
#######################################################
#                                                     #
#                        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 T0363TS035_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS035_2-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          5.283
LGA    Q      12      Q      12          3.651
LGA    I      13      I      13          2.422
LGA    N      14      N      14          0.437
LGA    I      15      I      15          1.012
LGA    E      16      E      16          1.678
LGA    I      17      I      17          3.110
LGA    A      18      A      18          2.555
LGA    Y      19      Y      19          2.750
LGA    A      20      A      20          2.735
LGA    F      21      F      21          4.219
LGA    P      22      -       -           -
LGA    E      23      P      22          2.090
LGA    R      24      E      23          1.994
LGA    Y      25      R      24          2.537
LGA    Y      26      Y      25          4.456
LGA    L      27      Y      26          2.082
LGA    K      28      L      27          4.139
LGA    S      29      K      28          1.257
LGA    F      30      S      29          4.649
LGA    Q      31      F      30          1.907
LGA    V      32      Q      31          5.085
LGA    D      33      V      32          2.061
LGA    -       -      D      33           -
LGA    E      34      E      34          1.807
LGA    G      35      G      35          2.280
LGA    I      36      I      36          1.719
LGA    T      37      T      37          2.138
LGA    V      38      V      38          2.661
LGA    Q      39      Q      39          2.136
LGA    T      40      T      40          2.028
LGA    A      41      A      41          2.802
LGA    I      42      I      42          2.639
LGA    T      43      T      43          2.153
LGA    Q      44      Q      44          2.600
LGA    S      45      S      45          3.044
LGA    G      46      G      46          1.720
LGA    I      47      I      47          1.370
LGA    L      48      L      48          1.245
LGA    S      49      S      49          1.665
LGA    Q      50      Q      50          1.248
LGA    F      51      F      51          1.522
LGA    P      52      P      52          2.975
LGA    E      53      E      53          3.480
LGA    I      54      I      54          4.383
LGA    -       -      D      55           -
LGA    D      55      L      56           #
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     43    2.79    76.74     63.654     1.490

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.518338 * X  +  -0.688141 * Y  +  -0.507729 * Z  +  26.336020
  Y_new =   0.529783 * X  +  -0.724452 * Y  +   0.441021 * Z  +  17.531185
  Z_new =  -0.671309 * X  +  -0.040388 * Y  +   0.740076 * Z  +   4.715477 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.054519    3.087074  [ DEG:    -3.1237    176.8763 ]
  Theta =   0.735974    2.405619  [ DEG:    42.1682    137.8318 ]
  Phi   =   2.345275   -0.796317  [ DEG:   134.3744    -45.6256 ]
 
# 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: T0363TS035_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS035_2-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   43   2.79   76.74  63.654
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS035_2-D1
PFRMAT TS
TARGET T0363
MODEL  2  REFINED
PARENT N/A
ATOM     41  N   ASN    11      12.096   3.351  14.303  1.00  0.00
ATOM     42  CA  ASN    11      12.557   2.843  13.025  1.00  0.00
ATOM     43  C   ASN    11      13.777   3.602  12.529  1.00  0.00
ATOM     44  O   ASN    11      14.449   4.293  13.292  1.00  0.00
ATOM     45  N   GLN    12      14.088   3.490  11.241  1.00  0.00
ATOM     46  CA  GLN    12      15.287   4.122  10.727  1.00  0.00
ATOM     47  C   GLN    12      14.960   5.359   9.907  1.00  0.00
ATOM     48  O   GLN    12      14.016   5.367   9.118  1.00  0.00
