
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0358TS383_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS383_3-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    P      11      P      11           -
LGA    F      12      F      12           -
LGA    T      13      T      13           -
LGA    R      14      -       -           -
LGA    R      15      R      14          5.188
LGA    Q      16      R      15          0.676
LGA    A      17      Q      16          1.935
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    Q      18      A      19          3.330
LGA    A      19      V      20          1.806
LGA    V      20      T      21          4.024
LGA    -       -      T      22           -
LGA    T      21      T      23          1.057
LGA    T      22      Y      24          1.142
LGA    T      23      S      25          2.206
LGA    Y      24      N      26          2.980
LGA    S      25      I      27          1.928
LGA    N      26      T      28          2.033
LGA    I      27      L      29          1.796
LGA    T      28      E      30          1.936
LGA    L      29      D      31          1.655
LGA    -       -      D      32           -
LGA    E      30      Q      33           #
LGA    D      31      G      34           -
LGA    D      32      S      35           -
LGA    F      37      H      36           #
LGA    R      38      -       -           -
LGA    L      39      F      37          1.464
LGA    V      40      R      38          1.141
LGA    V      41      L      39          0.926
LGA    R      42      V      40          0.718
LGA    D      43      V      41          1.446
LGA    T      44      R      42          1.600
LGA    E      45      D      43          3.156
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    G      46      V      49          1.824
LGA    R      47      W      50          2.383
LGA    M      48      R      51          3.561
LGA    V      49      A      52           #
LGA    W      50      -       -           -
LGA    R      51      W      53          2.842
LGA    A      52      N      54          0.878
LGA    N      54      F      55          1.935
LGA    F      55      E      56          4.879
LGA    E      56      P      57           -
LGA    P      57      D      58           -
LGA    D      58      A      59           -
LGA    A      59      G      60           -
LGA    G      60      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   65    5.0     29    2.44     6.90     32.195     1.141

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.619258 * X  +   0.677904 * Y  +   0.396189 * Z  + -33.422802
  Y_new =   0.218616 * X  +   0.633485 * Y  +  -0.742229 * Z  + -26.812136
  Z_new =  -0.754140 * X  +  -0.373018 * Y  +  -0.540491 * Z  +  78.046310 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.537511    0.604082  [ DEG:  -145.3887     34.6113 ]
  Theta =   0.854344    2.287249  [ DEG:    48.9503    131.0497 ]
  Phi   =   2.802222   -0.339371  [ DEG:   160.5555    -19.4445 ]
 
