
#######################################################
#                                                     #
#                        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   43 (  209),  selected   43 , name T0316TS102_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS102_3-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V     225      -       -           -
LGA    G     227      G     220          3.404
LGA    R     228      R     221          2.904
LGA    D     229      M     222          2.798
LGA    M     230      M     223          2.220
LGA    G     231      T     224          2.663
LGA    E     232      V     225          2.188
LGA    H     233      D     226          5.128
LGA    A     234      G     227           -
LGA    G     235      R     228          2.056
LGA    L     236      D     229          3.585
LGA    M     237      M     230          2.398
LGA    Y     238      G     231          2.584
LGA    Y     239      E     232          2.017
LGA    I     249      H     233          1.838
LGA    Q     252      A     234          2.753
LGA    N     257      G     235           #
LGA    A     258      L     236           #
LGA    P     259      M     237           -
LGA    W     260      Y     238           -
LGA    F     261      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    V     262      G     245          4.767
LGA    V     263      G     246          1.660
LGA    -       -      L     247           -
LGA    G     264      G     248           #
LGA    K     265      I     249          4.149
LGA    D     266      G     250          5.184
LGA    L     267      G     251          2.684
LGA    S     268      D     256          3.921
LGA    -       -      N     257           -
LGA    K     269      A     258          3.857
LGA    N     270      P     259          1.675
LGA    I     271      W     260          2.055
LGA    L     272      F     261          0.785
LGA    Y     273      V     262          3.072
LGA    V     274      V     263          3.193
LGA    G     275      G     264          3.632
LGA    Q     276      K     265          4.484
LGA    G     277      -       -           -
LGA    F     278      -       -           -
LGA    Y     279      D     266          3.047
LGA    H     280      L     267          2.736
LGA    D     281      S     268          3.168
LGA    S     282      K     269           -
LGA    L     283      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   60    5.0     31    3.16    19.35     31.206     0.950

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.472115 * X  +  -0.793550 * Y  +   0.383910 * Z  +  82.492615
  Y_new =  -0.852744 * X  +   0.521507 * Y  +   0.029302 * Z  +   8.543056
  Z_new =  -0.223464 * X  +  -0.313543 * Y  +  -0.922906 * Z  +   9.835714 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.814092    0.327500  [ DEG:  -161.2356     18.7644 ]
  Theta =   0.225367    2.916225  [ DEG:    12.9126    167.0874 ]
  Phi   =  -2.076431    1.065161  [ DEG:  -118.9707     61.0292 ]
 
# 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_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS102_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   60   5.0   31   3.16   19.35  31.206
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS102_3-D2
PFRMAT TS
TARGET T0316
MODEL 3
PARENT 1ake_A
ATOM    591  N   VAL   225      45.547  18.608 -17.740  1.00  1.00
ATOM    592  CA  VAL   225      44.656  18.842 -16.608  1.00  1.00