ATOM     49  N   ILE    13      15.731   6.429  10.076  1.00  0.00
ATOM     50  CA  ILE    13      15.460   7.644   9.329  1.00  0.00
ATOM     51  C   ILE    13      16.584   7.966   8.358  1.00  0.00
ATOM     52  O   ILE    13      17.756   8.002   8.732  1.00  0.00
ATOM     53  N   ASN    14      16.252   8.207   7.094  1.00  0.00
ATOM     54  CA  ASN    14      17.283   8.501   6.117  1.00  0.00
ATOM     55  C   ASN    14      17.568   9.991   6.033  1.00  0.00
ATOM     56  O   ASN    14      16.748  10.770   5.546  1.00  0.00
ATOM     57  N   ILE    15      18.734  10.421   6.507  1.00  0.00
ATOM     58  CA  ILE    15      19.041  11.838   6.500  1.00  0.00
ATOM     59  C   ILE    15      19.778  12.244   5.234  1.00  0.00
ATOM     60  O   ILE    15      20.657  11.530   4.753  1.00  0.00
ATOM     61  N   GLU    16      19.437  13.399   4.668  1.00  0.00
ATOM     62  CA  GLU    16      20.140  13.864   3.489  1.00  0.00
ATOM     63  C   GLU    16      20.448  15.350   3.570  1.00  0.00
ATOM     64  O   GLU    16      19.547  16.187   3.569  1.00  0.00
ATOM     65  N   ILE    17      21.726  15.710   3.644  1.00  0.00
ATOM     66  CA  ILE    17      22.079  17.108   3.785  1.00  0.00
ATOM     67  C   ILE    17      23.036  17.557   2.691  1.00  0.00
ATOM     68  O   ILE    17      24.054  16.915   2.434  1.00  0.00
ATOM     69  N   ALA    18      22.731  18.668   2.027  1.00  0.00
ATOM     70  CA  ALA    18      23.619  19.160   0.992  1.00  0.00
ATOM     71  C   ALA    18      24.204  20.516   1.354  1.00  0.00
ATOM     72  O   ALA    18      23.587  21.303   2.069  1.00  0.00
ATOM     73  N   TYR    19      25.406  20.815   0.869  1.00  0.00
ATOM     74  CA  TYR    19      26.017  22.092   1.186  1.00  0.00
ATOM     75  C   TYR    19      26.214  22.942  -0.059  1.00  0.00
ATOM     76  O   TYR    19      26.630  22.449  -1.106  1.00  0.00
ATOM     77  N   ALA    20      25.918  24.236   0.029  1.00  0.00
ATOM     78  CA  ALA    20      26.145  25.110  -1.106  1.00  0.00
ATOM     79  C   ALA    20      27.016  26.298  -0.730  1.00  0.00
ATOM     80  O   ALA    20      26.538  27.284  -0.172  1.00  0.00
ATOM     81  N   PHE    21      28.310  26.231  -1.029  1.00  0.00
ATOM     82  CA  PHE    21      29.199  27.313  -0.654  1.00  0.00
ATOM     83  C   PHE    21      29.152  28.451  -1.661  1.00  0.00
ATOM     84  O   PHE    21      28.699  28.279  -2.792  1.00  0.00
ATOM     85  N   PRO    22      29.617  29.635  -1.273  1.00  0.00
ATOM     86  CA  PRO    22      29.575  30.763  -2.183  1.00  0.00
ATOM     87  C   PRO    22      30.320  30.469  -3.474  1.00  0.00
ATOM     88  O   PRO    22      30.040  31.059  -4.518  1.00  0.00
ATOM     89  N   GLU    23      31.285  29.555  -3.433  1.00  0.00
ATOM     90  CA  GLU    23      32.056  29.260  -4.625  1.00  0.00
ATOM     91  C   GLU    23      31.388  28.191  -5.474  1.00  0.00
ATOM     92  O   GLU    23      31.756  27.974  -6.627  1.00  0.00
ATOM     93  N   ARG    24      30.393  27.502  -4.922  1.00  0.00
ATOM     94  CA  ARG    24      29.713  26.473  -5.686  1.00  0.00
ATOM     95  C   ARG    24      29.339  25.285  -4.815  1.00  0.00
ATOM     96  O   ARG    24      29.341  25.371  -3.588  1.00  0.00
ATOM     97  N   TYR    25      29.011  24.152  -5.429  1.00  0.00
ATOM     98  CA  TYR    25      28.639  22.986  -4.651  1.00  0.00
ATOM     99  C   TYR    25      29.603  21.833  -4.874  1.00  0.00
ATOM    100  O   TYR    25      29.978  21.527  -6.004  1.00  0.00
ATOM    101  N   TYR    26      30.024  21.170  -3.801  1.00  0.00
ATOM    102  CA  TYR    26      30.953  20.065  -3.951  1.00  0.00
ATOM    103  C   TYR    26      30.383  18.774  -3.386  1.00  0.00
ATOM    104  O   TYR    26      30.755  17.679  -3.804  1.00  0.00
ATOM    105  N   LEU    27      29.470  18.876  -2.424  1.00  0.00
ATOM    106  CA  LEU    27      28.917  17.678  -1.819  1.00  0.00
ATOM    107  C   LEU    27      27.638  17.240  -2.513  1.00  0.00