# 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: T0358TS383_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_3-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   65   5.0   29   2.44    6.90  32.195
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_3-D1
PFRMAT TS
TARGET T0358
MODEL 3
PARENT 1dlpA
ATOM     25  N   GLY    10       4.978   1.375 -22.424  1.00  0.00
ATOM     26  CA  GLY    10       5.045   0.041 -23.103  1.00  0.00
ATOM     27  C   GLY    10       5.481  -1.223 -22.361  1.00  0.00
ATOM     28  O   GLY    10       4.737  -1.802 -21.537  1.00  0.00
ATOM     29  N   PRO    11       6.636  -1.830 -22.740  1.00  0.00
ATOM     30  CA  PRO    11       7.124  -2.966 -21.915  1.00  0.00
ATOM     31  C   PRO    11       8.164  -2.107 -21.212  1.00  0.00
ATOM     32  O   PRO    11       7.454  -1.108 -20.955  1.00  0.00
ATOM     33  N   PHE    12       9.412  -1.966 -20.984  1.00  0.00
ATOM     34  CA  PHE    12      10.076  -0.940 -20.192  1.00  0.00
ATOM     35  C   PHE    12       9.110  -0.456 -19.109  1.00  0.00
ATOM     36  O   PHE    12       7.995  -0.044 -19.148  1.00  0.00
ATOM     37  N   THR    13       9.761  -0.689 -18.006  1.00  0.00
ATOM     38  CA  THR    13       9.272  -0.496 -16.707  1.00  0.00
ATOM     39  C   THR    13       9.844   0.692 -16.030  1.00  0.00
ATOM     40  O   THR    13      10.980   0.628 -15.580  1.00  0.00
ATOM     41  N   ARG    14       9.185   1.815 -15.845  1.00  0.00
ATOM     42  CA  ARG    14       9.942   2.722 -15.076  1.00  0.00
ATOM     43  C   ARG    14       9.877   2.971 -13.631  1.00  0.00
ATOM     44  O   ARG    14      10.976   3.243 -13.213  1.00  0.00
ATOM     45  N   ARG    15       8.914   3.183 -12.812  1.00  0.00
ATOM     46  CA  ARG    15       9.050   3.281 -11.372  1.00  0.00
ATOM     47  C   ARG    15       8.037   2.320 -10.741  1.00  0.00
ATOM     48  O   ARG    15       7.171   2.230 -11.658  1.00  0.00
ATOM     49  N   GLN    16       8.139   1.862  -9.498  1.00  0.00
ATOM     50  CA  GLN    16       7.127   1.016  -8.939  1.00  0.00
ATOM     51  C   GLN    16       7.220   0.959  -7.458  1.00  0.00
ATOM     52  O   GLN    16       7.691   2.072  -7.237  1.00  0.00
ATOM     53  N   ALA    17       6.449   0.287  -6.594  1.00  0.00
ATOM     54  CA  ALA    17       6.451   0.866  -5.165  1.00  0.00
ATOM     55  C   ALA    17       7.208  -0.259  -4.506  1.00  0.00
ATOM     56  O   ALA    17       7.864  -0.418  -3.443  1.00  0.00
ATOM     57  N   GLN    18       7.250  -1.317  -5.384  1.00  0.00
ATOM     58  CA  GLN    18       7.955  -2.546  -5.020  1.00  0.00
ATOM     59  C   GLN    18       7.161  -3.108  -3.837  1.00  0.00
ATOM     60  O   GLN    18       7.643  -3.538  -2.770  1.00  0.00
ATOM     61  N   ALA    19       5.855  -3.022  -3.968  1.00  0.00
ATOM     62  CA  ALA    19       5.143  -3.356  -2.749  1.00  0.00
ATOM     63  C   ALA    19       4.483  -4.618  -3.230  1.00  0.00
ATOM     64  O   ALA    19       3.225  -4.636  -3.017  1.00  0.00
ATOM     65  N   VAL    20       5.130  -5.663  -3.805  1.00  0.00
ATOM     66  CA  VAL    20       4.209  -6.775  -4.123  1.00  0.00
ATOM     67  C   VAL    20       4.090  -8.023  -3.304  1.00  0.00
ATOM     68  O   VAL    20       4.254  -8.266  -2.131  1.00  0.00
