
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0358TS383_5-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS383_5-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      -       -           -
LGA    R      14      T      13          4.824
LGA    R      15      R      14          2.608
LGA    Q      16      R      15          4.861
LGA    A      17      Q      16          3.825
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    Q      18      V      20          2.574
LGA    -       -      T      21           -
LGA    A      19      T      22           #
LGA    V      20      T      23          2.248
LGA    T      21      Y      24          2.972
LGA    T      22      S      25          1.559
LGA    T      23      N      26          2.582
LGA    Y      24      I      27          2.362
LGA    S      25      T      28          2.142
LGA    N      26      L      29          2.238
LGA    -       -      E      30           -
LGA    I      27      D      31          2.327
LGA    T      28      D      32          4.486
LGA    L      29      -       -           -
LGA    E      30      -       -           -
LGA    D      31      -       -           -
LGA    F      37      -       -           -
LGA    R      38      Q      33           #
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    L      39      F      37          2.174
LGA    V      40      R      38          0.919
LGA    V      41      L      39          1.215
LGA    R      42      V      40          0.955
LGA    D      43      V      41          1.432
LGA    T      44      R      42          1.099
LGA    E      45      D      43          4.359
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    G      46      V      49          3.062
LGA    R      47      W      50          1.823
LGA    M      48      R      51          2.851
LGA    V      49      A      52          4.755
LGA    W      50      W      53          4.174
LGA    R      51      N      54          2.173
LGA    A      52      -       -           -
LGA    W      53      F      55          3.890
LGA    N      54      E      56           -
LGA    F      55      P      57           -
LGA    P      57      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      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)   42   65    5.0     28    2.99     7.14     28.180     0.907

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.265986 * X  +  -0.955504 * Y  +   0.127529 * Z  +  18.175888
  Y_new =  -0.592782 * X  +   0.266451 * Y  +   0.760009 * Z  +  16.714132
  Z_new =  -0.760172 * X  +   0.126555 * Y  +  -0.637277 * Z  +  10.624746 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.945556   -0.196037  [ DEG:   168.7679    -11.2321 ]
  Theta =   0.863578    2.278015  [ DEG:    49.4794    130.5206 ]
  Phi   =  -1.992576    1.149017  [ DEG:  -114.1662     65.8338 ]
 
# 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_5-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_5-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   65   5.0   28   2.99    7.14  28.180
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_5-D1
PFRMAT TS
TARGET T0358
MODEL 5
PARENT 1xd6A
ATOM     25  N   GLY    10       8.121  -2.620 -22.194  1.00  0.00
ATOM     26  CA  GLY    10       8.247  -3.584 -21.101  1.00  0.00
ATOM     27  C   GLY    10       9.193  -3.112 -19.979  1.00  0.00
ATOM     28  O   GLY    10       9.304  -3.772 -18.931  1.00  0.00
ATOM     29  N   PRO    11      10.522  -0.753 -16.899  1.00  0.00
ATOM     30  CA  PRO    11      10.097   0.093 -15.781  1.00  0.00
ATOM     31  C   PRO    11      10.892   1.404 -15.781  1.00  0.00
