
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0356TS383_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_4-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      92      -       -           -
LGA    A      93      -       -           -
LGA    F      94      -       -           -
LGA    L      95      -       -           -
LGA    K      96      -       -           -
LGA    D     314      -       -           -
LGA    A     315      -       -           -
LGA    I     316      -       -           -
LGA    Y     317      -       -           -
LGA    H     318      -       -           -
LGA    S     319      N       7           #
LGA    T     320      D       8          3.250
LGA    Y     321      L       9          3.976
LGA    T     322      R      10          3.321
LGA    -       -      D      11           -
LGA    G     323      F      12          2.589
LGA    R     324      L      13          2.707
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    P     325      L      16          1.759
LGA    P     326      E      17          5.083
LGA    D     327      Q      18           #
LGA    E     328      Q      19           #
LGA    P     329      G      20          4.359
LGA    A     330      E      21           #
LGA    V     331      -       -           -
LGA    L     332      L      22          3.108
LGA    G     333      K      23          3.823
LGA    V     334      R      24          2.384
LGA    A     335      I      25          2.311
LGA    L     336      T      26          5.252
LGA    N     337      L      27          5.404
LGA    E     338      P      28          4.630
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    V     339      F      52          2.815
LGA    F     340      E      53          2.742
LGA    V     341      N      54          2.691
LGA    P     342      P      55          2.188
LGA    I     343      K      56          4.588
LGA    -       -      G      57           -
LGA    L     344      Y      58          3.004
LGA    Q     345      S      59          3.769
LGA    K     346      M      60          1.897
LGA    Q     347      P      61          3.371
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  124    5.0     24    3.53     8.33     11.064     0.661

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.443529 * X  +   0.592398 * Y  +   0.672567 * Z  +   0.528635
  Y_new =  -0.870779 * X  +   0.462488 * Y  +   0.166881 * Z  +  64.889435
  Z_new =  -0.212195 * X  +  -0.659673 * Y  +   0.720975 * Z  +  45.383911 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.741026    2.400566  [ DEG:   -42.4577    137.5423 ]
  Theta =   0.213820    2.927773  [ DEG:    12.2510    167.7490 ]
  Phi   =  -1.099698    2.041894  [ DEG:   -63.0081    116.9919 ]
 
# 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: T0356TS383_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_4-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  124   5.0   24   3.53    8.33  11.064
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_4-D1
PFRMAT TS
TARGET t0356
MODEL 4
PARENT 1ndoA
ATOM      1  N   LEU    92      83.681  49.188  60.582  1.00  0.00
ATOM      2  CA  LEU    92      83.408  49.918  61.818  1.00  0.00
ATOM      3  C   LEU    92      83.859  49.283  63.115  1.00  0.00
ATOM      4  O   LEU    92      83.518  49.810  64.194  1.00  0.00
ATOM      5  N   ALA    93      84.656  48.223  63.070  1.00  0.00
