       -           -
LGA    G     356      T     308          1.858
LGA    G     357      A     309          0.643
LGA    G     358      K     310          4.990
LGA    L     359      F     311           -
LGA    I     360      R     312           #
LGA    D     361      Y     313          4.756
LGA    N     362      -       -           -
LGA    A     363      -       -           -
LGA    Y     364      -       -           -
LGA    R     365      R     314          2.662
LGA    D     366      Q     315          2.660
LGA    G     367      P     316          4.155
LGA    Q     368      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    V     369      T     341           #
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    C     370      V     346          4.440
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    -       -      L     359           -
LGA    Q     371      I     360          2.209
LGA    Y     372      D     361          3.070
LGA    I     373      N     362          3.792
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
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)   35   90    5.0     23    3.34    13.04     14.832     0.669

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.897256 * X  +  -0.322722 * Y  +   0.301299 * Z  +  15.693297
  Y_new =  -0.116235 * X  +   0.485692 * Y  +   0.866368 * Z  + -25.008522
  Z_new =  -0.425935 * X  +  -0.812375 * Y  +   0.398279 * Z  +  37.534077 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.114968    2.026625  [ DEG:   -63.8829    116.1171 ]
  Theta =   0.439995    2.701598  [ DEG:    25.2098    154.7902 ]
  Phi   =  -0.128827    3.012766  [ DEG:    -7.3812    172.6188 ]
 
# 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: T0316TS102_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_4-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   90   5.0   23   3.34   13.04  14.832
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_4-D3
PFRMAT TS
TARGET T0316
MODEL 4
PARENT 2btw_A
ATOM    833  N   ALA   334      31.436   8.648  10.980  1.00  1.00
ATOM    834  CA  ALA   334      32.512   9.336  11.695  1.00  1.00
ATOM    835  C   ALA   334      32.101   9.923  13.074  1.00  1.00
ATOM    836  O   ALA   334      32.944  10.209  13.885  1.00  1.00
ATOM    837  CB  ALA   334      33.247  10.384  10.802  1.00  1.00
ATOM    838  N   GLU   335      30.800  10.029  13.367  1.00  1.00
ATOM    839  CA  GLU   335      30.339  10.375  14.724  1.00  1.00
ATOM    840  C   GLU   335      30.423   9.185  15.670  1.00  1.00
ATOM    841  O   GLU   335      29.450   8.820  16.243  1.00  1.00
ATOM    842  CB  GLU   335      28.874  10.833  14.661  1.00  1.00
ATOM    843  N   PRO   336      31.577   8.573  15.828  1.00  1.00
ATOM    844  CA  PRO   336      31.654   7.279  16.472  1.00  1.00
ATOM    845  C   PRO   336      31.253   7.242  17.942  1.00  1.00
ATOM    846  O   PRO   336      30.897   6.184  18.430  1.00  1.00
ATOM    847  CB  PRO   336      33.072   6.683  16.348  1.00  1.00
ATOM    848  N   GLN   337      31.430   8.364  18.643  1.00  1.00
ATOM    849  CA  GLN   337      30.932   8.509  20.023  1.00  1.00
ATOM    850  C   GLN   337      29.394   8.548  20.162  1.00  1.00
ATOM    851  O   GLN   337      28.882   8.473  21.287  1.00  1.00
ATOM    852  CB  GLN   337      31.488   9.797  20.671  1.00  1.00
