
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS393_2
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS393_2.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    E       2      -       -           -
LGA    I       3      -       -           -
LGA    Q       4      M       1           #
LGA    E       5      E       2          4.573
LGA    I       6      I       3          1.693
LGA    S       7      -       -           -
LGA    K       8      Q       4          1.372
LGA    L       9      E       5          0.871
LGA    A      10      I       6          1.202
LGA    I      11      S       7          1.964
LGA    E      12      K       8          1.754
LGA    A      13      L       9          1.837
LGA    L      14      A      10          3.236
LGA    E      15      I      11          4.282
LGA    D      16      E      12          4.500
LGA    I      17      A      13          4.747
LGA    K      18      L      14          4.786
LGA    G      19      E      15          2.124
LGA    K      20      D      16          5.333
LGA    D      21      I      17          1.968
LGA    I      22      K      18          3.936
LGA    I      23      G      19          3.476
LGA    E      24      K      20           -
LGA    L      25      D      21           -
LGA    D      26      I      22           -
LGA    T      27      -       -           -
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    T      31      -       -           -
LGA    S      32      -       -           -
LGA    L      33      I      23           #
LGA    F      34      E      24          4.709
LGA    Q      35      L      25           #
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      M      37           -
LGA    R      36      I      38          0.864
LGA    M      37      V      39          1.190
LGA    I      38      A      40           #
LGA    V      39      T      41           #
LGA    A      40      G      42           #
LGA    T      41      -       -           -
LGA    G      42      -       -           -
LGA    D      43      D      43           #
LGA    S      44      S      44          2.592
LGA    N      45      N      45          1.406
LGA    R      46      R      46          0.982
LGA    Q      47      Q      47          0.805
LGA    V      48      V      48          0.364
LGA    K      49      K      49          0.864
LGA    A      50      A      50          0.701
LGA    L      51      L      51          0.375
LGA    A      52      A      52          0.834
LGA    N      53      N      53          0.929
LGA    S      54      S      54          0.589
LGA    V      55      V      55          1.210
LGA    Q      56      Q      56          1.584
LGA    V      57      V      57          0.543
LGA    K      58      K      58          1.581
LGA    L      59      L      59          2.634
LGA    K      60      K      60          1.905
LGA    E      61      E      61          1.418
LGA    A      62      A      62          1.774
LGA    G      63      G      63          1.591
LGA    V      64      V      64          2.079
LGA    D      65      D      65          2.394
LGA    I      66      I      66          2.955
LGA    -       -      V      67           -
LGA    V      67      G      68          4.115
LGA    G      68      S      69          2.815
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    S      69      V      78          3.245
LGA    E      70      L      79           #
LGA    G      71      V      80           -
LGA    -       -      D      81           -
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    H      72      Y      97           #
LGA    E      73      Y      98          5.042
LGA    S      74      D      99          3.852
LGA    G      75      I     100          1.553
LGA    E      76      E     101          3.611
LGA    W      77      A     102          4.392
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    V      78      K     108          2.660
LGA    L      79      P     109          2.857
LGA    V      80      S     110           #
LGA    D      81      F     111          3.813
LGA    -       -      A     112           -
LGA    A      82      V     113           #
LGA    G      83      G     114           -
LGA    D      84      A     115           -
LGA    V      85      A     116           -
LGA    V      86      K     117           -