ATOM      6  CA  ALA    93      85.228  47.691  64.313  1.00  0.00
ATOM      7  C   ALA    93      86.560  48.454  64.440  1.00  0.00
ATOM      8  O   ALA    93      86.861  49.216  65.363  1.00  0.00
ATOM      9  N   PHE    94      87.256  48.359  63.294  1.00  0.00
ATOM     10  CA  PHE    94      88.491  49.044  63.031  1.00  0.00
ATOM     11  C   PHE    94      88.285  50.533  62.803  1.00  0.00
ATOM     12  O   PHE    94      89.210  51.272  63.196  1.00  0.00
ATOM     13  N   LEU    95      87.225  50.933  62.109  1.00  0.00
ATOM     14  CA  LEU    95      87.115  52.372  61.871  1.00  0.00
ATOM     15  C   LEU    95      86.862  53.110  63.208  1.00  0.00
ATOM     16  O   LEU    95      85.944  52.980  64.010  1.00  0.00
ATOM     17  N   LYS    96      87.895  53.904  63.410  1.00  0.00
ATOM     18  CA  LYS    96      88.105  54.765  64.567  1.00  0.00
ATOM     19  C   LYS    96      87.652  56.179  64.181  1.00  0.00
ATOM     20  O   LYS    96      88.312  56.937  63.472  1.00  0.00
ATOM    753  N   ASP   314      78.554  57.129  81.772  1.00  0.00
ATOM    754  CA  ASP   314      78.963  55.904  81.133  1.00  0.00
ATOM    755  C   ASP   314      78.275  55.611  79.829  1.00  0.00
ATOM    756  O   ASP   314      78.957  55.330  78.867  1.00  0.00
ATOM    757  N   ALA   315      74.981  59.989  78.323  1.00  0.00
ATOM    758  CA  ALA   315      74.173  61.145  78.687  1.00  0.00
ATOM    759  C   ALA   315      75.073  62.106  79.468  1.00  0.00
ATOM    760  O   ALA   315      75.946  61.655  80.212  1.00  0.00
ATOM    761  N   ILE   316      74.783  63.404  79.298  1.00  0.00
ATOM    762  CA  ILE   316      75.511  64.371  80.105  1.00  0.00
ATOM    763  C   ILE   316      74.841  65.731  80.079  1.00  0.00
ATOM    764  O   ILE   316      73.789  65.871  79.430  1.00  0.00
ATOM    765  N   TYR   317      75.465  66.700  80.753  1.00  0.00
ATOM    766  CA  TYR   317      74.766  68.013  80.816  1.00  0.00
ATOM    767  C   TYR   317      75.640  69.087  81.421  1.00  0.00
ATOM    768  O   TYR   317      76.557  68.779  82.163  1.00  0.00
ATOM    769  N   HIS   318      75.348  70.350  81.137  1.00  0.00
ATOM    770  CA  HIS   318      75.871  71.499  81.835  1.00  0.00
ATOM    771  C   HIS   318      74.834  71.932  82.905  1.00  0.00
ATOM    772  O   HIS   318      73.611  71.749  82.859  1.00  0.00
ATOM    773  N   SER   319      75.349  72.519  83.973  1.00  0.00
ATOM    774  CA  SER   319      74.605  73.064  85.107  1.00  0.00
ATOM    775  C   SER   319      74.940  74.547  85.218  1.00  0.00
ATOM    776  O   SER   319      76.107  74.879  85.417  1.00  0.00
ATOM    777  N   THR   320      73.965  75.450  85.248  1.00  0.00
ATOM    778  CA  THR   320      74.213  76.871  85.425  1.00  0.00
ATOM    779  C   THR   320      73.494  77.245  86.744  1.00  0.00
ATOM    780  O   THR   320      72.259  77.348  86.849  1.00  0.00
ATOM    781  N   TYR   321      74.314  77.484  87.761  1.00  0.00
ATOM    782  CA  TYR   321      73.776  77.627  89.124  1.00  0.00
ATOM    783  C   TYR   321      72.730  78.725  89.254  1.00  0.00
ATOM    784  O   TYR   321      72.900  79.891  88.843  1.00  0.00
ATOM    785  N   THR   322      71.570  78.396  89.828  1.00  0.00
ATOM    786  CA  THR   322      70.470  79.301  90.114  1.00  0.00
ATOM    787  C   THR   322      69.695  79.841  88.925  1.00  0.00