ATOM    853  N   ARG   338      28.686   8.620  19.029  1.00  1.00
ATOM    854  CA  ARG   338      27.227   8.871  18.996  1.00  1.00
ATOM    855  C   ARG   338      26.532   7.674  18.352  1.00  1.00
ATOM    856  O   ARG   338      25.606   7.097  18.901  1.00  1.00
ATOM    857  CB  ARG   338      26.951  10.141  18.196  1.00  1.00
ATOM    858  N   ALA   339      27.016   7.270  17.200  1.00  1.00
ATOM    859  CA  ALA   339      26.429   6.165  16.531  1.00  1.00
ATOM    860  C   ALA   339      27.468   5.147  16.052  1.00  1.00
ATOM    861  O   ALA   339      28.590   5.525  15.750  1.00  1.00
ATOM    862  CB  ALA   339      25.694   6.721  15.332  1.00  1.00
ATOM    863  N   ALA   345      27.045   3.877  15.890  1.00  1.00
ATOM    864  CA  ALA   345      27.885   2.884  15.223  1.00  1.00
ATOM    865  C   ALA   345      27.768   3.076  13.715  1.00  1.00
ATOM    866  O   ALA   345      26.902   3.803  13.265  1.00  1.00
ATOM    867  CB  ALA   345      27.219   1.579  15.618  1.00  1.00
ATOM    868  N   VAL   346      28.634   2.410  12.920  1.00  1.00
ATOM    869  CA  VAL   346      28.248   2.312  11.500  1.00  1.00
ATOM    870  C   VAL   346      26.869   1.602  11.398  1.00  1.00
ATOM    871  O   VAL   346      26.539   0.756  12.220  1.00  1.00
ATOM    872  CB  VAL   346      29.361   1.449  10.884  1.00  1.00
ATOM    873  N   VAL   347      26.095   1.953  10.378  1.00  1.00
ATOM    874  CA  VAL   347      24.725   1.551  10.258  1.00  1.00
ATOM    875  C   VAL   347      24.515   1.039   8.810  1.00  1.00
ATOM    876  O   VAL   347      25.096   1.558   7.845  1.00  1.00
ATOM    877  CB  VAL   347      23.940   2.811  10.672  1.00  1.00
ATOM    878  N   PHE   348      23.755  -0.028   8.695  1.00  1.00
ATOM    879  CA  PHE   348      23.254  -0.537   7.397  1.00  1.00
ATOM    880  C   PHE   348      21.883   0.059   7.117  1.00  1.00
ATOM    881  O   PHE   348      20.896  -0.282   7.766  1.00  1.00
ATOM    882  CB  PHE   348      23.173  -2.065   7.409  1.00  1.00
ATOM    883  N   TYR   349      21.818   0.941   6.126  1.00  1.00
ATOM    884  CA  TYR   349      20.610   1.714   5.863  1.00  1.00
ATOM    885  C   TYR   349      19.985   1.253   4.529  1.00  1.00
ATOM    886  O   TYR   349      20.692   1.094   3.513  1.00  1.00
ATOM    887  CB  TYR   349      20.895   3.235   5.894  1.00  1.00
ATOM    888  N   ASP   350      18.671   1.009   4.538  1.00  1.00
ATOM    889  CA  ASP   350      17.953   0.699   3.282  1.00  1.00
ATOM    890  C   ASP   350      18.221   1.793   2.265  1.00  1.00
ATOM    891  O   ASP   350      18.288   2.968   2.618  1.00  1.00
ATOM    892  CB  ASP   350      16.454   0.596   3.512  1.00  1.00
ATOM    893  N   GLY   351      18.438   1.412   1.017  1.00  1.00
ATOM    894  CA  GLY   351      18.727   2.412  -0.037  1.00  1.00
ATOM    895  C   GLY   351      17.594   3.459  -0.079  1.00  1.00
ATOM    896  O   GLY   351      17.844   4.657  -0.276  1.00  1.00
ATOM    897  N   GLU   352      16.348   3.026   0.145  1.00  1.00
ATOM    898  CA  GLU   352      15.234   3.980   0.073  1.00  1.00
ATOM    899  C   GLU   352      15.262   5.048   1.175  1.00  1.00
ATOM    900  O   GLU   352      14.862   6.152   0.934  1.00  1.00
ATOM    901  CB  GLU   352      13.869   3.301   0.081  1.00  1.00
ATOM    902  N   GLU   353      15.669   4.677   2.387  1.00  1.00