ATOM    593  C   VAL   225      43.706  20.019 -16.838  1.00  1.00
ATOM    594  O   VAL   225      42.642  20.133 -16.200  1.00  1.00
ATOM    595  CB  VAL   225      45.421  19.087 -15.214  1.00  1.00
ATOM    596  N   GLY   227      44.075  20.941 -17.727  1.00  1.00
ATOM    597  CA  GLY   227      43.194  22.034 -18.069  1.00  1.00
ATOM    598  C   GLY   227      42.310  21.630 -19.244  1.00  1.00
ATOM    599  O   GLY   227      41.557  22.492 -19.692  1.00  1.00
ATOM    600  N   ARG   228      42.350  20.412 -19.798  1.00  1.00
ATOM    601  CA  ARG   228      41.505  20.100 -20.926  1.00  1.00
ATOM    602  C   ARG   228      40.060  19.850 -20.503  1.00  1.00
ATOM    603  O   ARG   228      39.779  19.207 -19.492  1.00  1.00
ATOM    604  CB  ARG   228      42.032  18.893 -21.656  1.00  1.00
ATOM    605  N   ASP   229      39.131  20.391 -21.311  1.00  1.00
ATOM    606  CA  ASP   229      37.671  20.289 -21.178  1.00  1.00
ATOM    607  C   ASP   229      37.158  20.041 -22.607  1.00  1.00
ATOM    608  O   ASP   229      37.634  20.594 -23.627  1.00  1.00
ATOM    609  CB  ASP   229      37.098  21.606 -20.638  1.00  1.00
ATOM    610  N   MET   230      36.182  19.151 -22.700  1.00  1.00
ATOM    611  CA  MET   230      35.670  18.741 -23.979  1.00  1.00
ATOM    612  C   MET   230      34.136  18.852 -24.024  1.00  1.00
ATOM    613  O   MET   230      33.423  18.881 -23.015  1.00  1.00
ATOM    614  CB  MET   230      36.113  17.274 -24.275  1.00  1.00
ATOM    615  N   GLY   231      33.675  19.050 -25.252  1.00  1.00
ATOM    616  CA  GLY   231      32.292  18.881 -25.601  1.00  1.00
ATOM    617  C   GLY   231      32.205  17.465 -26.214  1.00  1.00
ATOM    618  O   GLY   231      32.442  17.240 -27.412  1.00  1.00
ATOM    619  N   GLU   232      31.750  16.489 -25.452  1.00  1.00
ATOM    620  CA  GLU   232      31.802  15.098 -25.874  1.00  1.00
ATOM    621  C   GLU   232      31.026  14.729 -27.100  1.00  1.00
ATOM    622  O   GLU   232      31.567  14.044 -27.978  1.00  1.00
ATOM    623  CB  GLU   232      31.346  14.212 -24.747  1.00  1.00
ATOM    624  N   HIS   233      29.809  15.248 -27.320  1.00  1.00
ATOM    625  CA  HIS   233      29.048  14.929 -28.509  1.00  1.00
ATOM    626  C   HIS   233      29.821  15.313 -29.764  1.00  1.00
ATOM    627  O   HIS   233      29.747  14.608 -30.774  1.00  1.00
ATOM    628  CB  HIS   233      27.753  15.697 -28.352  1.00  1.00
ATOM    629  N   ALA   234      30.615  16.380 -29.752  1.00  1.00
ATOM    630  CA  ALA   234      31.214  16.753 -30.997  1.00  1.00
ATOM    631  C   ALA   234      32.672  16.433 -31.034  1.00  1.00
ATOM    632  O   ALA   234      33.306  16.502 -32.109  1.00  1.00
ATOM    633  CB  ALA   234      31.026  18.218 -31.222  1.00  1.00
ATOM    634  N   GLY   235      33.214  16.188 -29.841  1.00  1.00
ATOM    635  CA  GLY   235      34.653  15.989 -29.768  1.00  1.00
ATOM    636  C   GLY   235      35.361  17.352 -29.808  1.00  1.00
ATOM    637  O   GLY   235      36.589  17.371 -29.916  1.00  1.00
ATOM    638  N   LEU   236      34.700  18.533 -29.724  1.00  1.00
ATOM    639  CA  LEU   236      35.479  19.775 -29.698  1.00  1.00
ATOM    640  C   LEU   236      36.196  19.843 -28.342  1.00  1.00
ATOM    641  O   LEU   236      35.635  19.446 -27.304  1.00  1.00
ATOM    642  CB  LEU   236      34.610  21.018 -29.840  1.00  1.00
ATOM    643  N   MET   237      37.426  20.351 -28.361  1.00  1.00
ATOM    644  CA  MET   237      38.282  20.444 -27.180  1.00  1.00