ATOM     69  N   THR    21       3.175  -8.757  -3.886  1.00  0.00
ATOM     70  CA  THR    21       2.508 -10.016  -3.663  1.00  0.00
ATOM     71  C   THR    21       1.367 -10.034  -2.697  1.00  0.00
ATOM     72  O   THR    21       1.434 -10.681  -1.678  1.00  0.00
ATOM     73  N   THR    22       0.327  -9.279  -2.893  1.00  0.00
ATOM     74  CA  THR    22      -0.658  -9.394  -1.814  1.00  0.00
ATOM     75  C   THR    22      -1.936  -9.146  -2.566  1.00  0.00
ATOM     76  O   THR    22      -1.902  -9.663  -3.725  1.00  0.00
ATOM     77  N   THR    23      -3.123  -8.922  -1.985  1.00  0.00
ATOM     78  CA  THR    23      -4.323  -8.699  -2.652  1.00  0.00
ATOM     79  C   THR    23      -5.413  -7.753  -2.032  1.00  0.00
ATOM     80  O   THR    23      -5.855  -7.201  -1.019  1.00  0.00
ATOM     81  N   TYR    24      -5.779  -7.207  -3.246  1.00  0.00
ATOM     82  CA  TYR    24      -6.788  -6.367  -3.634  1.00  0.00
ATOM     83  C   TYR    24      -6.400  -5.028  -3.131  1.00  0.00
ATOM     84  O   TYR    24      -7.250  -4.367  -2.563  1.00  0.00
ATOM     85  N   SER    25      -5.132  -4.715  -3.386  1.00  0.00
ATOM     86  CA  SER    25      -4.612  -3.386  -2.867  1.00  0.00
ATOM     87  C   SER    25      -5.254  -2.413  -3.820  1.00  0.00
ATOM     88  O   SER    25      -5.602  -2.745  -4.995  1.00  0.00
ATOM     89  N   ASN    26      -5.793  -1.288  -3.419  1.00  0.00
ATOM     90  CA  ASN    26      -6.291  -0.383  -4.437  1.00  0.00
ATOM     91  C   ASN    26      -5.404   0.845  -4.027  1.00  0.00
ATOM     92  O   ASN    26      -4.988   0.783  -2.885  1.00  0.00
ATOM     93  N   ILE    27      -5.257   1.699  -5.013  1.00  0.00
ATOM     94  CA  ILE    27      -4.553   2.930  -5.031  1.00  0.00
ATOM     95  C   ILE    27      -5.381   4.149  -4.779  1.00  0.00
ATOM     96  O   ILE    27      -4.703   4.672  -3.757  1.00  0.00
ATOM     97  N   THR    28      -6.461   4.891  -4.749  1.00  0.00
ATOM     98  CA  THR    28      -6.633   6.090  -3.897  1.00  0.00
ATOM     99  C   THR    28      -5.788   7.284  -3.423  1.00  0.00
ATOM    100  O   THR    28      -4.764   7.160  -2.788  1.00  0.00
ATOM    101  N   LEU    29      -6.468   8.498  -3.598  1.00  0.00
ATOM    102  CA  LEU    29      -5.679   9.633  -3.157  1.00  0.00
ATOM    103  C   LEU    29      -6.185  10.391  -2.043  1.00  0.00
ATOM    104  O   LEU    29      -7.122  11.061  -2.251  1.00  0.00
ATOM    105  N   GLU    30      -5.275  10.882  -1.183  1.00  0.00
ATOM    106  CA  GLU    30      -5.780  11.693  -0.132  1.00  0.00
ATOM    107  C   GLU    30      -6.025  13.077   0.010  1.00  0.00
ATOM    108  O   GLU    30      -6.462  13.443  -1.061  1.00  0.00
ATOM    109  N   ASP    31      -6.147  13.747   1.123  1.00  0.00
ATOM    110  CA  ASP    31      -6.691  15.027   1.187  1.00  0.00
ATOM    111  C   ASP    31      -5.631  15.935   1.728  1.00  0.00
ATOM    112  O   ASP    31      -5.851  17.033   2.268  1.00  0.00
ATOM    113  N   ASP    32      -4.488  15.297   1.882  1.00  0.00
ATOM    114  CA  ASP    32      -3.432  16.025   2.654  1.00  0.00
ATOM    115  C   ASP    32      -2.389  15.505   1.712  1.00  0.00