LGA    V      87      -       -           -
LGA    H      88      -       -           -
LGA    V      89      P     118          4.913
LGA    M      90      W     119           #
LGA    L      91      S     120          4.891
LGA    P      92      A     121           -
LGA    A      93      V     122           -
LGA    V      94      -       -           -
LGA    R      95      -       -           -
LGA    D      96      -       -           -
LGA    Y      97      -       -           -
LGA    Y      98      -       -           -
LGA    D      99      -       -           -
LGA    I     100      -       -           -
LGA    E     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    W     104      -       -           -
LGA    G     105      -       -           -
LGA    G     106      -       -           -
LGA    Q     107      -       -           -
LGA    K     108      -       -           -
LGA    P     109      -       -           -
LGA    S     110      -       -           -
LGA    F     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    G     114      -       -           -
LGA    A     115      -       -           -
LGA    A     116      -       -           -
LGA    K     117      -       -           -
LGA    P     118      -       -           -
LGA    W     119      -       -           -
LGA    S     120      -       -           -
LGA    A     121      -       -           -
LGA    V     122      -       -           -
LGA    L     123      -       -           -
LGA    E     124      -       -           -
LGA    H     125      -       -           -
LGA    H     126      -       -           -
LGA    H     127      -       -           -
LGA    H     128      -       -           -
LGA    H     129      -       -           -
LGA    H     130      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     57    2.86    45.61     30.935     1.924

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.393412 * X  +  -0.916038 * Y  +  -0.078112 * Z  +  42.560925
  Y_new =   0.061070 * X  +  -0.058737 * Y  +   0.996404 * Z  +  31.574207
  Z_new =  -0.917332 * X  +  -0.396768 * Y  +   0.032834 * Z  +  21.747328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.488230    1.653362  [ DEG:   -85.2693     94.7307 ]
  Theta =   1.161325    1.980267  [ DEG:    66.5390    113.4610 ]
  Phi   =   0.154001   -2.987591  [ DEG:     8.8236   -171.1764 ]
 
# 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: T0354TS393_2                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS393_2.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   57   2.86   45.61  30.935
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS393_2
PFRMAT TS
TARGET T0354
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      50.585  16.239  11.530  1.00 25.00           C
ATOM      2  CA  GLU     2      51.058  19.986  10.858  1.00 25.00           C
ATOM      3  CA  ILE     3      48.625  22.412  12.494  1.00 25.00           C
ATOM      4  CA  GLN     4      47.326  19.457  14.556  1.00 25.00           C
ATOM      5  CA  GLU     5      50.858  18.799  15.882  1.00 25.00           C
ATOM      6  CA  ILE     6      51.217  22.492  16.832  1.00 25.00           C
ATOM      7  CA  SER     7      47.847  22.378  18.648  1.00 25.00           C
ATOM      8  CA  LYS     8      48.946  19.234  20.541  1.00 25.00           C
ATOM      9  CA  LEU     9      52.221  20.950  21.539  1.00 25.00           C
ATOM     10  CA  ALA    10      50.271  24.008  22.772  1.00 25.00           C
ATOM     11  CA  ILE    11      47.961  21.740  24.818  1.00 25.00           C
ATOM     12  CA  GLU    12      50.999  19.980  26.346  1.00 25.00           C
ATOM     13  CA  ALA    13      52.542  23.369  27.241  1.00 25.00           C
ATOM     14  CA  LEU    14      49.254  24.461  28.874  1.00 25.00           C
ATOM     15  CA  GLU    15      49.141  21.203  30.883  1.00 25.00           C
ATOM     16  CA  ASP    16      52.755  21.752  32.025  1.00 25.00           C
ATOM     17  CA  ILE    17      51.914  25.221  33.342  1.00 25.00           C
ATOM     18  CA  LYS    18      48.290  24.933  34.282  1.00 25.00           C
ATOM     19  CA  GLY    19      44.832  23.595  33.257  1.00 25.00           C
ATOM     20  CA  LYS    20      44.071  23.679  37.010  1.00 25.00           C