ATOM    788  O   THR   322      68.759  80.615  89.257  1.00  0.00
ATOM    789  N   GLY   323      69.973  79.492  87.658  1.00  0.00
ATOM    790  CA  GLY   323      69.308  80.122  86.541  1.00  0.00
ATOM    791  C   GLY   323      67.923  79.619  86.226  1.00  0.00
ATOM    792  O   GLY   323      67.669  79.128  85.139  1.00  0.00
ATOM    793  N   ARG   324      66.988  79.752  87.183  1.00  0.00
ATOM    794  CA  ARG   324      65.662  79.134  87.099  1.00  0.00
ATOM    795  C   ARG   324      64.739  79.689  86.043  1.00  0.00
ATOM    796  O   ARG   324      63.911  78.946  85.501  1.00  0.00
ATOM    797  N   PRO   325      64.845  80.971  85.691  1.00  0.00
ATOM    798  CA  PRO   325      64.075  81.514  84.577  1.00  0.00
ATOM    799  C   PRO   325      64.694  81.238  83.204  1.00  0.00
ATOM    800  O   PRO   325      64.015  81.518  82.229  1.00  0.00
ATOM    801  N   PRO   326      60.439  87.301  86.945  1.00  0.00
ATOM    802  CA  PRO   326      60.081  87.474  88.352  1.00  0.00
ATOM    803  C   PRO   326      59.142  86.377  88.858  1.00  0.00
ATOM    804  O   PRO   326      59.375  85.793  89.935  1.00  0.00
ATOM    805  N   ASP   327      58.092  86.007  88.134  1.00  0.00
ATOM    806  CA  ASP   327      57.238  84.927  88.606  1.00  0.00
ATOM    807  C   ASP   327      58.000  83.593  88.733  1.00  0.00
ATOM    808  O   ASP   327      57.873  82.919  89.745  1.00  0.00
ATOM    809  N   GLU   328      58.813  83.247  87.744  1.00  0.00
ATOM    810  CA  GLU   328      59.536  81.984  87.760  1.00  0.00
ATOM    811  C   GLU   328      60.508  82.039  88.922  1.00  0.00
ATOM    812  O   GLU   328      60.525  81.141  89.789  1.00  0.00
ATOM    813  N   PRO   329      61.207  83.172  89.108  1.00  0.00
ATOM    814  CA  PRO   329      62.234  83.180  90.149  1.00  0.00
ATOM    815  C   PRO   329      61.550  83.022  91.501  1.00  0.00
ATOM    816  O   PRO   329      62.057  82.310  92.380  1.00  0.00
ATOM    817  N   ALA   330      60.354  83.589  91.692  1.00  0.00
ATOM    818  CA  ALA   330      59.664  83.473  92.966  1.00  0.00
ATOM    819  C   ALA   330      59.217  82.016  93.163  1.00  0.00
ATOM    820  O   ALA   330      59.362  81.416  94.224  1.00  0.00
ATOM    821  N   VAL   331      58.678  81.412  92.110  1.00  0.00
ATOM    822  CA  VAL   331      58.201  80.034  92.219  1.00  0.00
ATOM    823  C   VAL   331      59.319  79.044  92.529  1.00  0.00
ATOM    824  O   VAL   331      59.214  78.231  93.485  1.00  0.00
ATOM    825  N   LEU   332      60.466  79.131  91.848  1.00  0.00
ATOM    826  CA  LEU   332      61.521  78.175  92.068  1.00  0.00
ATOM    827  C   LEU   332      62.189  78.395  93.434  1.00  0.00
ATOM    828  O   LEU   332      62.627  77.424  94.070  1.00  0.00
ATOM    829  N   GLY   333      62.334  79.668  93.849  1.00  0.00
ATOM    830  CA  GLY   333      63.001  79.945  95.120  1.00  0.00
ATOM    831  C   GLY   333      62.182  79.340  96.275  1.00  0.00
ATOM    832  O   GLY   333      62.689  78.693  97.196  1.00  0.00
ATOM    833  N   VAL   334      60.867  79.459  96.211  1.00  0.00
ATOM    834  CA  VAL   334      59.960  78.976  97.240  1.00  0.00
ATOM    835  C   VAL   334      60.016  77.438  97.314  1.00  0.00
ATOM    836  O   VAL   334      60.233  76.841  98.388  1.00  0.00
ATOM    837  N   ALA   335      60.046  76.813  96.126  1.00  0.00
ATOM    838  CA  ALA   335      60.121  75.360  96.112  1.00  0.00
