
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0358TS383_3
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS383_3.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    S       4      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    V       5      R      14           #
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      R      15          2.903
LGA    Q      16      Q      16          3.010
LGA    A      17      A      17          2.150
LGA    -       -      Q      18           -
LGA    Q      18      A      19          3.902
LGA    A      19      V      20          2.167
LGA    V      20      T      21          4.606
LGA    -       -      T      22           -
LGA    T      21      T      23          2.654
LGA    T      22      Y      24          2.062
LGA    T      23      S      25          2.988
LGA    Y      24      N      26          2.786
LGA    S      25      I      27          2.025
LGA    N      26      T      28          2.145
LGA    I      27      L      29          1.649
LGA    T      28      E      30          1.340
LGA    L      29      D      31          0.627
LGA    E      30      D      32           #
LGA    D      31      -       -           -
LGA    D      32      -       -           -
LGA    F      37      Q      33          5.768
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    R      38      H      36          3.715
LGA    L      39      F      37          0.676
LGA    V      40      R      38          1.121
LGA    V      41      L      39          1.470
LGA    R      42      V      40          0.611
LGA    D      43      V      41          1.956
LGA    T      44      R      42          1.894
LGA    E      45      D      43          3.917
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    G      46      M      48          1.469
LGA    R      47      V      49          3.116
LGA    M      48      W      50          3.872
LGA    V      49      R      51           #
LGA    W      50      A      52          5.130
LGA    R      51      W      53          2.327
LGA    A      52      N      54          1.331
LGA    N      54      F      55          1.433
LGA    F      55      E      56           #
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           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   66    5.0     31    2.79    12.90     32.288     1.073

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.538397 * X  +   0.709452 * Y  +   0.454759 * Z  + -41.701458
  Y_new =   0.095071 * X  +   0.587343 * Y  +  -0.803735 * Z  + -15.854763
  Z_new =  -0.837311 * X  +  -0.389494 * Y  +  -0.383672 * Z  +  77.193291 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.348664    0.792929  [ DEG:  -134.5685     45.4315 ]
  Theta =   0.992346    2.149246  [ DEG:    56.8573    123.1427 ]
  Phi   =   2.966814   -0.174779  [ DEG:   169.9859    -10.0141 ]
 
# 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                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_3.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   66   5.0   31   2.79   12.90  32.288
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_3
PFRMAT TS
TARGET T0358
MODEL 3
PARENT 1dlpA
ATOM      1  N   SER     4       1.525  -4.886  -6.034  1.00  0.00
ATOM      2  CA  SER     4       2.651  -4.083  -6.431  1.00  0.00
ATOM      3  C   SER     4       2.059  -3.181  -7.488  1.00  0.00