ATOM     21  CA  ASP    21      44.448  27.480  36.549  1.00 25.00           C
ATOM     22  CA  ILE    22      40.965  28.509  35.513  1.00 25.00           C
ATOM     23  CA  ILE    23      41.356  27.041  31.964  1.00 25.00           C
ATOM     24  CA  GLU    24      43.386  27.947  28.838  1.00 25.00           C
ATOM     25  CA  LEU    25      40.943  30.137  27.028  1.00 25.00           C
ATOM     26  CA  ASP    26      39.447  30.186  23.484  1.00 25.00           C
ATOM     27  CA  THR    27      39.571  30.412  19.690  1.00 25.00           C
ATOM     28  CA  SER    28      39.361  31.959  16.221  1.00 25.00           C
ATOM     29  CA  LYS    29      36.169  31.397  14.343  1.00 25.00           C
ATOM     30  CA  LEU    30      34.137  29.748  17.078  1.00 25.00           C
ATOM     31  CA  THR    31      34.294  27.029  19.771  1.00 25.00           C
ATOM     32  CA  SER    32      36.417  23.864  19.481  1.00 25.00           C
ATOM     33  CA  LEU    33      36.079  20.974  22.020  1.00 25.00           C
ATOM     34  CA  PHE    34      36.510  20.103  25.706  1.00 25.00           C
ATOM     35  CA  GLN    35      40.145  20.114  26.838  1.00 25.00           C
ATOM     36  CA  ARG    36      40.289  23.314  24.825  1.00 25.00           C
ATOM     37  CA  MET    37      37.729  25.243  26.900  1.00 25.00           C
ATOM     38  CA  ILE    38      35.036  27.435  25.383  1.00 25.00           C
ATOM     39  CA  VAL    39      34.280  31.175  25.588  1.00 25.00           C
ATOM     40  CA  ALA    40      34.663  31.294  29.418  1.00 25.00           C
ATOM     41  CA  THR    41      31.944  34.004  29.363  1.00 25.00           C
ATOM     42  CA  GLY    42      29.768  36.371  31.416  1.00 25.00           C
ATOM     43  CA  ASP    43      29.418  33.439  33.874  1.00 25.00           C
ATOM     44  CA  SER    44      32.527  32.248  35.714  1.00 25.00           C
ATOM     45  CA  ASN    45      33.530  35.914  35.432  1.00 25.00           C
ATOM     46  CA  ARG    46      36.727  36.906  37.293  1.00 25.00           C
ATOM     47  CA  GLN    47      38.070  33.337  36.938  1.00 25.00           C
ATOM     48  CA  VAL    48      37.291  33.390  33.189  1.00 25.00           C
ATOM     49  CA  LYS    49      39.102  36.747  32.835  1.00 25.00           C
ATOM     50  CA  ALA    50      42.136  35.333  34.696  1.00 25.00           C
ATOM     51  CA  LEU    51      42.154  32.273  32.392  1.00 25.00           C
ATOM     52  CA  ALA    52      41.998  34.555  29.321  1.00 25.00           C
ATOM     53  CA  ASN    53      44.917  36.628  30.680  1.00 25.00           C
ATOM     54  CA  SER    54      46.944  33.432  31.269  1.00 25.00           C
ATOM     55  CA  VAL    55      46.204  32.275  27.694  1.00 25.00           C
ATOM     56  CA  GLN    56      47.318  35.678  26.336  1.00 25.00           C
ATOM     57  CA  VAL    57      50.554  35.459  28.372  1.00 25.00           C
ATOM     58  CA  LYS    58      51.200  31.938  27.012  1.00 25.00           C
ATOM     59  CA  LEU    59      50.623  33.185  23.437  1.00 25.00           C
ATOM     60  CA  LYS    60      53.061  36.079  24.028  1.00 25.00           C
ATOM     61  CA  GLU    61      55.675  33.631  25.386  1.00 25.00           C
ATOM     62  CA  ALA    62      57.975  31.456  23.329  1.00 25.00           C
ATOM     63  CA  GLY    63      55.902  32.282  20.298  1.00 25.00           C
ATOM     64  CA  VAL    64      52.489  32.974  18.801  1.00 25.00           C
ATOM     65  CA  ASP    65      50.096  35.870  19.123  1.00 25.00           C
ATOM     66  CA  ILE    66      46.877  35.755  21.221  1.00 25.00           C
ATOM     67  CA  VAL    67      43.195  34.688  21.422  1.00 25.00           C
ATOM     68  CA  GLY    68      39.641  35.448  20.301  1.00 25.00           C
ATOM     69  CA  SER    69      36.630  34.624  22.522  1.00 25.00           C
ATOM     70  CA  GLU    70      33.400  33.961  20.613  1.00 25.00           C
ATOM     71  CA  GLY    71      30.900  31.361  21.730  1.00 25.00           C
ATOM     72  CA  HIS    72      27.263  30.096  21.898  1.00 25.00           C
ATOM     73  CA  GLU    73      27.416  28.057  18.699  1.00 25.00           C
ATOM     74  CA  SER    74      26.569  24.649  20.172  1.00 25.00           C
ATOM     75  CA  GLY    75      29.635  25.293  22.418  1.00 25.00           C