ATOM     32  O   PRO    11      12.105   1.379 -15.856  1.00  0.00
ATOM     33  N   PHE    12      10.190   2.534 -15.701  1.00  0.00
ATOM     34  CA  PHE    12      10.799   3.861 -15.690  1.00  0.00
ATOM     35  C   PHE    12      10.949   4.384 -14.259  1.00  0.00
ATOM     36  O   PHE    12      11.872   5.159 -13.953  1.00  0.00
ATOM     37  N   THR    13      10.045   3.940 -13.387  1.00  0.00
ATOM     38  CA  THR    13       9.917   4.466 -12.033  1.00  0.00
ATOM     39  C   THR    13       9.035   3.519 -11.247  1.00  0.00
ATOM     40  O   THR    13       8.077   2.983 -11.786  1.00  0.00
ATOM     41  N   ARG    14       9.356   3.319  -9.974  1.00  0.00
ATOM     42  CA  ARG    14       8.547   2.481  -9.088  1.00  0.00
ATOM     43  C   ARG    14       8.433   3.096  -7.701  1.00  0.00
ATOM     44  O   ARG    14       9.381   3.734  -7.206  1.00  0.00
ATOM     45  N   ARG    15       7.292   2.862  -7.063  1.00  0.00
ATOM     46  CA  ARG    15       7.063   3.329  -5.700  1.00  0.00
ATOM     47  C   ARG    15       7.898   2.528  -4.686  1.00  0.00
ATOM     48  O   ARG    15       8.096   2.981  -3.550  1.00  0.00
ATOM     49  N   GLN    16       8.358   1.344  -5.095  1.00  0.00
ATOM     50  CA  GLN    16       9.202   0.472  -4.271  1.00  0.00
ATOM     51  C   GLN    16       8.517   0.094  -2.949  1.00  0.00
ATOM     52  O   GLN    16       9.132   0.135  -1.885  1.00  0.00
ATOM     53  N   ALA    17       7.238  -0.250  -3.048  1.00  0.00
ATOM     54  CA  ALA    17       6.431  -0.661  -1.911  1.00  0.00
ATOM     55  C   ALA    17       5.954  -2.037  -2.243  1.00  0.00
ATOM     56  O   ALA    17       4.768  -2.267  -2.498  1.00  0.00
ATOM     57  N   GLN    18       6.915  -2.955  -2.270  1.00  0.00
ATOM     58  CA  GLN    18       6.623  -4.333  -2.610  1.00  0.00
ATOM     59  C   GLN    18       6.100  -5.114  -1.404  1.00  0.00
ATOM     60  O   GLN    18       6.672  -5.069  -0.312  1.00  0.00
ATOM     61  N   ALA    19       4.974  -5.779  -1.629  1.00  0.00
ATOM     62  CA  ALA    19       4.421  -6.782  -0.740  1.00  0.00
ATOM     63  C   ALA    19       3.993  -7.887  -1.693  1.00  0.00
ATOM     64  O   ALA    19       4.639  -8.078  -2.730  1.00  0.00
ATOM     65  N   VAL    20       2.923  -8.609  -1.388  1.00  0.00
ATOM     66  CA  VAL    20       2.537  -9.719  -2.260  1.00  0.00
ATOM     67  C   VAL    20       1.213  -9.457  -2.951  1.00  0.00
ATOM     68  O   VAL    20       0.561  -8.452  -2.673  1.00  0.00
ATOM     69  N   THR    21       0.838 -10.361  -3.857  1.00  0.00
ATOM     70  CA  THR    21      -0.404 -10.249  -4.616  1.00  0.00
ATOM     71  C   THR    21      -1.584 -10.033  -3.671  1.00  0.00
ATOM     72  O   THR    21      -1.775 -10.797  -2.725  1.00  0.00
ATOM     73  N   THR    22      -2.351  -8.974  -3.909  1.00  0.00
ATOM     74  CA  THR    22      -3.464  -8.624  -3.051  1.00  0.00
ATOM     75  C   THR    22      -4.398  -7.643  -3.720  1.00  0.00
ATOM     76  O   THR    22      -4.420  -7.538  -4.952  1.00  0.00
ATOM     77  N   THR    23      -5.154  -6.907  -2.909  1.00  0.00
ATOM     78  CA  THR    23      -6.182  -6.016  -3.431  1.00  0.00
ATOM     79  C   THR    23      -5.952  -4.539  -3.123  1.00  0.00
ATOM     80  O   THR    23      -6.798  -3.864  -2.517  1.00  0.00
ATOM     81  N   TYR    24      -4.812  -4.040  -3.580  1.00  0.00
ATOM     82  CA  TYR    24      -4.421  -2.647  -3.391  1.00  0.00
ATOM     83  C   TYR    24      -5.189  -1.724  -4.291  1.00  0.00
ATOM     84  O   TYR    24      -5.747  -2.135  -5.305  1.00  0.00