ATOM    116  O   ASP    32      -1.374  14.996   1.948  1.00  0.00
ATOM    117  N   PHE    37      -2.756  15.365   0.453  1.00  0.00
ATOM    118  CA  PHE    37      -1.912  14.987  -0.582  1.00  0.00
ATOM    119  C   PHE    37      -1.391  13.580  -0.375  1.00  0.00
ATOM    120  O   PHE    37      -0.468  13.448  -1.065  1.00  0.00
ATOM    121  N   ARG    38      -1.757  12.611   0.467  1.00  0.00
ATOM    122  CA  ARG    38      -0.873  11.440   0.222  1.00  0.00
ATOM    123  C   ARG    38      -1.379  10.524  -0.843  1.00  0.00
ATOM    124  O   ARG    38      -2.544  10.286  -0.814  1.00  0.00
ATOM    125  N   LEU    39      -0.596   9.782  -1.531  1.00  0.00
ATOM    126  CA  LEU    39      -1.120   8.800  -2.450  1.00  0.00
ATOM    127  C   LEU    39      -0.799   7.575  -1.692  1.00  0.00
ATOM    128  O   LEU    39       0.100   7.862  -1.085  1.00  0.00
ATOM    129  N   VAL    40      -1.431   6.608  -1.209  1.00  0.00
ATOM    130  CA  VAL    40      -1.642   5.439  -0.511  1.00  0.00
ATOM    131  C   VAL    40      -2.428   4.357  -1.293  1.00  0.00
ATOM    132  O   VAL    40      -3.432   4.703  -1.800  1.00  0.00
ATOM    133  N   VAL    41      -1.750   3.222  -1.235  1.00  0.00
ATOM    134  CA  VAL    41      -2.063   1.885  -1.496  1.00  0.00
ATOM    135  C   VAL    41      -2.440   1.184  -0.293  1.00  0.00
ATOM    136  O   VAL    41      -1.839   0.560   0.532  1.00  0.00
ATOM    137  N   ARG    42      -3.722   1.016  -0.126  1.00  0.00
ATOM    138  CA  ARG    42      -4.721   0.588   0.740  1.00  0.00
ATOM    139  C   ARG    42      -5.042  -0.791   0.294  1.00  0.00
ATOM    140  O   ARG    42      -4.983  -1.395  -0.768  1.00  0.00
ATOM    141  N   ASP    43      -5.145  -1.250   1.532  1.00  0.00
ATOM    142  CA  ASP    43      -5.387  -2.681   1.488  1.00  0.00
ATOM    143  C   ASP    43      -6.848  -3.058   1.499  1.00  0.00
ATOM    144  O   ASP    43      -7.347  -2.736   2.508  1.00  0.00
ATOM    145  N   THR    44      -7.218  -4.121   0.893  1.00  0.00
ATOM    146  CA  THR    44      -8.193  -5.141   1.003  1.00  0.00
ATOM    147  C   THR    44      -8.847  -5.140   2.396  1.00  0.00
ATOM    148  O   THR    44     -10.081  -5.109   2.571  1.00  0.00
ATOM    149  N   GLU    45      -8.068  -4.839   3.455  1.00  0.00
ATOM    150  CA  GLU    45      -8.877  -4.660   4.628  1.00  0.00
ATOM    151  C   GLU    45      -8.567  -3.374   5.263  1.00  0.00
ATOM    152  O   GLU    45      -8.454  -3.408   6.499  1.00  0.00
ATOM    153  N   GLY    46      -8.257  -2.369   4.515  1.00  0.00
ATOM    154  CA  GLY    46      -8.114  -1.050   5.000  1.00  0.00
ATOM    155  C   GLY    46      -6.749  -0.817   5.641  1.00  0.00
ATOM    156  O   GLY    46      -6.386   0.349   6.082  1.00  0.00
ATOM    157  N   ARG    47      -5.771  -1.676   5.367  1.00  0.00
ATOM    158  CA  ARG    47      -4.528  -1.334   5.832  1.00  0.00
ATOM    159  C   ARG    47      -3.481  -0.761   4.948  1.00  0.00
ATOM    160  O   ARG    47      -2.589  -1.699   4.849  1.00  0.00
ATOM    161  N   MET    48      -3.022   0.498   4.823  1.00  0.00