ATOM     76  CA  GLU    76      28.501  22.030  24.024  1.00 25.00           C
ATOM     77  CA  TRP    77      31.614  19.876  24.122  1.00 25.00           C
ATOM     78  CA  VAL    78      31.723  20.668  27.827  1.00 25.00           C
ATOM     79  CA  LEU    79      32.375  20.652  31.562  1.00 25.00           C
ATOM     80  CA  VAL    80      32.471  21.344  35.279  1.00 25.00           C
ATOM     81  CA  ASP    81      29.461  23.662  34.938  1.00 25.00           C
ATOM     82  CA  ALA    82      31.219  25.831  37.482  1.00 25.00           C
ATOM     83  CA  GLY    83      33.787  27.256  39.975  1.00 25.00           C
ATOM     84  CA  ASP    84      36.503  25.683  37.850  1.00 25.00           C
ATOM     85  CA  VAL    85      36.645  25.868  34.015  1.00 25.00           C
ATOM     86  CA  VAL    86      33.359  27.712  33.254  1.00 25.00           C
ATOM     87  CA  VAL    87      31.139  27.639  30.205  1.00 25.00           C
ATOM     88  CA  HIS    88      29.575  29.862  27.504  1.00 25.00           C
ATOM     89  CA  VAL    89      27.100  32.410  28.766  1.00 25.00           C
ATOM     90  CA  MET    90      27.245  34.222  25.444  1.00 25.00           C
ATOM     91  CA  LEU    91      26.219  37.266  27.512  1.00 25.00           C
ATOM     92  CA  PRO    92      28.295  39.802  25.518  1.00 25.00           C
ATOM     93  CA  ALA    93      30.861  37.784  23.515  1.00 25.00           C
ATOM     94  CA  VAL    94      32.343  41.021  22.105  1.00 25.00           C
ATOM     95  CA  ARG    95      32.577  42.481  25.638  1.00 25.00           C
ATOM     96  CA  ASP    96      34.330  39.302  26.862  1.00 25.00           C
ATOM     97  CA  TYR    97      36.802  39.513  23.944  1.00 25.00           C
ATOM     98  CA  TYR    98      37.508  43.185  24.775  1.00 25.00           C
ATOM     99  CA  ASP    99      38.106  42.265  28.444  1.00 25.00           C
ATOM    100  CA  ILE   100      40.507  39.479  27.380  1.00 25.00           C
ATOM    101  CA  GLU   101      42.391  41.932  25.121  1.00 25.00           C
ATOM    102  CA  ALA   102      42.650  44.432  28.010  1.00 25.00           C
ATOM    103  CA  LEU   103      43.993  41.676  30.306  1.00 25.00           C
ATOM    104  CA  TRP   104      46.583  40.700  27.660  1.00 25.00           C
ATOM    105  CA  GLY   105      48.090  44.112  26.797  1.00 25.00           C
ATOM    106  CA  GLY   106      49.034  43.267  23.206  1.00 25.00           C
ATOM    107  CA  GLN   107      48.167  46.544  21.444  1.00 25.00           C
ATOM    108  CA  LYS   108      48.860  46.724  17.649  1.00 25.00           C
ATOM    109  CA  PRO   109      47.402  46.868  14.121  1.00 25.00           C
ATOM    110  CA  SER   110      46.666  43.318  12.908  1.00 25.00           C
ATOM    111  CA  PHE   111      44.489  40.709  11.199  1.00 25.00           C
ATOM    112  CA  ALA   112      43.213  38.210   8.631  1.00 25.00           C
ATOM    113  CA  VAL   113      41.218  38.404   5.433  1.00 25.00           C
ATOM    114  CA  GLY   114      42.346  38.459   1.847  1.00 25.00           C
ATOM    115  CA  ALA   115      44.174  41.462   0.273  1.00 25.00           C
ATOM    116  CA  ALA   116      43.710  39.661  -2.997  1.00 25.00           C
ATOM    117  CA  LYS   117      46.482  38.813  -5.454  1.00 25.00           C
ATOM    118  CA  PRO   118      48.881  37.607  -8.169  1.00 25.00           C
ATOM    119  CA  TRP   119      52.131  38.510  -6.564  1.00 25.00           C
ATOM    120  CA  SER   120      54.314  41.559  -7.034  1.00 25.00           C
ATOM    121  CA  ALA   121      56.911  39.413  -8.752  1.00 25.00           C
ATOM    122  CA  VAL   122      58.886  36.462 -10.200  1.00 25.00           C
ATOM    123  CA  LEU   123      57.917  34.436  -7.144  1.00 25.00           C
ATOM    124  CA  GLU   124      60.105  36.017  -4.427  1.00 25.00           C
ATOM    125  CA  HIS   125      62.768  33.318  -4.967  1.00 25.00           C
ATOM    126  CA  HIS   126      60.575  30.265  -5.542  1.00 25.00           C
ATOM    127  CA  HIS   127      61.460  28.537  -2.334  1.00 25.00           C
ATOM    128  CA  HIS   128      60.591  30.879   0.472  1.00 25.00           C
ATOM    129  CA  HIS   129      63.092  31.570   3.250  1.00 25.00           C
ATOM    130  CA  HIS   130      61.364  29.844   6.214  1.00 25.00           C
TER
END