ATOM    645  C   MET   237      38.782  21.875 -26.902  1.00  1.00
ATOM    646  O   MET   237      39.143  22.680 -27.770  1.00  1.00
ATOM    647  CB  MET   237      39.457  19.355 -27.399  1.00  1.00
ATOM    648  N   TYR   238      38.810  22.179 -25.611  1.00  1.00
ATOM    649  CA  TYR   238      39.189  23.472 -25.068  1.00  1.00
ATOM    650  C   TYR   238      40.239  23.300 -23.952  1.00  1.00
ATOM    651  O   TYR   238      40.449  22.212 -23.423  1.00  1.00
ATOM    652  CB  TYR   238      37.912  24.124 -24.497  1.00  1.00
ATOM    653  N   TYR   239      40.866  24.389 -23.512  1.00  1.00
ATOM    654  CA  TYR   239      41.778  24.378 -22.390  1.00  1.00
ATOM    655  C   TYR   239      41.416  25.588 -21.553  1.00  1.00
ATOM    656  O   TYR   239      41.447  26.719 -22.064  1.00  1.00
ATOM    657  CB  TYR   239      43.237  24.521 -22.843  1.00  1.00
ATOM    658  N   ILE   249      41.226  25.413 -20.252  1.00  1.00
ATOM    659  CA  ILE   249      40.847  26.535 -19.409  1.00  1.00
ATOM    660  C   ILE   249      41.739  27.764 -19.449  1.00  1.00
ATOM    661  O   ILE   249      41.258  28.876 -19.192  1.00  1.00
ATOM    662  CB  ILE   249      40.724  26.098 -17.943  1.00  1.00
ATOM    663  N   GLN   252      43.046  27.539 -19.726  1.00  1.00
ATOM    664  CA  GLN   252      44.036  28.627 -19.867  1.00  1.00
ATOM    665  C   GLN   252      44.427  28.903 -21.306  1.00  1.00
ATOM    666  O   GLN   252      44.385  30.031 -21.791  1.00  1.00
ATOM    667  CB  GLN   252      45.372  28.327 -19.141  1.00  1.00
ATOM    668  N   ASN   257      44.737  27.836 -22.060  1.00  1.00
ATOM    669  CA  ASN   257      45.436  28.057 -23.316  1.00  1.00
ATOM    670  C   ASN   257      44.523  28.282 -24.488  1.00  1.00
ATOM    671  O   ASN   257      44.960  28.765 -25.540  1.00  1.00
ATOM    672  CB  ASN   257      46.369  26.859 -23.628  1.00  1.00
ATOM    673  N   ALA   258      43.266  27.911 -24.348  1.00  1.00
ATOM    674  CA  ALA   258      42.379  28.016 -25.464  1.00  1.00
ATOM    675  C   ALA   258      40.979  27.883 -24.910  1.00  1.00
ATOM    676  O   ALA   258      40.263  26.899 -25.159  1.00  1.00
ATOM    677  CB  ALA   258      42.677  26.904 -26.437  1.00  1.00
ATOM    678  N   PRO   259      40.547  28.851 -24.097  1.00  1.00
ATOM    679  CA  PRO   259      39.308  28.736 -23.347  1.00  1.00
ATOM    680  C   PRO   259      38.056  28.880 -24.227  1.00  1.00
ATOM    681  O   PRO   259      38.157  29.457 -25.337  1.00  1.00
ATOM    682  CB  PRO   259      39.480  29.793 -22.273  1.00  1.00
ATOM    683  N   TRP   260      36.874  28.368 -23.836  1.00  1.00
ATOM    684  CA  TRP   260      35.615  28.685 -24.547  1.00  1.00
ATOM    685  C   TRP   260      35.257  30.196 -24.410  1.00  1.00
ATOM    686  O   TRP   260      35.768  30.860 -23.493  1.00  1.00
ATOM    687  CB  TRP   260      34.641  27.722 -23.908  1.00  1.00
ATOM    688  N   PHE   261      34.384  30.798 -25.258  1.00  1.00
ATOM    689  CA  PHE   261      34.010  32.224 -25.237  1.00  1.00
ATOM    690  C   PHE   261      33.175  32.488 -24.012  1.00  1.00
ATOM    691  O   PHE   261      33.166  33.581 -23.458  1.00  1.00
ATOM    692  CB  PHE   261      33.239  32.579 -26.529  1.00  1.00
ATOM    693  N   VAL   262      32.474  31.484 -23.517  1.00  1.00
ATOM    694  CA  VAL   262      31.724  31.576 -22.284  1.00  1.00
ATOM    695  C   VAL   262      32.230  30.371 -21.461  1.00  1.00
