
#######################################################
#                                                     #
#                        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   44 (  219),  selected   44 , name T0363TS239_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS239_4-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    N      11      I      15          3.870
LGA    Q      12      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    I      13      F      30           #
LGA    N      14      Q      31           #
LGA    I      15      -       -           -
LGA    E      16      V      32          1.570
LGA    I      17      D      33          4.823
LGA    A      18      E      34          2.348
LGA    Y      19      G      35          4.157
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      I      36          4.324
LGA    Y      26      T      37          5.042
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    L      27      T      40          4.843
LGA    K      28      -       -           -
LGA    S      29      -       -           -
LGA    F      30      -       -           -
LGA    Q      31      A      41          4.459
LGA    V      32      I      42           #
LGA    -       -      T      43           -
LGA    D      33      Q      44          3.762
LGA    E      34      S      45          1.660
LGA    G      35      -       -           -
LGA    I      36      -       -           -
LGA    T      37      G      46          2.074
LGA    V      38      I      47          0.583
LGA    Q      39      L      48          0.458
LGA    T      40      S      49          1.089
LGA    A      41      Q      50          1.683
LGA    I      42      F      51          1.755
LGA    T      43      P      52          1.041
LGA    Q      44      -       -           -
LGA    I      47      -       -           -
LGA    L      48      E      53          3.731
LGA    S      49      -       -           -
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      -       -           -
LGA    E      53      -       -           -
LGA    I      54      -       -           -
LGA    D      55      I      54           #
LGA    L      56      D      55          2.835
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   46    5.0     20    3.18     0.00     29.988     0.609

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.279370 * X  +  -0.573907 * Y  +   0.769795 * Z  +  25.643341
  Y_new =  -0.583236 * X  +  -0.738295 * Y  +  -0.338757 * Z  +  72.488876
  Z_new =   0.762750 * X  +  -0.354334 * Y  +  -0.540980 * Z  +  42.462654 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.561722    0.579871  [ DEG:  -146.7758     33.2242 ]
  Theta =  -0.867555   -2.274037  [ DEG:   -49.7073   -130.2927 ]
  Phi   =  -1.124090    2.017503  [ DEG:   -64.4056    115.5944 ]
 
# 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: T0363TS239_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS239_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   46   5.0   20   3.18    0.00  29.988
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS239_4-D1
PFRMAT TS
TARGET T0363
MODEL 4
PARENT 1qhs_A
ATOM     51  N   ASN    11      19.304   8.430   7.187  1.00  9.99
ATOM     52  CA  ASN    11      19.075   8.387   8.621  1.00  9.99
ATOM     53  C   ASN    11      18.114   7.288   9.064  1.00  9.99
ATOM     54  O   ASN    11      17.839   7.141  10.257  1.00  9.99
ATOM     55  CB  ASN    11      18.559   9.744   9.093  1.00  9.99
ATOM     56  N   GLN    12      17.606   6.515   8.113  1.00  9.99