ATOM      4  O   SER     4       1.030  -3.494  -8.029  1.00  0.00
ATOM      5  N   VAL     5       2.548  -1.911  -7.351  1.00  0.00
ATOM      6  CA  VAL     5       2.236  -0.665  -7.982  1.00  0.00
ATOM      7  C   VAL     5       3.414  -0.331  -8.798  1.00  0.00
ATOM      8  O   VAL     5       4.382  -0.032  -8.196  1.00  0.00
ATOM      9  N   LEU     6       3.437  -0.815  -9.992  1.00  0.00
ATOM     10  CA  LEU     6       4.565  -0.672 -10.925  1.00  0.00
ATOM     11  C   LEU     6       4.497   0.033 -12.300  1.00  0.00
ATOM     12  O   LEU     6       3.542  -0.088 -13.164  1.00  0.00
ATOM     13  N   LEU     7       5.710   0.679 -12.671  1.00  0.00
ATOM     14  CA  LEU     7       5.719   1.226 -14.013  1.00  0.00
ATOM     15  C   LEU     7       6.534   0.381 -15.036  1.00  0.00
ATOM     16  O   LEU     7       7.495   0.037 -14.428  1.00  0.00
ATOM     17  N   PRO     8       6.037   0.279 -16.219  1.00  0.00
ATOM     18  CA  PRO     8       6.766  -0.552 -17.059  1.00  0.00
ATOM     19  C   PRO     8       6.681   0.122 -18.449  1.00  0.00
ATOM     20  O   PRO     8       5.597   0.576 -18.720  1.00  0.00
ATOM     21  N   PRO     9       7.835  -0.028 -19.124  1.00  0.00
ATOM     22  CA  PRO     9       8.031   0.271 -20.494  1.00  0.00
ATOM     23  C   PRO     9       7.807  -1.030 -21.176  1.00  0.00
ATOM     24  O   PRO     9       8.704  -1.860 -21.263  1.00  0.00
ATOM     25  N   GLY    10       6.815  -1.595 -21.834  1.00  0.00
ATOM     26  CA  GLY    10       6.960  -3.012 -22.302  1.00  0.00
ATOM     27  C   GLY    10       7.323  -4.147 -21.343  1.00  0.00
ATOM     28  O   GLY    10       6.501  -4.616 -20.525  1.00  0.00
ATOM     29  N   PRO    11       8.515  -4.777 -21.510  1.00  0.00
ATOM     30  CA  PRO    11       8.921  -5.773 -20.483  1.00  0.00
ATOM     31  C   PRO    11       9.877  -4.800 -19.810  1.00  0.00
ATOM     32  O   PRO    11       9.138  -3.789 -19.774  1.00  0.00
ATOM     33  N   PHE    12      11.093  -4.601 -19.478  1.00  0.00
ATOM     34  CA  PHE    12      11.665  -3.459 -18.779  1.00  0.00
ATOM     35  C   PHE    12      10.588  -2.844 -17.882  1.00  0.00
ATOM     36  O   PHE    12       9.481  -2.466 -18.095  1.00  0.00
ATOM     37  N   THR    13      11.122  -2.903 -16.696  1.00  0.00
ATOM     38  CA  THR    13      10.499  -2.536 -15.495  1.00  0.00
ATOM     39  C   THR    13      10.990  -1.251 -14.943  1.00  0.00
ATOM     40  O   THR    13      12.073  -1.226 -14.375  1.00  0.00
ATOM     41  N   ARG    14      10.309  -0.127 -14.991  1.00  0.00
ATOM     42  CA  ARG    14      10.976   0.897 -14.289  1.00  0.00
ATOM     43  C   ARG    14      10.760   1.349 -12.910  1.00  0.00
ATOM     44  O   ARG    14      11.807   1.701 -12.425  1.00  0.00
ATOM     45  N   ARG    15       9.715   1.657 -12.233  1.00  0.00
ATOM     46  CA  ARG    15       9.700   1.963 -10.816  1.00  0.00
ATOM     47  C   ARG    15       8.632   1.082 -10.159  1.00  0.00
ATOM     48  O   ARG    15       7.866   0.843 -11.138  1.00  0.00
ATOM     49  N   GLN    16       8.606   0.809  -8.859  1.00  0.00
ATOM     50  CA  GLN    16       7.546   0.032  -8.290  1.00  0.00
ATOM     51  C   GLN    16       7.484   0.189  -6.815  1.00  0.00
ATOM     52  O   GLN    16       7.923   1.332  -6.711  1.00  0.00
ATOM     53  N   ALA    17       6.631  -0.367  -5.946  1.00  0.00
ATOM     54  CA  ALA    17       6.481   0.411  -4.624  1.00  0.00
ATOM     55  C   ALA    17       7.171  -0.592  -3.735  1.00  0.00