ATOM     85  N   SER    25      -5.213  -0.461  -3.910  1.00  0.00
ATOM     86  CA  SER    25      -5.762   0.552  -4.777  1.00  0.00
ATOM     87  C   SER    25      -5.087   1.881  -4.535  1.00  0.00
ATOM     88  O   SER    25      -4.638   2.172  -3.422  1.00  0.00
ATOM     89  N   ASN    26      -4.980   2.658  -5.609  1.00  0.00
ATOM     90  CA  ASN    26      -4.411   3.982  -5.552  1.00  0.00
ATOM     91  C   ASN    26      -5.597   4.915  -5.491  1.00  0.00
ATOM     92  O   ASN    26      -6.535   4.756  -6.259  1.00  0.00
ATOM     93  N   ILE    27      -5.550   5.884  -4.582  1.00  0.00
ATOM     94  CA  ILE    27      -6.630   6.850  -4.433  1.00  0.00
ATOM     95  C   ILE    27      -6.077   8.267  -4.340  1.00  0.00
ATOM     96  O   ILE    27      -5.144   8.523  -3.591  1.00  0.00
ATOM     97  N   THR    28      -6.650   9.181  -5.123  1.00  0.00
ATOM     98  CA  THR    28      -6.432  10.603  -4.907  1.00  0.00
ATOM     99  C   THR    28      -7.461  11.039  -3.858  1.00  0.00
ATOM    100  O   THR    28      -8.655  11.125  -4.145  1.00  0.00
ATOM    101  N   LEU    29      -6.986  11.309  -2.652  1.00  0.00
ATOM    102  CA  LEU    29      -7.878  11.641  -1.541  1.00  0.00
ATOM    103  C   LEU    29      -8.374  13.082  -1.541  1.00  0.00
ATOM    104  O   LEU    29      -7.726  13.979  -2.096  1.00  0.00
ATOM    105  N   GLU    30      -9.510  13.290  -0.876  1.00  0.00
ATOM    106  CA  GLU    30     -10.129  14.616  -0.732  1.00  0.00
ATOM    107  C   GLU    30      -9.179  15.613  -0.051  1.00  0.00
ATOM    108  O   GLU    30      -9.320  16.821  -0.207  1.00  0.00
ATOM    109  N   ASP    31      -8.217  15.112   0.712  1.00  0.00
ATOM    110  CA  ASP    31      -7.242  15.989   1.354  1.00  0.00
ATOM    111  C   ASP    31      -5.984  16.230   0.494  1.00  0.00
ATOM    112  O   ASP    31      -4.982  16.766   0.984  1.00  0.00
ATOM    113  N   PHE    37      -6.059  15.844  -0.783  1.00  0.00
ATOM    114  CA  PHE    37      -4.982  16.034  -1.769  1.00  0.00
ATOM    115  C   PHE    37      -3.809  15.053  -1.670  1.00  0.00
ATOM    116  O   PHE    37      -2.872  15.133  -2.470  1.00  0.00
ATOM    117  N   ARG    38      -3.829  14.162  -0.685  1.00  0.00
ATOM    118  CA  ARG    38      -2.830  13.091  -0.630  1.00  0.00
ATOM    119  C   ARG    38      -3.182  12.035  -1.684  1.00  0.00
ATOM    120  O   ARG    38      -4.362  11.794  -1.969  1.00  0.00
ATOM    121  N   LEU    39      -2.157  11.426  -2.269  1.00  0.00
ATOM    122  CA  LEU    39      -2.358  10.282  -3.134  1.00  0.00
ATOM    123  C   LEU    39      -1.773   9.093  -2.384  1.00  0.00
ATOM    124  O   LEU    39      -0.617   9.109  -2.010  1.00  0.00
ATOM    125  N   VAL    40      -2.574   8.061  -2.174  1.00  0.00
ATOM    126  CA  VAL    40      -2.200   7.015  -1.240  1.00  0.00
ATOM    127  C   VAL    40      -2.473   5.675  -1.893  1.00  0.00
ATOM    128  O   VAL    40      -3.444   5.533  -2.639  1.00  0.00
ATOM    129  N   VAL    41      -1.597   4.705  -1.634  1.00  0.00
ATOM    130  CA  VAL    41      -1.875   3.309  -1.965  1.00  0.00
ATOM    131  C   VAL    41      -2.291   2.596  -0.681  1.00  0.00
ATOM    132  O   VAL    41      -1.542   2.601   0.311  1.00  0.00
ATOM    133  N   ARG    42      -3.477   1.986  -0.712  1.00  0.00
ATOM    134  CA  ARG    42      -3.998   1.207   0.414  1.00  0.00
ATOM    135  C   ARG    42      -3.974  -0.295   0.120  1.00  0.00
ATOM    136  O   ARG    42      -4.109  -0.699  -1.033  1.00  0.00
ATOM    137  N   ASP    43      -3.802  -1.110   1.162  1.00  0.00
ATOM    138  CA  ASP    43      -3.877  -2.567   1.038  1.00  0.00