ATOM    903  CA  GLU   353      15.926   5.645   3.484  1.00  1.00
ATOM    904  C   GLU   353      17.074   6.569   3.183  1.00  1.00
ATOM    905  O   GLU   353      16.979   7.794   3.397  1.00  1.00
ATOM    906  CB  GLU   353      16.163   4.924   4.798  1.00  1.00
ATOM    907  N   CYS   354      18.168   6.014   2.660  1.00  1.00
ATOM    908  CA  CYS   354      19.329   6.853   2.338  1.00  1.00
ATOM    909  C   CYS   354      19.000   7.780   1.187  1.00  1.00
ATOM    910  O   CYS   354      19.429   8.927   1.205  1.00  1.00
ATOM    911  CB  CYS   354      20.569   6.026   1.996  1.00  1.00
ATOM    912  N   LEU   355      18.262   7.299   0.181  1.00  1.00
ATOM    913  CA  LEU   355      17.823   8.180  -0.900  1.00  1.00
ATOM    914  C   LEU   355      17.011   9.390  -0.381  1.00  1.00
ATOM    915  O   LEU   355      17.318  10.536  -0.704  1.00  1.00
ATOM    916  CB  LEU   355      17.014   7.423  -1.984  1.00  1.00
ATOM    917  N   GLY   356      16.973  10.649   2.545  1.00  1.00
ATOM    918  CA  GLY   356      17.853  11.481   3.372  1.00  1.00
ATOM    919  C   GLY   356      18.742  12.417   2.562  1.00  1.00
ATOM    920  O   GLY   356      19.049  13.529   3.034  1.00  1.00
ATOM    921  N   GLY   357      19.226  11.924   1.418  1.00  1.00
ATOM    922  CA  GLY   357      20.018  12.715   0.479  1.00  1.00
ATOM    923  C   GLY   357      19.183  13.696  -0.352  1.00  1.00
ATOM    924  O   GLY   357      19.679  14.762  -0.742  1.00  1.00
ATOM    925  N   GLY   358      17.930  13.320  -0.623  1.00  1.00
ATOM    926  CA  GLY   358      16.996  14.147  -1.406  1.00  1.00
ATOM    927  C   GLY   358      16.358  15.200  -0.513  1.00  1.00
ATOM    928  O   GLY   358      15.135  15.305  -0.390  1.00  1.00
ATOM    929  N   LEU   359      17.215  15.951   0.157  1.00  1.00
ATOM    930  CA  LEU   359      16.792  16.970   1.093  1.00  1.00
ATOM    931  C   LEU   359      17.588  18.206   0.789  1.00  1.00
ATOM    932  O   LEU   359      18.743  18.135   0.378  1.00  1.00
ATOM    933  CB  LEU   359      17.029  16.598   2.582  1.00  1.00
ATOM    934  N   ILE   360      16.965  19.354   1.000  1.00  1.00
ATOM    935  CA  ILE   360      17.609  20.613   0.670  1.00  1.00
ATOM    936  C   ILE   360      18.378  21.111   1.874  1.00  1.00
ATOM    937  O   ILE   360      17.836  21.296   2.965  1.00  1.00
ATOM    938  CB  ILE   360      16.613  21.713   0.131  1.00  1.00
ATOM    939  N   ASP   361      19.677  21.265   1.681  1.00  1.00
ATOM    940  CA  ASP   361      20.552  21.779   2.694  1.00  1.00
ATOM    941  C   ASP   361      20.333  23.305   2.660  1.00  1.00
ATOM    942  O   ASP   361      20.539  23.945   1.629  1.00  1.00
ATOM    943  CB  ASP   361      21.994  21.397   2.316  1.00  1.00
ATOM    944  N   ASN   362      19.900  23.868   3.782  1.00  1.00
ATOM    945  CA  ASN   362      19.545  25.292   3.859  1.00  1.00
ATOM    946  C   ASN   362      20.774  26.203   3.659  1.00  1.00
ATOM    947  O   ASN   362      20.661  27.313   3.113  1.00  1.00
ATOM    948  CB  ASN   362      18.845  25.604   5.186  1.00  1.00
ATOM    949  N   ALA   363      21.946  25.706   4.037  1.00  1.00
ATOM    950  CA  ALA   363      23.198  26.418   3.773  1.00  1.00
ATOM    951  C   ALA   363      23.485  26.539   2.263  1.00  1.00
ATOM    952  O   ALA   363      23.798  27.621   1.809  1.00  1.00