ATOM     56  O   ALA    17       7.714  -0.583  -2.598  1.00  0.00
ATOM     57  N   GLN    18       7.311  -1.764  -4.441  1.00  0.00
ATOM     58  CA  GLN    18       7.981  -2.913  -3.832  1.00  0.00
ATOM     59  C   GLN    18       7.071  -3.316  -2.668  1.00  0.00
ATOM     60  O   GLN    18       7.441  -3.578  -1.506  1.00  0.00
ATOM     61  N   ALA    19       5.785  -3.276  -2.943  1.00  0.00
ATOM     62  CA  ALA    19       4.952  -3.447  -1.768  1.00  0.00
ATOM     63  C   ALA    19       4.354  -4.778  -2.126  1.00  0.00
ATOM     64  O   ALA    19       3.080  -4.792  -2.043  1.00  0.00
ATOM     65  N   VAL    20       5.063  -5.882  -2.474  1.00  0.00
ATOM     66  CA  VAL    20       4.186  -7.047  -2.720  1.00  0.00
ATOM     67  C   VAL    20       3.990  -8.166  -1.746  1.00  0.00
ATOM     68  O   VAL    20       4.032  -8.235  -0.539  1.00  0.00
ATOM     69  N   THR    21       3.145  -8.995  -2.305  1.00  0.00
ATOM     70  CA  THR    21       2.466 -10.222  -1.972  1.00  0.00
ATOM     71  C   THR    21       1.230 -10.125  -1.136  1.00  0.00
ATOM     72  O   THR    21       1.194 -10.618  -0.032  1.00  0.00
ATOM     73  N   THR    22       0.212  -9.428  -1.545  1.00  0.00
ATOM     74  CA  THR    22      -0.879  -9.408  -0.567  1.00  0.00
ATOM     75  C   THR    22      -2.073  -9.297  -1.473  1.00  0.00
ATOM     76  O   THR    22      -1.916  -9.974  -2.536  1.00  0.00
ATOM     77  N   THR    23      -3.316  -9.016  -1.057  1.00  0.00
ATOM     78  CA  THR    23      -4.441  -8.917  -1.867  1.00  0.00
ATOM     79  C   THR    23      -5.596  -7.915  -1.507  1.00  0.00
ATOM     80  O   THR    23      -6.144  -7.232  -0.635  1.00  0.00
ATOM     81  N   TYR    24      -5.835  -7.557  -2.818  1.00  0.00
ATOM     82  CA  TYR    24      -6.803  -6.802  -3.425  1.00  0.00
ATOM     83  C   TYR    24      -6.478  -5.397  -3.084  1.00  0.00
ATOM     84  O   TYR    24      -7.387  -4.678  -2.708  1.00  0.00
ATOM     85  N   SER    25      -5.192  -5.097  -3.251  1.00  0.00
ATOM     86  CA  SER    25      -4.737  -3.697  -2.879  1.00  0.00
ATOM     87  C   SER    25      -5.281  -2.885  -4.024  1.00  0.00
ATOM     88  O   SER    25      -5.503  -3.389  -5.168  1.00  0.00
ATOM     89  N   ASN    26      -5.866  -1.725  -3.847  1.00  0.00
ATOM     90  CA  ASN    26      -6.260  -0.987  -5.032  1.00  0.00
ATOM     91  C   ASN    26      -5.428   0.306  -4.715  1.00  0.00
ATOM     92  O   ASN    26      -5.134   0.418  -3.540  1.00  0.00
ATOM     93  N   ILE    27      -5.183   1.013  -5.794  1.00  0.00
ATOM     94  CA  ILE    27      -4.489   2.242  -5.918  1.00  0.00
ATOM     95  C   ILE    27      -5.346   3.467  -5.932  1.00  0.00
ATOM     96  O   ILE    27      -4.781   4.146  -4.933  1.00  0.00
ATOM     97  N   THR    28      -6.428   4.184  -6.121  1.00  0.00
ATOM     98  CA  THR    28      -6.695   5.489  -5.474  1.00  0.00
ATOM     99  C   THR    28      -5.910   6.756  -5.094  1.00  0.00
ATOM    100  O   THR    28      -4.958   6.746  -4.346  1.00  0.00
ATOM    101  N   LEU    29      -6.575   7.917  -5.512  1.00  0.00
ATOM    102  CA  LEU    29      -5.843   9.120  -5.161  1.00  0.00
ATOM    103  C   LEU    29      -6.467  10.019  -4.227  1.00  0.00
ATOM    104  O   LEU    29      -7.381  10.633  -4.626  1.00  0.00
ATOM    105  N   GLU    30      -5.655  10.648  -3.359  1.00  0.00
ATOM    106  CA  GLU    30      -6.272  11.590  -2.494  1.00  0.00