ATOM    839  C   ALA   335      61.490  74.892  96.597  1.00  0.00
ATOM    840  O   ALA   335      61.574  73.906  97.366  1.00  0.00
ATOM    841  N   LEU   336      62.550  75.607  96.237  1.00  0.00
ATOM    842  CA  LEU   336      63.882  75.260  96.679  1.00  0.00
ATOM    843  C   LEU   336      63.881  75.236  98.223  1.00  0.00
ATOM    844  O   LEU   336      64.507  74.367  98.888  1.00  0.00
ATOM    845  N   ASN   337      63.322  76.281  98.823  1.00  0.00
ATOM    846  CA  ASN   337      63.316  76.441 100.276  1.00  0.00
ATOM    847  C   ASN   337      62.664  75.222 100.935  1.00  0.00
ATOM    848  O   ASN   337      63.222  74.602 101.869  1.00  0.00
ATOM    849  N   GLU   338      61.607  74.652 100.348  1.00  0.00
ATOM    850  CA  GLU   338      61.064  73.411 100.899  1.00  0.00
ATOM    851  C   GLU   338      61.910  72.201 100.582  1.00  0.00
ATOM    852  O   GLU   338      61.998  71.262 101.404  1.00  0.00
ATOM    853  N   VAL   339      62.660  72.181  99.483  1.00  0.00
ATOM    854  CA  VAL   339      63.428  71.005  99.137  1.00  0.00
ATOM    855  C   VAL   339      64.682  70.887 100.005  1.00  0.00
ATOM    856  O   VAL   339      65.180  69.766 100.209  1.00  0.00
ATOM    857  N   PHE   340      65.210  72.000 100.528  1.00  0.00
ATOM    858  CA  PHE   340      66.421  71.976 101.336  1.00  0.00
ATOM    859  C   PHE   340      66.328  70.896 102.421  1.00  0.00
ATOM    860  O   PHE   340      67.249  70.125 102.695  1.00  0.00
ATOM    861  N   VAL   341      65.199  70.844 103.107  1.00  0.00
ATOM    862  CA  VAL   341      64.930  69.887 104.136  1.00  0.00
ATOM    863  C   VAL   341      64.795  68.466 103.599  1.00  0.00
ATOM    864  O   VAL   341      65.119  67.498 104.312  1.00  0.00
ATOM    865  N   PRO   342      64.201  68.246 102.431  1.00  0.00
ATOM    866  CA  PRO   342      64.015  66.892 101.949  1.00  0.00
ATOM    867  C   PRO   342      65.318  66.315 101.421  1.00  0.00
ATOM    868  O   PRO   342      65.658  65.159 101.704  1.00  0.00
ATOM    869  N   ILE   343      66.099  67.067 100.605  1.00  0.00
ATOM    870  CA  ILE   343      67.214  66.459  99.887  1.00  0.00
ATOM    871  C   ILE   343      68.520  67.192 100.133  1.00  0.00
ATOM    872  O   ILE   343      69.533  66.785  99.535  1.00  0.00
ATOM    873  N   LEU   344      68.603  68.130 101.052  1.00  0.00
ATOM    874  CA  LEU   344      69.826  68.885 101.320  1.00  0.00
ATOM    875  C   LEU   344      69.936  70.086 100.362  1.00  0.00
ATOM    876  O   LEU   344      69.311  70.114  99.304  1.00  0.00
ATOM    877  N   GLN   345      70.768  71.037 100.679  1.00  0.00
ATOM    878  CA  GLN   345      71.100  72.271 100.014  1.00  0.00
ATOM    879  C   GLN   345      71.603  72.139  98.571  1.00  0.00
ATOM    880  O   GLN   345      71.250  72.970  97.757  1.00  0.00
ATOM    881  N   LYS   346      72.500  71.194  98.337  1.00  0.00
ATOM    882  CA  LYS   346      73.111  70.988  97.029  1.00  0.00
ATOM    883  C   LYS   346      72.072  70.514  96.020  1.00  0.00
ATOM    884  O   LYS   346      71.810  71.204  95.044  1.00  0.00
ATOM    885  N   GLN   347      71.347  69.439  96.354  1.00  0.00
ATOM    886  CA  GLN   347      70.332  68.913  95.427  1.00  0.00
ATOM    887  C   GLN   347      69.157  69.865  95.239  1.00  0.00
ATOM    888  O   GLN   347      68.669  70.012  94.116  1.00  0.00
TER
END