ATOM    696  O   VAL   262      32.129  29.185 -21.834  1.00  1.00
ATOM    697  CB  VAL   262      30.189  31.489 -22.612  1.00  1.00
ATOM    698  N   VAL   263      32.817  30.672 -20.322  1.00  1.00
ATOM    699  CA  VAL   263      33.383  29.667 -19.458  1.00  1.00
ATOM    700  C   VAL   263      32.458  28.486 -19.163  1.00  1.00
ATOM    701  O   VAL   263      31.291  28.619 -18.779  1.00  1.00
ATOM    702  CB  VAL   263      33.820  30.398 -18.195  1.00  1.00
ATOM    703  N   GLY   264      32.983  27.296 -19.451  1.00  1.00
ATOM    704  CA  GLY   264      32.294  26.046 -19.189  1.00  1.00
ATOM    705  C   GLY   264      31.317  25.626 -20.264  1.00  1.00
ATOM    706  O   GLY   264      30.651  24.598 -20.097  1.00  1.00
ATOM    707  N   LYS   265      31.193  26.324 -21.383  1.00  1.00
ATOM    708  CA  LYS   265      30.137  25.977 -22.322  1.00  1.00
ATOM    709  C   LYS   265      30.770  25.844 -23.672  1.00  1.00
ATOM    710  O   LYS   265      31.716  26.548 -24.035  1.00  1.00
ATOM    711  CB  LYS   265      29.051  27.055 -22.450  1.00  1.00
ATOM    712  N   ASP   266      30.241  24.940 -24.476  1.00  1.00
ATOM    713  CA  ASP   266      30.746  24.804 -25.798  1.00  1.00
ATOM    714  C   ASP   266      30.259  26.020 -26.611  1.00  1.00
ATOM    715  O   ASP   266      29.093  26.387 -26.518  1.00  1.00
ATOM    716  CB  ASP   266      30.220  23.470 -26.274  1.00  1.00
ATOM    717  N   LEU   267      31.113  26.601 -27.448  1.00  1.00
ATOM    718  CA  LEU   267      30.882  27.746 -28.318  1.00  1.00
ATOM    719  C   LEU   267      29.713  27.643 -29.273  1.00  1.00
ATOM    720  O   LEU   267      28.924  28.572 -29.429  1.00  1.00
ATOM    721  CB  LEU   267      32.127  28.000 -29.145  1.00  1.00
ATOM    722  N   SER   268      29.578  26.464 -29.868  1.00  1.00
ATOM    723  CA  SER   268      28.547  26.166 -30.838  1.00  1.00
ATOM    724  C   SER   268      27.205  25.831 -30.209  1.00  1.00
ATOM    725  O   SER   268      26.178  26.420 -30.513  1.00  1.00
ATOM    726  CB  SER   268      29.092  25.010 -31.711  1.00  1.00
ATOM    727  N   LYS   269      27.145  24.913 -29.294  1.00  1.00
ATOM    728  CA  LYS   269      25.877  24.492 -28.803  1.00  1.00
ATOM    729  C   LYS   269      25.541  25.098 -27.479  1.00  1.00
ATOM    730  O   LYS   269      24.427  24.867 -26.982  1.00  1.00
ATOM    731  CB  LYS   269      25.839  22.950 -28.673  1.00  1.00
ATOM    732  N   ASN   270      26.467  25.755 -26.780  1.00  1.00
ATOM    733  CA  ASN   270      26.133  26.255 -25.446  1.00  1.00
ATOM    734  C   ASN   270      25.979  25.184 -24.375  1.00  1.00
ATOM    735  O   ASN   270      25.559  25.421 -23.236  1.00  1.00
ATOM    736  CB  ASN   270      24.784  26.989 -25.556  1.00  1.00
ATOM    737  N   ILE   271      26.361  23.956 -24.728  1.00  1.00
ATOM    738  CA  ILE   271      26.336  22.852 -23.795  1.00  1.00
ATOM    739  C   ILE   271      27.563  22.849 -22.891  1.00  1.00
ATOM    740  O   ILE   271      28.664  23.250 -23.270  1.00  1.00
ATOM    741  CB  ILE   271      26.270  21.580 -24.580  1.00  1.00
ATOM    742  N   LEU   272      27.324  22.339 -21.698  1.00  1.00
ATOM    743  CA  LEU   272      28.298  22.278 -20.637  1.00  1.00
ATOM    744  C   LEU   272      29.483  21.372 -21.042  1.00  1.00
ATOM    745  O   LEU   272      29.320  20.300 -21.665  1.00  1.00
ATOM    746  CB  LEU   272      27.526  21.787 -19.417  1.00  1.00
ATOM    747  N   TYR   273      30.695  21.875 -20.812  1.00  1.00