ATOM     57  CA  GLN    12      16.670   5.448   8.440  1.00  9.99
ATOM     58  C   GLN    12      17.115   4.128   7.812  1.00  9.99
ATOM     59  O   GLN    12      16.416   3.115   7.897  1.00  9.99
ATOM     60  CB  GLN    12      15.276   5.779   7.907  1.00  9.99
ATOM     61  N   ILE    13      18.278   4.164   7.189  1.00  9.99
ATOM     62  CA  ILE    13      18.839   2.979   6.511  1.00  9.99
ATOM     63  C   ILE    13      19.940   2.370   7.387  1.00  9.99
ATOM     64  O   ILE    13      20.804   3.080   7.915  1.00  9.99
ATOM     65  CB  ILE    13      19.409   3.380   5.158  1.00  9.99
ATOM     66  N   ASN    14      19.887   1.058   7.505  1.00  9.99
ATOM     67  CA  ASN    14      20.787   0.301   8.395  1.00  9.99
ATOM     68  C   ASN    14      22.282   0.670   8.261  1.00  9.99
ATOM     69  O   ASN    14      22.963   0.940   9.255  1.00  9.99
ATOM     70  CB  ASN    14      20.694  -1.199   8.164  1.00  9.99
ATOM     71  N   ILE    15      22.813   0.665   7.048  1.00  9.99
ATOM     72  CA  ILE    15      24.257   0.964   6.830  1.00  9.99
ATOM     73  C   ILE    15      24.498   2.475   6.729  1.00  9.99
ATOM     74  O   ILE    15      25.522   2.929   6.199  1.00  9.99
ATOM     75  CB  ILE    15      24.747   0.245   5.562  1.00  9.99
ATOM     76  N   GLU    16      23.537   3.216   7.232  1.00  9.99
ATOM     77  CA  GLU    16      23.592   4.678   7.228  1.00  9.99
ATOM     78  C   GLU    16      23.908   5.160   8.625  1.00  9.99
ATOM     79  O   GLU    16      24.782   4.609   9.287  1.00  9.99
ATOM     80  CB  GLU    16      22.262   5.257   6.718  1.00  9.99
ATOM     81  N   ILE    17      23.204   6.180   9.088  1.00  9.99
ATOM     82  CA  ILE    17      23.448   6.685  10.426  1.00  9.99
ATOM     83  C   ILE    17      22.174   6.521  11.242  1.00  9.99
ATOM     84  O   ILE    17      21.081   6.829  10.769  1.00  9.99
ATOM     85  CB  ILE    17      23.876   8.169  10.387  1.00  9.99
ATOM     86  N   ALA    18      22.312   6.026  12.465  1.00  9.99
ATOM     87  CA  ALA    18      21.156   5.813  13.320  1.00  9.99
ATOM     88  C   ALA    18      21.279   6.527  14.662  1.00  9.99
ATOM     89  O   ALA    18      22.331   6.502  15.300  1.00  9.99
ATOM     90  CB  ALA    18      20.967   4.322  13.560  1.00  9.99
ATOM     91  N   TYR    19      20.193   7.152  15.098  1.00  9.99
ATOM     92  CA  TYR    19      20.211   7.859  16.366  1.00  9.99
ATOM     93  C   TYR    19      19.376   7.157  17.424  1.00  9.99
ATOM     94  O   TYR    19      18.154   7.251  17.417  1.00  9.99
ATOM     95  CB  TYR    19      19.701   9.289  16.185  1.00  9.99
ATOM     96  N   ALA    20      20.043   6.455  18.337  1.00  9.99
ATOM     97  CA  ALA    20      19.358   5.756  19.416  1.00  9.99
ATOM     98  C   ALA    20      18.583   6.801  20.211  1.00  9.99
ATOM     99  O   ALA    20      18.929   7.984  20.190  1.00  9.99
ATOM    100  CB  ALA    20      20.377   5.065  20.320  1.00  9.99
ATOM    101  N   PHE    21      17.538   6.377  20.908  1.00  9.99
ATOM    102  CA  PHE    21      16.736   7.312  21.685  1.00  9.99
ATOM    103  C   PHE    21      17.475   7.828  22.913  1.00  9.99
ATOM    104  O   PHE    21      17.127   8.869  23.458  1.00  9.99
ATOM    105  CB  PHE    21      15.434   6.661  22.103  1.00  9.99
ATOM    106  N   PRO    22      18.494   7.097  23.346  1.00  9.99
ATOM    107  CA  PRO    22      19.264   7.512  24.511  1.00  9.99
ATOM    108  C   PRO    22      20.440   8.423  24.133  1.00  9.99
ATOM    109  O   PRO    22      21.259   8.790  24.982  1.00  9.99
