
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0358TS383_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS383_2-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    G      10      T      13          3.675
LGA    P      11      R      14          3.769
LGA    F      12      -       -           -
LGA    T      13      R      15          4.116
LGA    R      14      Q      16          4.043
LGA    -       -      A      17           -
LGA    R      15      Q      18          2.568
LGA    Q      16      A      19          2.194
LGA    A      17      V      20          3.399
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    Q      18      T      23          1.200
LGA    A      19      Y      24          3.443
LGA    V      20      S      25          4.313
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      -       -           -
LGA    T      28      N      26          3.896
LGA    L      29      I      27          4.160
LGA    E      30      T      28           #
LGA    D      31      L      29          4.768
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    D      32      R      38          5.566
LGA    H      36      L      39          1.857
LGA    F      37      V      40          4.626
LGA    R      38      V      41          2.497
LGA    L      39      R      42          2.644
LGA    V      40      D      43          4.193
LGA    V      41      T      44          4.069
LGA    R      42      E      45          2.522
LGA    D      43      G      46           #
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    V      49      -       -           -
LGA    W      50      R      47          1.743
LGA    R      51      M      48          0.755
LGA    A      52      V      49          2.231
LGA    W      53      W      50          2.678
LGA    N      54      R      51          4.142
LGA    F      55      A      52          3.074
LGA    E      56      W      53          3.305
LGA    P      57      N      54          2.849
LGA    D      58      F      55          3.337
LGA    A      59      E      56          1.460
LGA    G      60      P      57          5.128
LGA    -       -      D      58           -
LGA    E      61      A      59          2.074
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    G      62      L      63           #
LGA    L      63      N      64           #
LGA    -       -      R      65           -
LGA    N      64      Y      66           #
LGA    R      65      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)   53   65    5.0     33    3.42     3.03     28.474     0.938

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.288210 * X  +   0.952370 * Y  +   0.099629 * Z  + -50.517166
  Y_new =  -0.683418 * X  +  -0.277457 * Y  +   0.675246 * Z  + -11.773669
  Z_new =   0.670727 * X  +   0.126525 * Y  +   0.730833 * Z  + -52.515785 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.171425   -2.970168  [ DEG:     9.8219   -170.1781 ]
  Theta =  -0.735189   -2.406404  [ DEG:   -42.1232   -137.8768 ]
  Phi   =  -1.969885    1.171708  [ DEG:  -112.8661     67.1339 ]
 
# 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_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_2-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   65   5.0   33   3.42    3.03  28.474
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_2-D1
PFRMAT TS
TARGET T0358
MODEL 2
PARENT 1flgA
ATOM     25  N   GLY    10       4.323   7.450  -3.682  1.00  0.00
ATOM     26  CA  GLY    10       5.736   7.387  -4.021  1.00  0.00
