
#######################################################
#                                                     #
#                        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   41 (  205),  selected   41 , name T0320TS102_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS102_3-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    N     229      A     244          3.258
LGA    S     230      L     245          3.063
LGA    L     231      -       -           -
LGA    P     232      -       -           -
LGA    N     233      -       -           -
LGA    P     234      H     246          3.888
LGA    H     235      F     247          0.937
LGA    L     236      E     248          0.768
LGA    R     237      W     249          0.816
LGA    K     238      E     250          0.871
LGA    D     239      I     251          1.152
LGA    S     240      I     252          1.144
LGA    N     241      H     253          0.634
LGA    N     242      A     254          1.873
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    P     243      K     257          3.397
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    A     244      S     264          1.175
LGA    L     245      S     265          1.804
LGA    -       -      A     266           -
LGA    H     246      I     267          3.191
LGA    F     247      N     268           -
LGA    E     248      T     269           -
LGA    W     249      S     270           -
LGA    E     250      P     271           -
LGA    I     251      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    I     252      G     290           #
LGA    H     253      -       -           -
LGA    A     254      W     291           #
LGA    F     255      Y     292          4.109
LGA    S     264      L     293          5.076
LGA    S     265      V     294          3.142
LGA    A     266      D     295          3.447
LGA    I     267      -       -           -
LGA    N     268      D     296          4.099
LGA    T     269      T     297          3.157
LGA    S     270      L     298          3.228
LGA    P     271      E     299           -
LGA    I     272      R     300           #
LGA    Y     287      A     301          0.604
LGA    Y     288      G     302           #
LGA    P     289      -       -           -
LGA    W     291      R     303          4.483
LGA    Y     292      I     304          4.019

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   73    5.0     25    2.89     4.00     23.475     0.836

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.406990 * X  +  -0.070642 * Y  +   0.910697 * Z  +   1.366822
  Y_new =   0.503464 * X  +   0.849238 * Y  +  -0.159123 * Z  +  -7.717045
  Z_new =  -0.762157 * X  +   0.523264 * Y  +   0.381197 * Z  + -20.127447 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.941199   -2.200393  [ DEG:    53.9267   -126.0733 ]
  Theta =   0.866639    2.274954  [ DEG:    49.6547    130.3452 ]
  Phi   =   0.890967   -2.250626  [ DEG:    51.0486   -128.9514 ]
 
# 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: T0320TS102_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS102_3-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   73   5.0   25   2.89    4.00  23.475
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS102_3-D2
PFRMAT TS
TARGET T0320
MODEL 3
PARENT 1vjg_A
ATOM    690  N   ASN   229       4.274  11.650   5.901  1.00  1.00