ATOM    139  C   ASP    43      -5.317  -3.045   1.314  1.00  0.00
ATOM    140  O   ASP    43      -6.219  -2.217   1.497  1.00  0.00
ATOM    141  N   THR    44      -5.541  -4.362   1.308  1.00  0.00
ATOM    142  CA  THR    44      -6.887  -4.900   1.525  1.00  0.00
ATOM    143  C   THR    44      -7.517  -4.497   2.872  1.00  0.00
ATOM    144  O   THR    44      -8.742  -4.500   3.010  1.00  0.00
ATOM    145  N   GLU    45      -6.667  -4.132   3.831  1.00  0.00
ATOM    146  CA  GLU    45      -7.083  -3.756   5.183  1.00  0.00
ATOM    147  C   GLU    45      -7.255  -2.242   5.350  1.00  0.00
ATOM    148  O   GLU    45      -7.567  -1.774   6.446  1.00  0.00
ATOM    149  N   GLY    46      -7.045  -1.482   4.281  1.00  0.00
ATOM    150  CA  GLY    46      -7.177  -0.035   4.330  1.00  0.00
ATOM    151  C   GLY    46      -6.058   0.628   5.111  1.00  0.00
ATOM    152  O   GLY    46      -6.232   1.705   5.673  1.00  0.00
ATOM    153  N   ARG    47      -4.914  -0.035   5.150  1.00  0.00
ATOM    154  CA  ARG    47      -3.703   0.573   5.649  1.00  0.00
ATOM    155  C   ARG    47      -2.887   1.135   4.494  1.00  0.00
ATOM    156  O   ARG    47      -2.699   0.467   3.481  1.00  0.00
ATOM    157  N   MET    48      -2.460   2.382   4.660  1.00  0.00
ATOM    158  CA  MET    48      -1.560   3.073   3.745  1.00  0.00
ATOM    159  C   MET    48      -0.167   2.428   3.698  1.00  0.00
ATOM    160  O   MET    48       0.518   2.335   4.728  1.00  0.00
ATOM    161  N   VAL    49       0.252   2.021   2.503  1.00  0.00
ATOM    162  CA  VAL    49       1.607   1.504   2.285  1.00  0.00
ATOM    163  C   VAL    49       2.526   2.508   1.566  1.00  0.00
ATOM    164  O   VAL    49       3.750   2.389   1.635  1.00  0.00
ATOM    165  N   TRP    50       1.933   3.503   0.903  1.00  0.00
ATOM    166  CA  TRP    50       2.676   4.549   0.218  1.00  0.00
ATOM    167  C   TRP    50       1.790   5.799   0.161  1.00  0.00
ATOM    168  O   TRP    50       0.576   5.689  -0.012  1.00  0.00
ATOM    169  N   ARG    51       2.395   6.974   0.320  1.00  0.00
ATOM    170  CA  ARG    51       1.677   8.240   0.166  1.00  0.00
ATOM    171  C   ARG    51       2.582   9.234  -0.545  1.00  0.00
ATOM    172  O   ARG    51       3.789   9.157  -0.410  1.00  0.00
ATOM    173  N   ALA    52       2.001  10.154  -1.310  1.00  0.00
ATOM    174  CA  ALA    52       2.784  11.233  -1.916  1.00  0.00
ATOM    175  C   ALA    52       3.178  12.304  -0.896  1.00  0.00
ATOM    176  O   ALA    52       4.089  13.084  -1.149  1.00  0.00
ATOM    177  N   TRP    53       2.465  12.359   0.231  1.00  0.00
ATOM    178  CA  TRP    53       2.697  13.366   1.256  1.00  0.00
ATOM    179  C   TRP    53       2.278  14.761   0.842  1.00  0.00
ATOM    180  O   TRP    53       2.883  15.749   1.258  1.00  0.00
ATOM    181  N   ASN    54       1.240  14.855   0.014  1.00  0.00
ATOM    182  CA  ASN    54       0.823  16.145  -0.515  1.00  0.00
ATOM    183  C   ASN    54      -0.493  16.619   0.093  1.00  0.00
ATOM    184  O   ASN    54      -1.172  17.471  -0.480  1.00  0.00
ATOM    185  N   PHE    55      -0.842  16.074   1.253  1.00  0.00
ATOM    186  CA  PHE    55      -2.027  16.502   1.982  1.00  0.00
ATOM    187  C   PHE    55      -1.969  17.967   2.433  1.00  0.00
ATOM    188  O   PHE    55      -0.921  18.461   2.846  1.00  0.00
ATOM    189  N   PRO    57      -3.109  18.645   2.327  1.00  0.00
ATOM    190  CA  PRO    57      -3.260  20.018   2.803  1.00  0.00
ATOM    191  C   PRO    57      -4.093  20.033   4.084  1.00  0.00
ATOM    192  O   PRO    57      -4.800  19.064   4.392  1.00  0.00
TER
END