ATOM     27  C   GLY    10       6.432   6.083  -3.624  1.00  0.00
ATOM     28  O   GLY    10       7.427   6.040  -2.942  1.00  0.00
ATOM     29  N   PRO    11       6.094   4.985  -4.304  1.00  0.00
ATOM     30  CA  PRO    11       6.851   3.731  -4.119  1.00  0.00
ATOM     31  C   PRO    11       8.290   3.945  -4.538  1.00  0.00
ATOM     32  O   PRO    11       8.621   4.857  -5.283  1.00  0.00
ATOM     33  N   PHE    12       9.312   3.301  -4.009  1.00  0.00
ATOM     34  CA  PHE    12      10.671   3.610  -4.378  1.00  0.00
ATOM     35  C   PHE    12      11.196   2.955  -5.649  1.00  0.00
ATOM     36  O   PHE    12      12.105   3.302  -6.305  1.00  0.00
ATOM     37  N   THR    13      10.728   1.741  -5.912  1.00  0.00
ATOM     38  CA  THR    13      11.219   0.724  -6.779  1.00  0.00
ATOM     39  C   THR    13      10.324  -0.001  -7.747  1.00  0.00
ATOM     40  O   THR    13      10.333  -1.245  -7.852  1.00  0.00
ATOM     41  N   ARG    14       9.422   0.783  -8.307  1.00  0.00
ATOM     42  CA  ARG    14       8.433   0.525  -9.298  1.00  0.00
ATOM     43  C   ARG    14       7.031   0.261  -8.694  1.00  0.00
ATOM     44  O   ARG    14       6.905  -0.055  -7.489  1.00  0.00
ATOM     45  N   ARG    15       5.981   0.455  -9.496  1.00  0.00
ATOM     46  CA  ARG    15       4.616   0.241  -9.098  1.00  0.00
ATOM     47  C   ARG    15       4.060  -1.184  -8.930  1.00  0.00
ATOM     48  O   ARG    15       2.964  -1.570  -9.375  1.00  0.00
ATOM     49  N   GLN    16       4.709  -2.048  -8.146  1.00  0.00
ATOM     50  CA  GLN    16       4.548  -3.484  -8.090  1.00  0.00
ATOM     51  C   GLN    16       3.858  -4.038  -6.853  1.00  0.00
ATOM     52  O   GLN    16       3.683  -3.500  -5.750  1.00  0.00
ATOM     53  N   ALA    17       3.424  -5.279  -7.033  1.00  0.00
ATOM     54  CA  ALA    17       2.769  -6.110  -6.080  1.00  0.00
ATOM     55  C   ALA    17       3.148  -7.552  -6.118  1.00  0.00
ATOM     56  O   ALA    17       3.367  -8.117  -7.165  1.00  0.00
ATOM     57  N   GLN    18       3.267  -8.216  -5.024  1.00  0.00
ATOM     58  CA  GLN    18       3.830  -9.552  -4.926  1.00  0.00
ATOM     59  C   GLN    18       2.814 -10.651  -4.648  1.00  0.00
ATOM     60  O   GLN    18       3.199 -11.740  -4.695  1.00  0.00
ATOM     61  N   ALA    19       1.555 -10.366  -4.462  1.00  0.00
ATOM     62  CA  ALA    19       0.463 -11.225  -4.181  1.00  0.00
ATOM     63  C   ALA    19      -0.631 -10.963  -3.097  1.00  0.00
ATOM     64  O   ALA    19      -0.374 -10.274  -2.137  1.00  0.00
ATOM     65  N   VAL    20      -1.719 -11.670  -3.222  1.00  0.00
ATOM     66  CA  VAL    20      -2.855 -11.733  -2.407  1.00  0.00
ATOM     67  C   VAL    20      -2.762 -12.901  -1.413  1.00  0.00
ATOM     68  O   VAL    20      -1.829 -13.698  -1.439  1.00  0.00
ATOM     69  N   THR    21      -3.768 -12.923  -0.506  1.00  0.00
ATOM     70  CA  THR    21      -3.811 -14.021   0.396  1.00  0.00
ATOM     71  C   THR    21      -5.269 -14.527   0.396  1.00  0.00
ATOM     72  O   THR    21      -6.059 -13.795  -0.242  1.00  0.00
ATOM     73  N   THR    22      -5.573 -15.581   1.074  1.00  0.00
ATOM     74  CA  THR    22      -6.938 -16.013   1.081  1.00  0.00
ATOM     75  C   THR    22      -7.330 -16.718   2.359  1.00  0.00
ATOM     76  O   THR    22      -6.604 -17.466   2.989  1.00  0.00
ATOM     77  N   THR    23      -8.571 -16.428   2.676  1.00  0.00
ATOM     78  CA  THR    23      -9.185 -17.045   3.844  1.00  0.00