ATOM    691  CA  ASN   229       3.558  12.752   6.524  1.00  1.00
ATOM    692  C   ASN   229       2.117  12.913   6.035  1.00  1.00
ATOM    693  O   ASN   229       1.438  13.838   6.467  1.00  1.00
ATOM    694  CB  ASN   229       4.333  14.046   6.334  1.00  1.00
ATOM    695  N   SER   230       1.675  12.061   5.101  1.00  1.00
ATOM    696  CA  SER   230       0.240  11.944   4.781  1.00  1.00
ATOM    697  C   SER   230      -0.444  11.082   5.839  1.00  1.00
ATOM    698  O   SER   230       0.223  10.410   6.667  1.00  1.00
ATOM    699  CB  SER   230       0.005  11.310   3.392  1.00  1.00
ATOM    700  N   LEU   231      -1.775  11.073   5.797  1.00  1.00
ATOM    701  CA  LEU   231      -2.565  10.374   6.810  1.00  1.00
ATOM    702  C   LEU   231      -2.111   8.904   6.876  1.00  1.00
ATOM    703  O   LEU   231      -1.787   8.328   5.825  1.00  1.00
ATOM    704  CB  LEU   231      -4.076  10.521   6.525  1.00  1.00
ATOM    705  N   PRO   232      -2.057   8.302   8.081  1.00  1.00
ATOM    706  CA  PRO   232      -2.606   8.856   9.343  1.00  1.00
ATOM    707  C   PRO   232      -1.690   9.802  10.164  1.00  1.00
ATOM    708  O   PRO   232      -1.998  10.100  11.317  1.00  1.00
ATOM    709  CB  PRO   232      -2.877   7.590  10.165  1.00  1.00
ATOM    710  N   ASN   233      -0.579  10.255   9.595  1.00  1.00
ATOM    711  CA  ASN   233       0.262  11.285  10.226  1.00  1.00
ATOM    712  C   ASN   233      -0.578  12.473  10.689  1.00  1.00
ATOM    713  O   ASN   233      -1.523  12.864   9.981  1.00  1.00
ATOM    714  CB  ASN   233       1.300  11.791   9.216  1.00  1.00
ATOM    715  N   PRO   234      -0.218  13.069  11.833  1.00  1.00
ATOM    716  CA  PRO   234      -0.949  14.248  12.325  1.00  1.00
ATOM    717  C   PRO   234      -0.610  15.576  11.591  1.00  1.00
ATOM    718  O   PRO   234      -1.292  16.562  11.775  1.00  1.00
ATOM    719  CB  PRO   234      -0.781  14.449  13.864  1.00  1.00
ATOM    720  N   HIS   235       0.427  15.579  10.763  1.00  1.00
ATOM    721  CA  HIS   235       0.839  16.756   9.999  1.00  1.00
ATOM    722  C   HIS   235      -0.325  17.603   9.444  1.00  1.00
ATOM    723  O   HIS   235      -0.447  18.785   9.779  1.00  1.00
ATOM    724  CB  HIS   235       1.795  16.286   8.873  1.00  1.00
ATOM    725  N   LEU   236      -1.180  17.017   8.611  1.00  1.00
ATOM    726  CA  LEU   236      -2.228  17.804   7.921  1.00  1.00
ATOM    727  C   LEU   236      -3.338  18.226   8.878  1.00  1.00
ATOM    728  O   LEU   236      -3.920  19.296   8.720  1.00  1.00
ATOM    729  CB  LEU   236      -2.832  17.055   6.706  1.00  1.00
ATOM    730  N   ARG   237      -3.607  17.404   9.880  1.00  1.00
ATOM    731  CA  ARG   237      -4.615  17.758  10.871  1.00  1.00
ATOM    732  C   ARG   237      -4.169  19.046  11.587  1.00  1.00
ATOM    733  O   ARG   237      -4.946  20.000  11.737  1.00  1.00
ATOM    734  CB  ARG   237      -4.888  16.620  11.881  1.00  1.00
ATOM    735  N   LYS   238      -2.906  19.093  11.971  1.00  1.00
ATOM    736  CA  LYS   238      -2.391  20.262  12.677  1.00  1.00
ATOM    737  C   LYS   238      -2.373  21.483  11.812  1.00  1.00
ATOM    738  O   LYS   238      -2.772  22.560  12.266  1.00  1.00
ATOM    739  CB  LYS   238      -1.013  19.971  13.240  1.00  1.00
ATOM    740  N   ASP   239      -1.953  21.316  10.552  1.00  1.00
ATOM    741  CA  ASP   239      -1.906  22.421   9.629  1.00  1.00