ATOM    108  O   LEU    27      26.693  18.015  -2.653  1.00  0.00
ATOM    109  N   LYS    28      27.580  15.989  -2.962  1.00  0.00
ATOM    110  CA  LYS    28      26.375  15.505  -3.606  1.00  0.00
ATOM    111  C   LYS    28      25.293  15.173  -2.591  1.00  0.00
ATOM    112  O   LYS    28      24.155  15.625  -2.705  1.00  0.00
ATOM    113  N   SER    29      25.624  14.376  -1.579  1.00  0.00
ATOM    114  CA  SER    29      24.635  14.027  -0.579  1.00  0.00
ATOM    115  C   SER    29      25.281  13.433   0.663  1.00  0.00
ATOM    116  O   SER    29      26.431  12.996   0.634  1.00  0.00
ATOM    117  N   PHE    30      24.557  13.405   1.778  1.00  0.00
ATOM    118  CA  PHE    30      25.058  12.712   2.950  1.00  0.00
ATOM    119  C   PHE    30      24.034  11.731   3.500  1.00  0.00
ATOM    120  O   PHE    30      23.341  12.016   4.475  1.00  0.00
ATOM    121  N   GLN    31      23.919  10.556   2.887  1.00  0.00
ATOM    122  CA  GLN    31      23.016   9.551   3.411  1.00  0.00
ATOM    123  C   GLN    31      23.590   8.870   4.643  1.00  0.00
ATOM    124  O   GLN    31      24.783   8.581   4.710  1.00  0.00
ATOM    125  N   VAL    32      22.754   8.601   5.641  1.00  0.00
ATOM    126  CA  VAL    32      23.265   8.078   6.893  1.00  0.00
ATOM    127  C   VAL    32      22.335   7.031   7.483  1.00  0.00
ATOM    128  O   VAL    32      21.124   7.062   7.268  1.00  0.00
ATOM    129  N   ASP    33      22.879   6.082   8.241  1.00  0.00
ATOM    130  CA  ASP    33      22.031   5.141   8.945  1.00  0.00
ATOM    131  C   ASP    33      21.749   5.596  10.367  1.00  0.00
ATOM    132  O   ASP    33      22.542   6.314  10.974  1.00  0.00
ATOM    133  N   GLU    34      20.613   5.190  10.927  1.00  0.00
ATOM    134  CA  GLU    34      20.314   5.548  12.300  1.00  0.00
ATOM    135  C   GLU    34      21.325   4.953  13.267  1.00  0.00
ATOM    136  O   GLU    34      21.390   5.337  14.434  1.00  0.00
ATOM    137  N   GLY    35      22.134   4.006  12.803  1.00  0.00
ATOM    138  CA  GLY    35      23.103   3.384  13.684  1.00  0.00
ATOM    139  C   GLY    35      24.527   3.625  13.212  1.00  0.00
ATOM    140  O   GLY    35      25.429   2.835  13.482  1.00  0.00
ATOM    141  N   ILE    36      24.758   4.723  12.498  1.00  0.00
ATOM    142  CA  ILE    36      26.118   5.096  12.162  1.00  0.00
ATOM    143  C   ILE    36      26.407   6.545  12.519  1.00  0.00
ATOM    144  O   ILE    36      25.558   7.420  12.357  1.00  0.00
ATOM    145  N   THR    37      27.609   6.828  13.014  1.00  0.00
ATOM    146  CA  THR    37      28.002   8.209  13.218  1.00  0.00
ATOM    147  C   THR    37      28.117   8.958  11.899  1.00  0.00
ATOM    148  O   THR    37      28.492   8.387  10.876  1.00  0.00
ATOM    149  N   VAL    38      27.799  10.248  11.897  1.00  0.00
ATOM    150  CA  VAL    38      27.897  11.017  10.671  1.00  0.00
ATOM    151  C   VAL    38      29.309  10.996  10.108  1.00  0.00
ATOM    152  O   VAL    38      29.513  10.793   8.912  1.00  0.00
ATOM    153  N   GLN    39      30.311  11.203  10.957  1.00  0.00
ATOM    154  CA  GLN    39      31.677  11.241  10.470  1.00  0.00
ATOM    155  C   GLN    39      32.085   9.917   9.846  1.00  0.00
ATOM    156  O   GLN    39      32.756   9.879   8.815  1.00  0.00
ATOM    157  N   THR    40      31.690   8.803  10.457  1.00  0.00
ATOM    158  CA  THR    40      32.021   7.510   9.889  1.00  0.00
ATOM    159  C   THR    40      31.471   7.360   8.481  1.00  0.00
ATOM    160  O   THR    40      32.166   6.908   7.572  1.00  0.00
ATOM    161  N   ALA    41      30.212   7.735   8.270  1.00  0.00
ATOM    162  CA  ALA    41      29.619   7.577   6.956  1.00  0.00
ATOM    163  C   ALA    41      30.304   8.456   5.922  1.00  0.00
ATOM    164  O   ALA    41      30.586   8.023   4.806  1.00  0.00
ATOM    165  N   ILE    42      30.586   9.708   6.272  1.00  0.00