ATOM    107  C   GLU    30      -6.538  12.975  -2.580  1.00  0.00
ATOM    108  O   GLU    30      -6.863  13.174  -3.732  1.00  0.00
ATOM    109  N   ASP    31      -6.779  13.795  -1.595  1.00  0.00
ATOM    110  CA  ASP    31      -7.335  15.060  -1.773  1.00  0.00
ATOM    111  C   ASP    31      -6.342  16.058  -1.263  1.00  0.00
ATOM    112  O   ASP    31      -6.624  17.218  -0.914  1.00  0.00
ATOM    113  N   ASP    32      -5.218  15.473  -0.902  1.00  0.00
ATOM    114  CA  ASP    32      -4.253  16.326  -0.140  1.00  0.00
ATOM    115  C   ASP    32      -3.114  15.698  -0.885  1.00  0.00
ATOM    116  O   ASP    32      -2.126  15.249  -0.475  1.00  0.00
ATOM    117  N   PHE    37      -3.347  15.371  -2.141  1.00  0.00
ATOM    118  CA  PHE    37      -2.397  14.866  -3.018  1.00  0.00
ATOM    119  C   PHE    37      -1.892  13.515  -2.557  1.00  0.00
ATOM    120  O   PHE    37      -0.902  13.304  -3.122  1.00  0.00
ATOM    121  N   ARG    38      -2.338  12.669  -1.626  1.00  0.00
ATOM    122  CA  ARG    38      -1.427  11.494  -1.606  1.00  0.00
ATOM    123  C   ARG    38      -1.813  10.424  -2.573  1.00  0.00
ATOM    124  O   ARG    38      -2.974  10.168  -2.630  1.00  0.00
ATOM    125  N   LEU    39      -0.959   9.607  -3.062  1.00  0.00
ATOM    126  CA  LEU    39      -1.378   8.493  -3.878  1.00  0.00
ATOM    127  C   LEU    39      -1.132   7.396  -2.922  1.00  0.00
ATOM    128  O   LEU    39      -0.302   7.786  -2.274  1.00  0.00
ATOM    129  N   VAL    40      -1.805   6.496  -2.371  1.00  0.00
ATOM    130  CA  VAL    40      -2.081   5.435  -1.536  1.00  0.00
ATOM    131  C   VAL    40      -2.774   4.236  -2.229  1.00  0.00
ATOM    132  O   VAL    40      -3.722   4.484  -2.881  1.00  0.00
ATOM    133  N   VAL    41      -2.099   3.135  -1.939  1.00  0.00
ATOM    134  CA  VAL    41      -2.375   1.768  -2.034  1.00  0.00
ATOM    135  C   VAL    41      -2.873   1.240  -0.786  1.00  0.00
ATOM    136  O   VAL    41      -2.357   0.754   0.178  1.00  0.00
ATOM    137  N   ARG    42      -4.163   1.071  -0.729  1.00  0.00
ATOM    138  CA  ARG    42      -5.245   0.751   0.083  1.00  0.00
ATOM    139  C   ARG    42      -5.510  -0.685  -0.189  1.00  0.00
ATOM    140  O   ARG    42      -5.336  -1.434  -1.141  1.00  0.00
ATOM    141  N   ASP    43      -5.739  -0.963   1.085  1.00  0.00
ATOM    142  CA  ASP    43      -5.966  -2.390   1.224  1.00  0.00
ATOM    143  C   ASP    43      -7.419  -2.792   1.141  1.00  0.00
ATOM    144  O   ASP    43      -8.022  -2.339   2.036  1.00  0.00
ATOM    145  N   THR    44      -7.717  -3.939   0.660  1.00  0.00
ATOM    146  CA  THR    44      -8.692  -4.952   0.817  1.00  0.00
ATOM    147  C   THR    44      -9.488  -4.765   2.121  1.00  0.00
ATOM    148  O   THR    44     -10.733  -4.735   2.162  1.00  0.00
ATOM    149  N   GLU    45      -8.826  -4.298   3.199  1.00  0.00
ATOM    150  CA  GLU    45      -9.753  -3.970   4.245  1.00  0.00
ATOM    151  C   GLU    45      -9.519  -2.600   4.714  1.00  0.00
ATOM    152  O   GLU    45      -9.536  -2.454   5.947  1.00  0.00
ATOM    153  N   GLY    46      -9.138  -1.706   3.865  1.00  0.00
ATOM    154  CA  GLY    46      -9.055  -0.329   4.165  1.00  0.00
ATOM    155  C   GLY    46      -7.766   0.022   4.902  1.00  0.00
ATOM    156  O   GLY    46      -7.457   1.246   5.204  1.00  0.00
ATOM    157  N   ARG    47      -6.760  -0.847   4.857  1.00  0.00