ATOM    742  C   ASP   239      -3.283  23.045   9.469  1.00  1.00
ATOM    743  O   ASP   239      -3.416  24.255   9.422  1.00  1.00
ATOM    744  CB  ASP   239      -1.362  21.968   8.248  1.00  1.00
ATOM    745  N   SER   240      -4.313  22.218   9.380  1.00  1.00
ATOM    746  CA  SER   240      -5.634  22.711   9.077  1.00  1.00
ATOM    747  C   SER   240      -6.286  23.366  10.288  1.00  1.00
ATOM    748  O   SER   240      -7.215  24.165  10.139  1.00  1.00
ATOM    749  CB  SER   240      -6.507  21.578   8.492  1.00  1.00
ATOM    750  N   ASN   241      -5.825  23.008  11.482  1.00  1.00
ATOM    751  CA  ASN   241      -6.318  23.630  12.724  1.00  1.00
ATOM    752  C   ASN   241      -5.499  24.897  13.103  1.00  1.00
ATOM    753  O   ASN   241      -5.823  25.588  14.056  1.00  1.00
ATOM    754  CB  ASN   241      -6.303  22.620  13.858  1.00  1.00
ATOM    755  N   ASN   242      -4.461  25.190  12.322  1.00  1.00
ATOM    756  CA  ASN   242      -3.643  26.374  12.480  1.00  1.00
ATOM    757  C   ASN   242      -3.980  27.384  11.383  1.00  1.00
ATOM    758  O   ASN   242      -5.025  27.966  11.422  1.00  1.00
ATOM    759  CB  ASN   242      -2.186  25.928  12.447  1.00  1.00
ATOM    760  N   PRO   243      -3.135  27.556  10.371  1.00  1.00
ATOM    761  CA  PRO   243      -3.387  28.534   9.296  1.00  1.00
ATOM    762  C   PRO   243      -3.669  27.865   7.921  1.00  1.00
ATOM    763  O   PRO   243      -3.676  28.542   6.893  1.00  1.00
ATOM    764  CB  PRO   243      -2.179  29.484   9.186  1.00  1.00
ATOM    765  N   ALA   244      -3.876  26.540   7.920  1.00  1.00
ATOM    766  CA  ALA   244      -4.086  25.766   6.700  1.00  1.00
ATOM    767  C   ALA   244      -2.871  25.113   6.054  1.00  1.00
ATOM    768  O   ALA   244      -3.016  24.181   5.235  1.00  1.00
ATOM    769  CB  ALA   244      -4.671  26.737   5.657  1.00  1.00
ATOM    770  N   LEU   245      -1.686  25.590   6.434  1.00  1.00
ATOM    771  CA  LEU   245      -0.428  25.267   5.794  1.00  1.00
ATOM    772  C   LEU   245       0.578  24.630   6.758  1.00  1.00
ATOM    773  O   LEU   245       1.163  23.596   6.450  1.00  1.00
ATOM    774  CB  LEU   245       0.268  26.558   5.181  1.00  1.00
ATOM    775  N   HIS   246       0.817  25.276   7.891  1.00  1.00
ATOM    776  CA  HIS   246       1.905  24.881   8.782  1.00  1.00
ATOM    777  C   HIS   246       1.375  24.130   9.985  1.00  1.00
ATOM    778  O   HIS   246       0.434  24.556  10.639  1.00  1.00
ATOM    779  CB  HIS   246       2.648  26.118   9.270  1.00  1.00
ATOM    780  N   PHE   247       2.000  23.014  10.293  1.00  1.00
ATOM    781  CA  PHE   247       1.614  22.235  11.449  1.00  1.00
ATOM    782  C   PHE   247       2.243  22.849  12.682  1.00  1.00
ATOM    783  O   PHE   247       2.857  23.933  12.635  1.00  1.00
ATOM    784  CB  PHE   247       2.241  20.877  11.136  1.00  1.00
ATOM    785  N   GLU   248       2.104  22.156  13.784  1.00  1.00
ATOM    786  CA  GLU   248       2.556  22.663  15.091  1.00  1.00
ATOM    787  C   GLU   248       3.475  21.608  15.649  1.00  1.00
ATOM    788  O   GLU   248       4.145  20.946  14.857  1.00  1.00
ATOM    789  CB  GLU   248       1.374  22.993  15.999  1.00  1.00
ATOM    790  N   TRP   249       3.547  21.437  16.967  1.00  1.00
ATOM    791  CA  TRP   249       4.669  20.716  17.570  1.00  1.00
ATOM    792  C   TRP   249       4.611  19.269  17.155  1.00  1.00