ATOM    110  CB  PRO    22      19.764   6.282  25.270  1.00  9.99
ATOM    111  N   GLU    23      20.525   8.784  22.856  1.00  9.99
ATOM    112  CA  GLU    23      21.584   9.668  22.414  1.00  9.99
ATOM    113  C   GLU    23      22.784   8.995  21.778  1.00  9.99
ATOM    114  O   GLU    23      23.778   9.656  21.471  1.00  9.99
ATOM    115  CB  GLU    23      22.029  10.510  23.622  1.00  9.99
ATOM    116  N   ARG    24      22.711   7.685  21.588  1.00  9.99
ATOM    117  CA  ARG    24      23.822   6.994  20.965  1.00  9.99
ATOM    118  C   ARG    24      23.809   7.234  19.462  1.00  9.99
ATOM    119  O   ARG    24      22.770   7.579  18.890  1.00  9.99
ATOM    120  CB  ARG    24      23.745   5.494  21.299  1.00  9.99
ATOM    121  N   TYR    25      24.957   7.060  18.813  1.00  9.99
ATOM    122  CA  TYR    25      25.033   7.260  17.374  1.00  9.99
ATOM    123  C   TYR    25      25.773   6.104  16.726  1.00  9.99
ATOM    124  O   TYR    25      26.900   5.794  17.111  1.00  9.99
ATOM    125  CB  TYR    25      25.758   8.573  17.043  1.00  9.99
ATOM    126  N   TYR    26      25.138   5.466  15.746  1.00  9.99
ATOM    127  CA  TYR    26      25.734   4.326  15.047  1.00  9.99
ATOM    128  C   TYR    26      25.975   4.679  13.588  1.00  9.99
ATOM    129  O   TYR    26      25.131   5.307  12.951  1.00  9.99
ATOM    130  CB  TYR    26      24.801   3.121  15.120  1.00  9.99
ATOM    131  N   LEU    27      27.120   4.271  13.057  1.00  9.99
ATOM    132  CA  LEU    27      27.449   4.563  11.670  1.00  9.99
ATOM    133  C   LEU    27      27.687   3.283  10.883  1.00  9.99
ATOM    134  O   LEU    27      28.475   2.437  11.293  1.00  9.99
ATOM    135  CB  LEU    27      28.712   5.432  11.569  1.00  9.99
ATOM    136  N   LYS    28      27.004   3.149   9.751  1.00  9.99
ATOM    137  CA  LYS    28      27.154   1.967   8.923  1.00  9.99
ATOM    138  C   LYS    28      28.071   2.228   7.744  1.00  9.99
ATOM    139  O   LYS    28      28.483   3.365   7.511  1.00  9.99
ATOM    140  CB  LYS    28      25.765   1.502   8.453  1.00  9.99
ATOM    141  N   SER    29      28.400   1.192   6.966  1.00  9.99
ATOM    142  CA  SER    29      29.280   1.318   5.802  1.00  9.99
ATOM    143  C   SER    29      28.780   2.198   4.675  1.00  9.99
ATOM    144  O   SER    29      29.582   2.832   3.991  1.00  9.99
ATOM    145  CB  SER    29      29.485  -0.128   5.363  1.00  9.99
ATOM    146  N   PHE    30      27.468   2.236   4.456  1.00  9.99
ATOM    147  CA  PHE    30      26.940   3.073   3.382  1.00  9.99
ATOM    148  C   PHE    30      27.259   4.519   3.712  1.00  9.99
ATOM    149  O   PHE    30      27.719   5.282   2.853  1.00  9.99
ATOM    150  CB  PHE    30      25.434   2.875   3.223  1.00  9.99
ATOM    151  N   GLN    31      27.036   4.879   4.972  1.00  9.99
ATOM    152  CA  GLN    31      27.321   6.222   5.440  1.00  9.99
ATOM    153  C   GLN    31      28.825   6.477   5.351  1.00  9.99
ATOM    154  O   GLN    31      29.263   7.477   4.782  1.00  9.99
ATOM    155  CB  GLN    31      26.851   6.386   6.889  1.00  9.99
ATOM    156  N   VAL    32      29.612   5.562   5.914  1.00  9.99
ATOM    157  CA  VAL    32      31.063   5.701   5.918  1.00  9.99
ATOM    158  C   VAL    32      31.632   5.872   4.506  1.00  9.99
ATOM    159  O   VAL    32      32.510   6.708   4.275  1.00  9.99
ATOM    160  CB  VAL    32      31.706   4.494   6.605  1.00  9.99
ATOM    161  N   ASP    33      31.125   5.094   3.560  1.00  9.99
ATOM    162  CA  ASP    33      31.597   5.171   2.182  1.00  9.99
ATOM    163  C   ASP    33      31.438   6.572   1.625  1.00  9.99