ATOM    158  CA  ARG    47      -5.574  -0.415   5.393  1.00  0.00
ATOM    159  C   ARG    47      -4.443   0.046   4.546  1.00  0.00
ATOM    160  O   ARG    47      -3.540  -0.878   4.677  1.00  0.00
ATOM    161  N   MET    48      -3.981   1.283   4.288  1.00  0.00
ATOM    162  CA  MET    48      -2.721   1.707   3.632  1.00  0.00
ATOM    163  C   MET    48      -1.529   0.882   3.323  1.00  0.00
ATOM    164  O   MET    48      -0.501   1.025   3.927  1.00  0.00
ATOM    165  N   VAL    49      -1.263   0.039   2.287  1.00  0.00
ATOM    166  CA  VAL    49       0.006  -0.744   2.222  1.00  0.00
ATOM    167  C   VAL    49       1.237   0.099   2.051  1.00  0.00
ATOM    168  O   VAL    49       2.317  -0.397   1.921  1.00  0.00
ATOM    169  N   TRP    50       1.219   1.324   1.681  1.00  0.00
ATOM    170  CA  TRP    50       2.149   2.213   1.109  1.00  0.00
ATOM    171  C   TRP    50       1.572   3.578   0.815  1.00  0.00
ATOM    172  O   TRP    50       0.547   3.348   0.190  1.00  0.00
ATOM    173  N   ARG    51       2.174   4.712   1.064  1.00  0.00
ATOM    174  CA  ARG    51       1.762   6.057   0.789  1.00  0.00
ATOM    175  C   ARG    51       2.842   6.584  -0.191  1.00  0.00
ATOM    176  O   ARG    51       3.697   5.891  -0.769  1.00  0.00
ATOM    177  N   ALA    52       2.672   7.825  -0.459  1.00  0.00
ATOM    178  CA  ALA    52       3.585   8.636  -1.228  1.00  0.00
ATOM    179  C   ALA    52       4.069   9.666  -0.244  1.00  0.00
ATOM    180  O   ALA    52       5.241   9.762  -0.447  1.00  0.00
ATOM    181  N   ASN    54       3.768  10.615   0.540  1.00  0.00
ATOM    182  CA  ASN    54       4.451  11.119   1.697  1.00  0.00
ATOM    183  C   ASN    54       4.447  12.612   1.746  1.00  0.00
ATOM    184  O   ASN    54       4.800  13.441   2.580  1.00  0.00
ATOM    185  N   PHE    55       3.885  12.839   0.554  1.00  0.00
ATOM    186  CA  PHE    55       3.981  14.329   0.424  1.00  0.00
ATOM    187  C   PHE    55       2.593  14.755   0.453  1.00  0.00
ATOM    188  O   PHE    55       2.020  13.921  -0.126  1.00  0.00
ATOM    189  N   GLU    56       2.202  15.857   0.748  1.00  0.00
ATOM    190  CA  GLU    56       0.790  16.007   0.891  1.00  0.00
ATOM    191  C   GLU    56       0.597  17.464   0.563  1.00  0.00
ATOM    192  O   GLU    56       1.637  18.101   0.660  1.00  0.00
ATOM    193  N   PRO    57      -0.625  17.934   0.234  1.00  0.00
ATOM    194  CA  PRO    57      -0.753  19.294  -0.052  1.00  0.00
ATOM    195  C   PRO    57      -1.969  19.925   0.561  1.00  0.00
ATOM    196  O   PRO    57      -2.340  19.775   1.823  1.00  0.00
ATOM    197  N   ASP    58      -2.582  20.506  -0.482  1.00  0.00
ATOM    198  CA  ASP    58      -3.755  21.339  -0.151  1.00  0.00
ATOM    199  C   ASP    58      -5.208  21.072  -0.374  1.00  0.00
ATOM    200  O   ASP    58      -5.250  19.875   0.110  1.00  0.00
ATOM    201  N   ALA    59      -6.406  21.745  -0.750  1.00  0.00
ATOM    202  CA  ALA    59      -7.378  20.738  -0.574  1.00  0.00
ATOM    203  C   ALA    59      -7.769  20.076  -1.753  1.00  0.00
ATOM    204  O   ALA    59      -7.307  18.949  -2.122  1.00  0.00
ATOM    205  N   GLY    60      -8.302  20.526  -2.774  1.00  0.00
ATOM    206  CA  GLY    60      -8.450  19.685  -3.900  1.00  0.00
ATOM    207  C   GLY    60      -8.253  18.411  -4.536  1.00  0.00
ATOM    208  O   GLY    60      -8.242  17.131  -4.533  1.00  0.00
TER
END