ATOM    953  CB  ALA   363      24.371  25.845   4.575  1.00  1.00
ATOM    954  N   TYR   364      23.379  25.455   1.485  1.00  1.00
ATOM    955  CA  TYR   364      23.612  25.576   0.029  1.00  1.00
ATOM    956  C   TYR   364      22.367  25.969  -0.800  1.00  1.00
ATOM    957  O   TYR   364      22.505  26.351  -1.949  1.00  1.00
ATOM    958  CB  TYR   364      24.162  24.275  -0.533  1.00  1.00
ATOM    959  N   ARG   365      21.170  25.838  -0.231  1.00  1.00
ATOM    960  CA  ARG   365      19.899  25.898  -1.002  1.00  1.00
ATOM    961  C   ARG   365      19.909  24.876  -2.155  1.00  1.00
ATOM    962  O   ARG   365      19.217  25.020  -3.187  1.00  1.00
ATOM    963  CB  ARG   365      19.627  27.323  -1.485  1.00  1.00
ATOM    964  N   ASP   366      20.694  23.821  -1.957  1.00  1.00
ATOM    965  CA  ASP   366      20.766  22.738  -2.934  1.00  1.00
ATOM    966  C   ASP   366      20.535  21.433  -2.220  1.00  1.00
ATOM    967  O   ASP   366      20.630  21.320  -0.994  1.00  1.00
ATOM    968  CB  ASP   366      22.089  22.715  -3.724  1.00  1.00
ATOM    969  N   GLY   367      20.159  20.452  -3.006  1.00  1.00
ATOM    970  CA  GLY   367      19.945  19.117  -2.509  1.00  1.00
ATOM    971  C   GLY   367      21.298  18.518  -1.972  1.00  1.00
ATOM    972  O   GLY   367      22.380  18.899  -2.412  1.00  1.00
ATOM    973  N   GLN   368      21.211  17.634  -0.972  1.00  1.00
ATOM    974  CA  GLN   368      22.362  16.806  -0.574  1.00  1.00
ATOM    975  C   GLN   368      22.586  15.695  -1.653  1.00  1.00
ATOM    976  O   GLN   368      22.018  15.758  -2.735  1.00  1.00
ATOM    977  CB  GLN   368      22.132  16.252   0.847  1.00  1.00
ATOM    978  N   VAL   369      23.461  14.738  -1.392  1.00  1.00
ATOM    979  CA  VAL   369      23.811  13.741  -2.385  1.00  1.00
ATOM    980  C   VAL   369      25.071  12.987  -2.015  1.00  1.00
ATOM    981  O   VAL   369      25.337  12.733  -0.807  1.00  1.00
ATOM    982  CB  VAL   369      24.064  14.465  -3.721  1.00  1.00
ATOM    983  N   CYS   370      25.826  12.593  -3.039  1.00  1.00
ATOM    984  CA  CYS   370      26.998  11.766  -2.859  1.00  1.00
ATOM    985  C   CYS   370      28.135  12.184  -3.803  1.00  1.00
ATOM    986  O   CYS   370      27.921  12.781  -4.846  1.00  1.00
ATOM    987  CB  CYS   370      26.654  10.277  -3.042  1.00  1.00
ATOM    988  N   GLN   371      29.349  11.864  -3.403  1.00  1.00
ATOM    989  CA  GLN   371      30.517  12.228  -4.173  1.00  1.00
ATOM    990  C   GLN   371      31.298  10.939  -4.420  1.00  1.00
ATOM    991  O   GLN   371      31.447  10.135  -3.502  1.00  1.00
ATOM    992  CB  GLN   371      31.393  13.198  -3.400  1.00  1.00
ATOM    993  N   TYR   372      31.758  10.757  -5.657  1.00  1.00
ATOM    994  CA  TYR   372      32.711   9.711  -6.006  1.00  1.00
ATOM    995  C   TYR   372      34.122  10.296  -6.034  1.00  1.00
ATOM    996  O   TYR   372      34.345  11.434  -6.517  1.00  1.00
ATOM    997  CB  TYR   372      32.426   9.137  -7.407  1.00  1.00
ATOM    998  N   ILE   373      35.080   9.506  -5.578  1.00  1.00
ATOM    999  CA  ILE   373      36.436   9.964  -5.397  1.00  1.00
ATOM   1000  C   ILE   373      37.329   8.857  -5.932  1.00  1.00
ATOM   1001  O   ILE   373      37.182   7.685  -5.561  1.00  1.00
ATOM   1002  CB  ILE   373      36.799  10.316  -3.887  1.00  1.00
TER
END