ATOM     79  C   THR    23     -10.702 -16.961   3.793  1.00  0.00
ATOM     80  O   THR    23     -11.235 -16.033   3.187  1.00  0.00
ATOM     81  N   TYR    24     -11.422 -18.001   4.214  1.00  0.00
ATOM     82  CA  TYR    24     -12.862 -18.063   4.061  1.00  0.00
ATOM     83  C   TYR    24     -13.450 -17.804   2.691  1.00  0.00
ATOM     84  O   TYR    24     -13.332 -18.536   1.728  1.00  0.00
ATOM     85  N   SER    25     -14.287 -16.793   2.522  1.00  0.00
ATOM     86  CA  SER    25     -14.847 -16.382   1.231  1.00  0.00
ATOM     87  C   SER    25     -14.148 -15.123   0.735  1.00  0.00
ATOM     88  O   SER    25     -14.745 -14.284   0.044  1.00  0.00
ATOM     89  N   ASN    26     -12.919 -14.893   1.277  1.00  0.00
ATOM     90  CA  ASN    26     -12.259 -13.649   0.911  1.00  0.00
ATOM     91  C   ASN    26     -10.843 -13.618   0.375  1.00  0.00
ATOM     92  O   ASN    26      -9.909 -14.374   0.648  1.00  0.00
ATOM     93  N   ILE    27     -10.593 -12.640  -0.515  1.00  0.00
ATOM     94  CA  ILE    27      -9.226 -12.421  -0.976  1.00  0.00
ATOM     95  C   ILE    27      -8.785 -11.007  -0.433  1.00  0.00
ATOM     96  O   ILE    27      -9.199  -9.941  -0.744  1.00  0.00
ATOM     97  N   THR    28      -7.459 -11.035  -0.270  1.00  0.00
ATOM     98  CA  THR    28      -6.788  -9.920   0.361  1.00  0.00
ATOM     99  C   THR    28      -5.523  -9.441  -0.337  1.00  0.00
ATOM    100  O   THR    28      -4.703 -10.274  -0.731  1.00  0.00
ATOM    101  N   LEU    29      -5.270  -8.123  -0.425  1.00  0.00
ATOM    102  CA  LEU    29      -3.982  -7.608  -0.954  1.00  0.00
ATOM    103  C   LEU    29      -3.624  -6.210  -0.485  1.00  0.00
ATOM    104  O   LEU    29      -4.434  -5.312  -0.222  1.00  0.00
ATOM    105  N   GLU    30      -2.347  -5.844  -0.504  1.00  0.00
ATOM    106  CA  GLU    30      -1.925  -4.465  -0.183  1.00  0.00
ATOM    107  C   GLU    30      -1.987  -3.597  -1.459  1.00  0.00
ATOM    108  O   GLU    30      -1.962  -4.180  -2.507  1.00  0.00
ATOM    109  N   ASP    31      -2.199  -2.317  -1.470  1.00  0.00
ATOM    110  CA  ASP    31      -2.202  -1.247  -2.361  1.00  0.00
ATOM    111  C   ASP    31      -1.122  -0.147  -2.153  1.00  0.00
ATOM    112  O   ASP    31      -0.667   0.077  -1.032  1.00  0.00
ATOM    113  N   ASP    32      -0.785   0.571  -3.249  1.00  0.00
ATOM    114  CA  ASP    32       0.305   1.529  -3.220  1.00  0.00
ATOM    115  C   ASP    32       0.140   2.860  -2.473  1.00  0.00
ATOM    116  O   ASP    32       1.082   3.656  -2.385  1.00  0.00
ATOM    117  N   HIS    36      -0.977   3.183  -1.904  1.00  0.00
ATOM    118  CA  HIS    36      -1.255   4.376  -1.157  1.00  0.00
ATOM    119  C   HIS    36      -1.349   4.053   0.333  1.00  0.00
ATOM    120  O   HIS    36      -2.140   4.547   1.069  1.00  0.00
ATOM    121  N   PHE    37      -0.700   3.007   0.734  1.00  0.00
ATOM    122  CA  PHE    37      -0.709   2.227   1.922  1.00  0.00
ATOM    123  C   PHE    37      -2.068   1.886   2.517  1.00  0.00
ATOM    124  O   PHE    37      -2.404   2.410   3.598  1.00  0.00
ATOM    125  N   ARG    38      -2.758   0.968   1.860  1.00  0.00
ATOM    126  CA  ARG    38      -4.006   0.424   2.332  1.00  0.00
ATOM    127  C   ARG    38      -3.927  -1.100   2.145  1.00  0.00
ATOM    128  O   ARG    38      -3.130  -1.633   1.392  1.00  0.00
ATOM    129  N   LEU    39      -4.829  -1.788   2.807  1.00  0.00
ATOM    130  CA  LEU    39      -5.149  -3.163   2.760  1.00  0.00
ATOM    131  C   LEU    39      -6.644  -3.245   2.355  1.00  0.00