ATOM    162  CA  MET    48      -1.827   1.005   4.107  1.00  0.00
ATOM    163  C   MET    48      -0.690   0.226   3.559  1.00  0.00
ATOM    164  O   MET    48       0.397   0.274   4.067  1.00  0.00
ATOM    165  N   VAL    49      -0.550  -0.459   2.391  1.00  0.00
ATOM    166  CA  VAL    49       0.689  -1.231   2.082  1.00  0.00
ATOM    167  C   VAL    49       1.914  -0.380   1.907  1.00  0.00
ATOM    168  O   VAL    49       2.964  -0.858   1.594  1.00  0.00
ATOM    169  N   TRP    50       1.883   0.886   1.721  1.00  0.00
ATOM    170  CA  TRP    50       2.768   1.843   1.188  1.00  0.00
ATOM    171  C   TRP    50       2.192   3.240   1.155  1.00  0.00
ATOM    172  O   TRP    50       1.104   3.108   0.614  1.00  0.00
ATOM    173  N   ARG    51       2.840   4.322   1.500  1.00  0.00
ATOM    174  CA  ARG    51       2.430   5.695   1.465  1.00  0.00
ATOM    175  C   ARG    51       3.416   6.353   0.464  1.00  0.00
ATOM    176  O   ARG    51       4.192   5.745  -0.294  1.00  0.00
ATOM    177  N   ALA    52       3.245   7.620   0.396  1.00  0.00
ATOM    178  CA  ALA    52       4.091   8.529  -0.339  1.00  0.00
ATOM    179  C   ALA    52       4.694   9.402   0.726  1.00  0.00
ATOM    180  O   ALA    52       5.841   9.520   0.418  1.00  0.00
ATOM    181  N   ASN    54       4.496  10.229   1.666  1.00  0.00
ATOM    182  CA  ASN    54       5.303  10.556   2.805  1.00  0.00
ATOM    183  C   ASN    54       5.335  12.027   3.069  1.00  0.00
ATOM    184  O   ASN    54       5.790  12.723   3.972  1.00  0.00
ATOM    185  N   PHE    55       4.660  12.427   1.987  1.00  0.00
ATOM    186  CA  PHE    55       4.773  13.919   2.063  1.00  0.00
ATOM    187  C   PHE    55       3.404  14.345   2.297  1.00  0.00
ATOM    188  O   PHE    55       2.757  13.607   1.667  1.00  0.00
ATOM    189  N   GLU    56       3.068  15.395   2.787  1.00  0.00
ATOM    190  CA  GLU    56       1.683  15.531   3.097  1.00  0.00
ATOM    191  C   GLU    56       1.486  17.021   3.003  1.00  0.00
ATOM    192  O   GLU    56       2.545  17.631   3.081  1.00  0.00
ATOM    193  N   PRO    57       0.247  17.540   2.874  1.00  0.00
ATOM    194  CA  PRO    57       0.119  18.929   2.801  1.00  0.00
ATOM    195  C   PRO    57      -1.014  19.471   3.622  1.00  0.00
ATOM    196  O   PRO    57      -1.257  19.141   4.881  1.00  0.00
ATOM    197  N   ASP    58      -1.718  20.201   2.744  1.00  0.00
ATOM    198  CA  ASP    58      -2.834  20.984   3.311  1.00  0.00
ATOM    199  C   ASP    58      -4.307  20.760   3.206  1.00  0.00
ATOM    200  O   ASP    58      -4.325  19.505   3.514  1.00  0.00
ATOM    201  N   ALA    59      -5.523  21.488   3.057  1.00  0.00
ATOM    202  CA  ALA    59      -6.493  20.471   3.187  1.00  0.00
ATOM    203  C   ALA    59      -7.016  19.989   1.973  1.00  0.00
ATOM    204  O   ALA    59      -6.618  18.925   1.400  1.00  0.00
ATOM    205  N   GLY    60      -7.642  20.586   1.088  1.00  0.00
ATOM    206  CA  GLY    60      -7.921  19.918  -0.125  1.00  0.00
ATOM    207  C   GLY    60      -7.817  18.748  -0.955  1.00  0.00
ATOM    208  O   GLY    60      -7.833  17.482  -1.137  1.00  0.00
TER
END