ATOM    164  O   ASP    33      32.359   7.121   1.014  1.00  9.99
ATOM    165  CB  ASP    33      30.831   4.199   1.319  1.00  9.99
ATOM    166  N   GLU    34      30.255   7.142   1.828  1.00  9.99
ATOM    167  CA  GLU    34      29.957   8.473   1.336  1.00  9.99
ATOM    168  C   GLU    34      30.879   9.477   1.991  1.00  9.99
ATOM    169  O   GLU    34      31.508  10.299   1.321  1.00  9.99
ATOM    170  CB  GLU    34      28.511   8.836   1.644  1.00  9.99
ATOM    171  N   GLY    35      30.952   9.398   3.315  1.00  9.99
ATOM    172  CA  GLY    35      31.799  10.289   4.087  1.00  9.99
ATOM    173  C   GLY    35      33.208  10.313   3.494  1.00  9.99
ATOM    174  O   GLY    35      33.822  11.375   3.357  1.00  9.99
ATOM    175  N   ILE    36      33.705   9.131   3.132  1.00  9.99
ATOM    176  CA  ILE    36      35.031   9.026   2.548  1.00  9.99
ATOM    177  C   ILE    36      35.233   9.907   1.328  1.00  9.99
ATOM    178  O   ILE    36      36.176  10.705   1.279  1.00  9.99
ATOM    179  CB  ILE    36      35.293   7.550   2.200  1.00  9.99
ATOM    180  N   THR    37      34.358   9.768   0.338  1.00  9.99
ATOM    181  CA  THR    37      34.473  10.579  -0.867  1.00  9.99
ATOM    182  C   THR    37      34.366  12.051  -0.489  1.00  9.99
ATOM    183  O   THR    37      35.022  12.906  -1.084  1.00  9.99
ATOM    184  CB  THR    37      33.385  10.208  -1.860  1.00  9.99
ATOM    185  N   VAL    38      33.531  12.343   0.503  1.00  9.99
ATOM    186  CA  VAL    38      33.356  13.713   0.965  1.00  9.99
ATOM    187  C   VAL    38      34.689  14.225   1.512  1.00  9.99
ATOM    188  O   VAL    38      35.148  15.307   1.147  1.00  9.99
ATOM    189  CB  VAL    38      32.293  13.759   2.065  1.00  9.99
ATOM    190  N   GLN    39      35.304  13.436   2.387  1.00  9.99
ATOM    191  CA  GLN    39      36.583  13.808   2.979  1.00  9.99
ATOM    192  C   GLN    39      37.592  14.140   1.884  1.00  9.99
ATOM    193  O   GLN    39      38.271  15.167   1.936  1.00  9.99
ATOM    194  CB  GLN    39      37.103  12.670   3.849  1.00  9.99
ATOM    195  N   THR    40      37.684  13.268   0.887  1.00  9.99
ATOM    196  CA  THR    40      38.607  13.494  -0.210  1.00  9.99
ATOM    197  C   THR    40      38.320  14.820  -0.900  1.00  9.99
ATOM    198  O   THR    40      39.243  15.561  -1.247  1.00  9.99
ATOM    199  CB  THR    40      38.522  12.345  -1.210  1.00  9.99
ATOM    200  N   ALA    41      37.037  15.124  -1.084  1.00  9.99
ATOM    201  CA  ALA    41      36.661  16.368  -1.734  1.00  9.99
ATOM    202  C   ALA    41      37.094  17.590  -0.945  1.00  9.99
ATOM    203  O   ALA    41      37.556  18.585  -1.512  1.00  9.99
ATOM    204  CB  ALA    41      35.139  16.371  -1.957  1.00  9.99
ATOM    205  N   ILE    42      36.938  17.522   0.370  1.00  9.99
ATOM    206  CA  ILE    42      37.322  18.628   1.232  1.00  9.99
ATOM    207  C   ILE    42      38.833  18.856   1.127  1.00  9.99
ATOM    208  O   ILE    42      39.297  19.996   1.037  1.00  9.99
ATOM    209  CB  ILE    42      36.916  18.340   2.704  1.00  9.99
ATOM    210  N   THR    43      39.597  17.765   1.127  1.00  9.99
ATOM    211  CA  THR    43      41.047  17.857   1.022  1.00  9.99
ATOM    212  C   THR    43      41.392  18.491  -0.317  1.00  9.99
ATOM    213  O   THR    43      42.327  19.290  -0.425  1.00  9.99
ATOM    214  CB  THR    43      41.698  16.458   1.109  1.00  9.99
ATOM    215  N   GLN    44      40.615  18.129  -1.332  1.00  9.99
ATOM    216  CA  GLN    44      40.801  18.647  -2.677  1.00  9.99