ATOM    132  O   LEU    39      -7.520  -2.597   2.958  1.00  0.00
ATOM    133  N   VAL    40      -6.960  -4.113   1.382  1.00  0.00
ATOM    134  CA  VAL    40      -8.318  -4.224   0.923  1.00  0.00
ATOM    135  C   VAL    40      -8.874  -5.637   1.040  1.00  0.00
ATOM    136  O   VAL    40      -8.105  -6.537   0.663  1.00  0.00
ATOM    137  N   VAL    41     -10.167  -5.745   1.353  1.00  0.00
ATOM    138  CA  VAL    41     -10.747  -7.090   1.345  1.00  0.00
ATOM    139  C   VAL    41     -11.898  -7.246   0.342  1.00  0.00
ATOM    140  O   VAL    41     -12.776  -6.403   0.159  1.00  0.00
ATOM    141  N   ARG    42     -11.732  -8.311  -0.492  1.00  0.00
ATOM    142  CA  ARG    42     -12.709  -8.581  -1.548  1.00  0.00
ATOM    143  C   ARG    42     -13.506  -9.888  -1.453  1.00  0.00
ATOM    144  O   ARG    42     -12.897 -10.856  -0.992  1.00  0.00
ATOM    145  N   ASP    43     -14.812  -9.888  -1.773  1.00  0.00
ATOM    146  CA  ASP    43     -15.546 -11.144  -1.755  1.00  0.00
ATOM    147  C   ASP    43     -14.992 -12.123  -2.799  1.00  0.00
ATOM    148  O   ASP    43     -14.787 -11.669  -3.885  1.00  0.00
ATOM    149  N   THR    44     -14.595 -13.325  -2.605  1.00  0.00
ATOM    150  CA  THR    44     -13.990 -14.234  -3.544  1.00  0.00
ATOM    151  C   THR    44     -14.776 -14.502  -4.843  1.00  0.00
ATOM    152  O   THR    44     -14.199 -14.722  -5.919  1.00  0.00
ATOM    153  N   GLU    45     -16.116 -14.575  -4.742  1.00  0.00
ATOM    154  CA  GLU    45     -16.972 -14.994  -5.834  1.00  0.00
ATOM    155  C   GLU    45     -17.261 -13.899  -6.829  1.00  0.00
ATOM    156  O   GLU    45     -17.371 -14.100  -8.022  1.00  0.00
ATOM    157  N   GLY    46     -16.092  -9.347  -7.146  1.00  0.00
ATOM    158  CA  GLY    46     -14.893  -8.679  -6.576  1.00  0.00
ATOM    159  C   GLY    46     -15.434  -7.583  -5.691  1.00  0.00
ATOM    160  O   GLY    46     -14.682  -6.607  -5.653  1.00  0.00
ATOM    161  N   ARG    47     -16.595  -7.740  -5.071  1.00  0.00
ATOM    162  CA  ARG    47     -16.952  -6.528  -4.320  1.00  0.00
ATOM    163  C   ARG    47     -16.069  -6.299  -3.062  1.00  0.00
ATOM    164  O   ARG    47     -15.770  -7.317  -2.436  1.00  0.00
ATOM    165  N   MET    48     -15.793  -5.061  -2.768  1.00  0.00
ATOM    166  CA  MET    48     -15.140  -4.710  -1.540  1.00  0.00
ATOM    167  C   MET    48     -15.935  -4.979  -0.265  1.00  0.00
ATOM    168  O   MET    48     -17.075  -4.532  -0.142  1.00  0.00
ATOM    169  N   VAL    49     -15.412  -5.737   0.678  1.00  0.00
ATOM    170  CA  VAL    49     -15.992  -5.942   2.007  1.00  0.00
ATOM    171  C   VAL    49     -15.580  -4.917   3.054  1.00  0.00
ATOM    172  O   VAL    49     -16.361  -4.317   3.749  1.00  0.00
ATOM    173  N   TRP    50     -14.312  -4.522   3.186  1.00  0.00
ATOM    174  CA  TRP    50     -13.703  -3.576   4.032  1.00  0.00
ATOM    175  C   TRP    50     -12.404  -3.086   3.349  1.00  0.00
ATOM    176  O   TRP    50     -11.910  -3.725   2.470  1.00  0.00
ATOM    177  N   ARG    51     -11.840  -1.966   3.857  1.00  0.00
ATOM    178  CA  ARG    51     -10.583  -1.460   3.371  1.00  0.00
ATOM    179  C   ARG    51     -10.046  -0.440   4.325  1.00  0.00
ATOM    180  O   ARG    51     -10.681   0.244   5.080  1.00  0.00
ATOM    181  N   ALA    52      -8.775  -0.484   4.746  1.00  0.00
ATOM    182  CA  ALA    52      -8.128   0.223   5.838  1.00  0.00
ATOM    183  C   ALA    52      -6.919   0.948   5.306  1.00  0.00
ATOM    184  O   ALA    52      -6.052   0.267   4.804  1.00  0.00