ATOM    166  CA  ILE    42      31.236  10.596   5.327  1.00  0.00
ATOM    167  C   ILE    42      32.607  10.079   4.924  1.00  0.00
ATOM    168  O   ILE    42      32.969  10.087   3.749  1.00  0.00
ATOM    169  N   THR    43      33.398   9.620   5.890  1.00  0.00
ATOM    170  CA  THR    43      34.726   9.135   5.570  1.00  0.00
ATOM    171  C   THR    43      34.672   7.865   4.736  1.00  0.00
ATOM    172  O   THR    43      35.363   7.739   3.726  1.00  0.00
ATOM    173  N   GLN    44      33.853   6.899   5.142  1.00  0.00
ATOM    174  CA  GLN    44      33.772   5.657   4.397  1.00  0.00
ATOM    175  C   GLN    44      33.284   5.888   2.976  1.00  0.00
ATOM    176  O   GLN    44      33.730   5.230   2.036  1.00  0.00
ATOM    177  N   SER    45      32.360   6.825   2.789  1.00  0.00
ATOM    178  CA  SER    45      31.852   7.086   1.455  1.00  0.00
ATOM    179  C   SER    45      32.857   7.855   0.615  1.00  0.00
ATOM    180  O   SER    45      32.763   7.893  -0.611  1.00  0.00
ATOM    181  N   GLY    46      33.838   8.486   1.254  1.00  0.00
ATOM    182  CA  GLY    46      34.820   9.246   0.506  1.00  0.00
ATOM    183  C   GLY    46      34.448  10.719   0.430  1.00  0.00
ATOM    184  O   GLY    46      35.140  11.516  -0.202  1.00  0.00
ATOM    185  N   ILE    47      33.351  11.109   1.070  1.00  0.00
ATOM    186  CA  ILE    47      32.957  12.504   1.051  1.00  0.00
ATOM    187  C   ILE    47      33.968  13.380   1.771  1.00  0.00
ATOM    188  O   ILE    47      34.367  14.432   1.272  1.00  0.00
ATOM    189  N   LEU    48      34.404  12.968   2.959  1.00  0.00
ATOM    190  CA  LEU    48      35.376  13.758   3.688  1.00  0.00
ATOM    191  C   LEU    48      36.666  13.925   2.901  1.00  0.00
ATOM    192  O   LEU    48      37.291  14.984   2.925  1.00  0.00
ATOM    193  N   SER    49      37.090  12.885   2.189  1.00  0.00
ATOM    194  CA  SER    49      38.301  12.993   1.398  1.00  0.00
ATOM    195  C   SER    49      38.153  14.016   0.283  1.00  0.00
ATOM    196  O   SER    49      39.041  14.834   0.050  1.00  0.00
ATOM    197  N   GLN    50      37.030  13.991  -0.427  1.00  0.00
ATOM    198  CA  GLN    50      36.836  14.933  -1.512  1.00  0.00
ATOM    199  C   GLN    50      36.691  16.355  -0.999  1.00  0.00
ATOM    200  O   GLN    50      37.112  17.312  -1.648  1.00  0.00
ATOM    201  N   PHE    51      36.090  16.526   0.176  1.00  0.00
ATOM    202  CA  PHE    51      35.827  17.864   0.668  1.00  0.00
ATOM    203  C   PHE    51      36.376  18.062   2.072  1.00  0.00
ATOM    204  O   PHE    51      35.628  18.099   3.047  1.00  0.00
ATOM    205  N   PRO    52      37.693  18.194   2.203  1.00  0.00
ATOM    206  CA  PRO    52      38.275  18.381   3.519  1.00  0.00
ATOM    207  C   PRO    52      37.868  19.713   4.126  1.00  0.00
ATOM    208  O   PRO    52      38.044  19.946   5.321  1.00  0.00
ATOM    209  N   GLU    53      37.314  20.613   3.319  1.00  0.00
ATOM    210  CA  GLU    53      36.876  21.889   3.848  1.00  0.00
ATOM    211  C   GLU    53      35.387  21.886   4.156  1.00  0.00
ATOM    212  O   GLU    53      34.874  22.785   4.821  1.00  0.00
ATOM    213  N   ILE    54      34.663  20.878   3.679  1.00  0.00
ATOM    214  CA  ILE    54      33.239  20.819   3.942  1.00  0.00
ATOM    215  C   ILE    54      32.948  20.253   5.323  1.00  0.00
ATOM    216  O   ILE    54      33.257  19.099   5.615  1.00  0.00
ATOM    217  N   ASP    55      32.346  21.052   6.200  1.00  0.00
ATOM    218  CA  ASP    55      32.233  20.649   7.588  1.00  0.00
ATOM    219  C   ASP    55      30.793  20.342   7.966  1.00  0.00
ATOM    220  O   ASP    55      29.972  21.243   8.128  1.00  0.00
ATOM    221  N   LEU    56      30.457  19.063   8.114  1.00  0.00
ATOM    222  CA  LEU    56      29.111  18.710   8.523  1.00  0.00
ATOM    223  C   LEU    56      28.841  19.114   9.963  1.00  0.00
ATOM    224  O   LEU    56      27.735  19.526  10.310  1.00  0.00
TER
END