ATOM    793  O   TRP   249       5.646  18.669  16.827  1.00  1.00
ATOM    794  CB  TRP   249       4.666  20.829  19.114  1.00  1.00
ATOM    795  N   GLU   250       3.410  18.730  17.127  1.00  1.00
ATOM    796  CA  GLU   250       3.200  17.337  16.775  1.00  1.00
ATOM    797  C   GLU   250       3.695  16.986  15.384  1.00  1.00
ATOM    798  O   GLU   250       4.389  15.988  15.173  1.00  1.00
ATOM    799  CB  GLU   250       1.685  17.066  16.817  1.00  1.00
ATOM    800  N   ILE   251       3.362  17.819  14.418  1.00  1.00
ATOM    801  CA  ILE   251       3.779  17.593  13.045  1.00  1.00
ATOM    802  C   ILE   251       5.282  17.754  12.903  1.00  1.00
ATOM    803  O   ILE   251       5.942  16.928  12.270  1.00  1.00
ATOM    804  CB  ILE   251       3.093  18.643  12.151  1.00  1.00
ATOM    805  N   ILE   252       5.861  18.797  13.476  1.00  1.00
ATOM    806  CA  ILE   252       7.297  18.949  13.318  1.00  1.00
ATOM    807  C   ILE   252       8.050  17.844  14.049  1.00  1.00
ATOM    808  O   ILE   252       9.133  17.440  13.621  1.00  1.00
ATOM    809  CB  ILE   252       7.746  20.327  13.760  1.00  1.00
ATOM    810  N   HIS   253       7.454  17.297  15.101  1.00  1.00
ATOM    811  CA  HIS   253       8.060  16.172  15.788  1.00  1.00
ATOM    812  C   HIS   253       8.091  14.906  14.926  1.00  1.00
ATOM    813  O   HIS   253       9.118  14.213  14.914  1.00  1.00
ATOM    814  CB  HIS   253       7.376  15.956  17.132  1.00  1.00
ATOM    815  N   ALA   254       7.016  14.652  14.172  1.00  1.00
ATOM    816  CA  ALA   254       6.954  13.514  13.260  1.00  1.00
ATOM    817  C   ALA   254       7.966  13.652  12.133  1.00  1.00
ATOM    818  O   ALA   254       8.679  12.703  11.794  1.00  1.00
ATOM    819  CB  ALA   254       5.539  13.328  12.676  1.00  1.00
ATOM    820  N   PHE   255       8.081  14.847  11.589  1.00  1.00
ATOM    821  CA  PHE   255       9.075  15.127  10.554  1.00  1.00
ATOM    822  C   PHE   255      10.495  14.850  11.072  1.00  1.00
ATOM    823  O   PHE   255      11.268  14.141  10.423  1.00  1.00
ATOM    824  CB  PHE   255       8.937  16.584  10.145  1.00  1.00
ATOM    825  N   SER   264      10.847  15.414  12.233  1.00  1.00
ATOM    826  CA  SER   264      12.145  15.111  12.874  1.00  1.00
ATOM    827  C   SER   264      12.439  13.636  13.058  1.00  1.00
ATOM    828  O   SER   264      13.583  13.203  12.803  1.00  1.00
ATOM    829  CB  SER   264      12.258  15.819  14.220  1.00  1.00
ATOM    830  N   SER   265      11.450  12.866  13.539  1.00  1.00
ATOM    831  CA  SER   265      11.650  11.423  13.754  1.00  1.00
ATOM    832  C   SER   265      11.999  10.677  12.441  1.00  1.00
ATOM    833  O   SER   265      12.830   9.764  12.434  1.00  1.00
ATOM    834  CB  SER   265      10.448  10.835  14.485  1.00  1.00
ATOM    835  N   ALA   266      11.420  11.106  11.317  1.00  1.00
ATOM    836  CA  ALA   266      11.772  10.545  10.022  1.00  1.00
ATOM    837  C   ALA   266      13.238  10.814   9.682  1.00  1.00
ATOM    838  O   ALA   266      13.979   9.902   9.279  1.00  1.00
ATOM    839  CB  ALA   266      10.871  11.105   8.880  1.00  1.00
ATOM    840  N   ILE   267      13.636  12.062   9.825  1.00  1.00
ATOM    841  CA  ILE   267      15.018  12.479   9.555  1.00  1.00
ATOM    842  C   ILE   267      16.014  11.693  10.423  1.00  1.00
ATOM    843  O   ILE   267      17.042  11.230   9.943  1.00  1.00