ATOM    185  N   TRP    53      -6.805   2.250   5.317  1.00  0.00
ATOM    186  CA  TRP    53      -5.684   3.058   4.839  1.00  0.00
ATOM    187  C   TRP    53      -4.835   3.095   6.110  1.00  0.00
ATOM    188  O   TRP    53      -5.445   3.601   7.043  1.00  0.00
ATOM    189  N   ASN    54      -3.639   2.541   6.178  1.00  0.00
ATOM    190  CA  ASN    54      -3.058   2.375   7.515  1.00  0.00
ATOM    191  C   ASN    54      -1.947   3.372   7.744  1.00  0.00
ATOM    192  O   ASN    54      -1.362   3.360   8.804  1.00  0.00
ATOM    193  N   PHE    55      -1.645   4.226   6.780  1.00  0.00
ATOM    194  CA  PHE    55      -0.553   5.159   6.978  1.00  0.00
ATOM    195  C   PHE    55      -0.720   6.178   5.866  1.00  0.00
ATOM    196  O   PHE    55      -1.413   5.984   4.898  1.00  0.00
ATOM    197  N   GLU    56       0.086   7.202   5.910  1.00  0.00
ATOM    198  CA  GLU    56       0.067   8.298   4.954  1.00  0.00
ATOM    199  C   GLU    56       0.978   8.178   3.752  1.00  0.00
ATOM    200  O   GLU    56       2.192   8.340   3.871  1.00  0.00
ATOM    201  N   PRO    57       0.542   7.946   2.533  1.00  0.00
ATOM    202  CA  PRO    57       1.419   7.894   1.368  1.00  0.00
ATOM    203  C   PRO    57       2.250   9.151   1.005  1.00  0.00
ATOM    204  O   PRO    57       3.393   9.171   0.444  1.00  0.00
ATOM    205  N   ASP    58       1.702  10.311   1.380  1.00  0.00
ATOM    206  CA  ASP    58       2.372  11.591   1.139  1.00  0.00
ATOM    207  C   ASP    58       3.666  11.670   1.939  1.00  0.00
ATOM    208  O   ASP    58       4.586  12.387   1.469  1.00  0.00
ATOM    209  N   ALA    59       3.778  10.953   3.089  1.00  0.00
ATOM    210  CA  ALA    59       5.009  10.992   3.829  1.00  0.00
ATOM    211  C   ALA    59       5.958   9.839   3.420  1.00  0.00
ATOM    212  O   ALA    59       6.888   9.511   4.180  1.00  0.00
ATOM    213  N   GLY    60       5.560   9.045   2.445  1.00  0.00
ATOM    214  CA  GLY    60       6.417   8.004   1.977  1.00  0.00
ATOM    215  C   GLY    60       6.058   6.613   2.318  1.00  0.00
ATOM    216  O   GLY    60       6.867   5.734   1.987  1.00  0.00
ATOM    217  N   GLU    61       4.988   6.269   2.971  1.00  0.00
ATOM    218  CA  GLU    61       4.631   4.879   3.226  1.00  0.00
ATOM    219  C   GLU    61       3.968   4.316   1.980  1.00  0.00
ATOM    220  O   GLU    61       3.350   5.165   1.320  1.00  0.00
ATOM    221  N   GLY    62       4.199   3.097   1.575  1.00  0.00
ATOM    222  CA  GLY    62       3.454   2.295   0.654  1.00  0.00
ATOM    223  C   GLY    62       3.195   0.860   1.225  1.00  0.00
ATOM    224  O   GLY    62       3.575   0.566   2.324  1.00  0.00
ATOM    225  N   LEU    63       2.779  -0.051   0.361  1.00  0.00
ATOM    226  CA  LEU    63       2.751  -1.464   0.530  1.00  0.00
ATOM    227  C   LEU    63       3.021  -2.202  -0.800  1.00  0.00
ATOM    228  O   LEU    63       2.261  -1.967  -1.742  1.00  0.00
ATOM    229  N   ASN    64       3.897  -3.258  -0.825  1.00  0.00
ATOM    230  CA  ASN    64       4.281  -3.942  -2.055  1.00  0.00
ATOM    231  C   ASN    64       4.216  -5.464  -1.881  1.00  0.00
ATOM    232  O   ASN    64       4.034  -6.197  -2.864  1.00  0.00
ATOM    233  N   ARG    65       4.527  -6.015  -0.668  1.00  0.00
ATOM    234  CA  ARG    65       4.562  -7.391  -0.257  1.00  0.00
ATOM    235  C   ARG    65       3.173  -8.044  -0.043  1.00  0.00
ATOM    236  O   ARG    65       2.086  -7.440   0.092  1.00  0.00
TER
END