ATOM    748  CA  TYR   273      31.895  21.110 -21.124  1.00  1.00
ATOM    749  C   TYR   273      32.194  20.144 -19.966  1.00  1.00
ATOM    750  O   TYR   273      31.780  20.380 -18.822  1.00  1.00
ATOM    751  CB  TYR   273      33.036  22.072 -21.347  1.00  1.00
ATOM    752  N   VAL   274      32.878  19.017 -20.193  1.00  1.00
ATOM    753  CA  VAL   274      33.166  18.051 -19.152  1.00  1.00
ATOM    754  C   VAL   274      34.675  17.763 -19.212  1.00  1.00
ATOM    755  O   VAL   274      35.391  18.258 -20.122  1.00  1.00
ATOM    756  CB  VAL   274      32.314  16.728 -19.385  1.00  1.00
ATOM    757  N   GLY   275      35.164  16.985 -18.243  1.00  1.00
ATOM    758  CA  GLY   275      36.545  16.526 -18.292  1.00  1.00
ATOM    759  C   GLY   275      36.544  15.060 -18.695  1.00  1.00
ATOM    760  O   GLY   275      35.581  14.328 -18.486  1.00  1.00
ATOM    761  N   GLN   276      37.544  14.581 -19.386  1.00  1.00
ATOM    762  CA  GLN   276      37.636  13.182 -19.683  1.00  1.00
ATOM    763  C   GLN   276      38.099  12.456 -18.423  1.00  1.00
ATOM    764  O   GLN   276      38.891  12.936 -17.580  1.00  1.00
ATOM    765  CB  GLN   276      38.606  13.002 -20.831  1.00  1.00
ATOM    766  N   GLY   277      37.566  11.239 -18.346  1.00  1.00
ATOM    767  CA  GLY   277      37.794  10.335 -17.209  1.00  1.00
ATOM    768  C   GLY   277      39.269   9.928 -17.108  1.00  1.00
ATOM    769  O   GLY   277      39.794   9.754 -16.020  1.00  1.00
ATOM    770  N   PHE   278      39.944   9.758 -18.260  1.00  1.00
ATOM    771  CA  PHE   278      41.332   9.356 -18.345  1.00  1.00
ATOM    772  C   PHE   278      42.290  10.558 -18.340  1.00  1.00
ATOM    773  O   PHE   278      43.479  10.469 -18.627  1.00  1.00
ATOM    774  CB  PHE   278      41.407   8.489 -19.609  1.00  1.00
ATOM    775  N   TYR   279      41.830  11.779 -18.051  1.00  1.00
ATOM    776  CA  TYR   279      42.720  12.916 -17.971  1.00  1.00
ATOM    777  C   TYR   279      43.058  13.252 -16.530  1.00  1.00
ATOM    778  O   TYR   279      42.689  14.305 -15.992  1.00  1.00
ATOM    779  CB  TYR   279      42.115  14.145 -18.636  1.00  1.00
ATOM    780  N   HIS   280      43.634  12.274 -15.826  1.00  1.00
ATOM    781  CA  HIS   280      44.268  12.578 -14.545  1.00  1.00
ATOM    782  C   HIS   280      45.735  12.247 -14.750  1.00  1.00
ATOM    783  O   HIS   280      46.086  11.402 -15.604  1.00  1.00
ATOM    784  CB  HIS   280      43.813  11.736 -13.386  1.00  1.00
ATOM    785  N   ASP   281      46.541  12.917 -13.925  1.00  1.00
ATOM    786  CA  ASP   281      47.986  12.831 -13.916  1.00  1.00
ATOM    787  C   ASP   281      48.537  11.409 -14.050  1.00  1.00
ATOM    788  O   ASP   281      49.366  11.160 -14.942  1.00  1.00
ATOM    789  CB  ASP   281      48.348  13.500 -12.657  1.00  1.00
ATOM    790  N   SER   282      48.045  10.403 -13.299  1.00  1.00
ATOM    791  CA  SER   282      48.647   9.093 -13.442  1.00  1.00
ATOM    792  C   SER   282      48.276   8.341 -14.696  1.00  1.00
ATOM    793  O   SER   282      49.132   7.629 -15.220  1.00  1.00
ATOM    794  CB  SER   282      48.329   8.266 -12.231  1.00  1.00
ATOM    795  N   LEU   283      47.055   8.485 -15.232  1.00  1.00
ATOM    796  CA  LEU   283      46.677   7.853 -16.477  1.00  1.00
ATOM    797  C   LEU   283      47.421   8.530 -17.599  1.00  1.00
ATOM    798  O   LEU   283      47.837   7.787 -18.470  1.00  1.00
ATOM    799  CB  LEU   283      45.211   7.984 -16.774  1.00  1.00
TER
END