ATOM    844  CB  ILE   267      15.208  13.975   9.816  1.00  1.00
ATOM    845  N   ASN   268      15.701  11.550  11.697  1.00  1.00
ATOM    846  CA  ASN   268      16.524  10.776  12.649  1.00  1.00
ATOM    847  C   ASN   268      16.720   9.266  12.329  1.00  1.00
ATOM    848  O   ASN   268      17.721   8.679  12.724  1.00  1.00
ATOM    849  CB  ASN   268      15.960  10.951  14.084  1.00  1.00
ATOM    850  N   THR   269      15.761   8.656  11.638  1.00  1.00
ATOM    851  CA  THR   269      15.864   7.282  11.141  1.00  1.00
ATOM    852  C   THR   269      16.396   7.124   9.709  1.00  1.00
ATOM    853  O   THR   269      16.402   6.024   9.152  1.00  1.00
ATOM    854  CB  THR   269      14.478   6.645  11.229  1.00  1.00
ATOM    855  N   SER   270      16.845   8.220   9.112  1.00  1.00
ATOM    856  CA  SER   270      17.371   8.192   7.766  1.00  1.00
ATOM    857  C   SER   270      18.829   7.741   7.810  1.00  1.00
ATOM    858  O   SER   270      19.635   8.328   8.557  1.00  1.00
ATOM    859  CB  SER   270      17.268   9.601   7.209  1.00  1.00
ATOM    860  N   PRO   271      19.157   6.705   7.029  1.00  1.00
ATOM    861  CA  PRO   271      20.506   6.164   7.019  1.00  1.00
ATOM    862  C   PRO   271      21.560   7.228   6.744  1.00  1.00
ATOM    863  O   PRO   271      22.573   7.263   7.441  1.00  1.00
ATOM    864  CB  PRO   271      20.671   4.963   6.050  1.00  1.00
ATOM    865  N   ILE   272      21.308   8.141   5.807  1.00  1.00
ATOM    866  CA  ILE   272      22.315   9.152   5.488  1.00  1.00
ATOM    867  C   ILE   272      22.590  10.061   6.688  1.00  1.00
ATOM    868  O   ILE   272      23.704  10.550   6.887  1.00  1.00
ATOM    869  CB  ILE   272      21.879   9.968   4.340  1.00  1.00
ATOM    870  N   TYR   287      21.559  10.307   7.477  1.00  1.00
ATOM    871  CA  TYR   287      21.676  11.148   8.657  1.00  1.00
ATOM    872  C   TYR   287      22.417  10.378   9.708  1.00  1.00
ATOM    873  O   TYR   287      23.323  10.900  10.324  1.00  1.00
ATOM    874  CB  TYR   287      20.275  11.565   9.170  1.00  1.00
ATOM    875  N   TYR   288      22.058   9.123   9.901  1.00  1.00
ATOM    876  CA  TYR   288      22.685   8.287  10.921  1.00  1.00
ATOM    877  C   TYR   288      24.159   8.031  10.620  1.00  1.00
ATOM    878  O   TYR   288      25.016   8.184  11.486  1.00  1.00
ATOM    879  CB  TYR   288      21.987   6.950  10.977  1.00  1.00
ATOM    880  N   PRO   289      24.409   7.670   9.359  1.00  1.00
ATOM    881  CA  PRO   289      25.728   7.285   8.857  1.00  1.00
ATOM    882  C   PRO   289      26.626   8.483   8.680  1.00  1.00
ATOM    883  O   PRO   289      27.808   8.325   8.419  1.00  1.00
ATOM    884  CB  PRO   289      25.618   6.511   7.529  1.00  1.00
ATOM    885  N   TRP   291      26.085   9.685   8.837  1.00  1.00
ATOM    886  CA  TRP   291      26.938  10.847   8.887  1.00  1.00
ATOM    887  C   TRP   291      27.320  11.191  10.341  1.00  1.00
ATOM    888  O   TRP   291      28.481  11.401  10.607  1.00  1.00
ATOM    889  CB  TRP   291      26.326  12.038   8.142  1.00  1.00
ATOM    890  N   TYR   292      26.362  11.221  11.259  1.00  1.00
ATOM    891  CA  TYR   292      26.643  11.391  12.673  1.00  1.00
ATOM    892  C   TYR   292      27.218  10.098  13.264  1.00  1.00
ATOM    893  O   TYR   292      27.601  10.079  14.431  1.00  1.00
ATOM    894  CB  TYR   292      25.368  11.805  13.434  1.00  1.00
TER
END