ATOM    217  C   GLN    44      40.564  20.154  -2.695  1.00  9.99
ATOM    218  O   GLN    44      41.184  20.874  -3.474  1.00  9.99
ATOM    219  CB  GLN    44      39.846  17.960  -3.629  1.00  9.99
ATOM    220  N   ILE    47      39.658  20.628  -1.849  1.00  9.99
ATOM    221  CA  ILE    47      39.383  22.057  -1.792  1.00  9.99
ATOM    222  C   ILE    47      40.594  22.770  -1.211  1.00  9.99
ATOM    223  O   ILE    47      40.974  23.847  -1.674  1.00  9.99
ATOM    224  CB  ILE    47      38.147  22.338  -0.938  1.00  9.99
ATOM    225  N   LEU    48      41.199  22.162  -0.193  1.00  9.99
ATOM    226  CA  LEU    48      42.378  22.737   0.438  1.00  9.99
ATOM    227  C   LEU    48      43.456  22.827  -0.631  1.00  9.99
ATOM    228  O   LEU    48      44.048  23.887  -0.855  1.00  9.99
ATOM    229  CB  LEU    48      42.845  21.855   1.589  1.00  9.99
ATOM    230  N   SER    49      43.691  21.701  -1.295  1.00  9.99
ATOM    231  CA  SER    49      44.678  21.628  -2.361  1.00  9.99
ATOM    232  C   SER    49      44.426  22.707  -3.414  1.00  9.99
ATOM    233  O   SER    49      45.356  23.319  -3.928  1.00  9.99
ATOM    234  CB  SER    49      44.622  20.256  -3.018  1.00  9.99
ATOM    235  N   GLN    50      43.156  22.940  -3.733  1.00  9.99
ATOM    236  CA  GLN    50      42.788  23.943  -4.724  1.00  9.99
ATOM    237  C   GLN    50      43.039  25.352  -4.202  1.00  9.99
ATOM    238  O   GLN    50      42.888  26.333  -4.932  1.00  9.99
ATOM    239  CB  GLN    50      41.320  23.780  -5.113  1.00  9.99
ATOM    240  N   PHE    51      43.404  25.457  -2.929  1.00  9.99
ATOM    241  CA  PHE    51      43.682  26.766  -2.371  1.00  9.99
ATOM    242  C   PHE    51      42.642  27.381  -1.454  1.00  9.99
ATOM    243  O   PHE    51      42.718  28.565  -1.142  1.00  9.99
ATOM    244  CB  PHE    51      43.955  27.714  -3.551  1.00  9.99
ATOM    245  N   PRO    52      41.659  26.606  -1.022  1.00  9.99
ATOM    246  CA  PRO    52      40.665  27.157  -0.115  1.00  9.99
ATOM    247  C   PRO    52      41.092  26.775   1.291  1.00  9.99
ATOM    248  O   PRO    52      41.519  25.644   1.523  1.00  9.99
ATOM    249  CB  PRO    52      39.288  26.579  -0.414  1.00  9.99
ATOM    250  N   GLU    53      41.012  27.720   2.222  1.00  9.99
ATOM    251  CA  GLU    53      41.364  27.420   3.608  1.00  9.99
ATOM    252  C   GLU    53      40.144  26.731   4.218  1.00  9.99
ATOM    253  O   GLU    53      39.059  27.308   4.276  1.00  9.99
ATOM    254  CB  GLU    53      41.698  28.705   4.355  1.00  9.99
ATOM    255  N   ILE    54      40.324  25.497   4.673  1.00  9.99
ATOM    256  CA  ILE    54      39.208  24.735   5.217  1.00  9.99
ATOM    257  C   ILE    54      39.244  24.426   6.712  1.00  9.99
ATOM    258  O   ILE    54      40.282  24.046   7.257  1.00  9.99
ATOM    259  CB  ILE    54      39.076  23.377   4.476  1.00  9.99
ATOM    260  N   ASP    55      38.093  24.585   7.363  1.00  9.99
ATOM    261  CA  ASP    55      37.942  24.259   8.781  1.00  9.99
ATOM    262  C   ASP    55      36.979  23.078   8.816  1.00  9.99
ATOM    263  O   ASP    55      35.922  23.119   8.183  1.00  9.99
ATOM    264  CB  ASP    55      37.283  25.391   9.603  1.00  9.99
ATOM    265  N   LEU    56      37.339  22.033   9.547  1.00  9.99
ATOM    266  CA  LEU    56      36.484  20.862   9.661  1.00  9.99
ATOM    267  C   LEU    56      36.020  20.674  11.102  1.00  9.99
ATOM    268  O   LEU    56      36.833  20.527  12.015  1.00  9.99
ATOM    269  CB  LEU    56      37.222  19.587   9.201  1.00  9.99
TER
END
