
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0304TS393_4
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS393_4.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D      16           -
LGA    S       2      R      17           -
LGA    D       3      P      18           -
LGA    T       4      W      19           -
LGA    L       5      W      20           -
LGA    P       6      G      21           -
LGA    G       7      L      22           -
LGA    T       8      P      23           -
LGA    T       9      C      24           -
LGA    L      10      T      25           -
LGA    P      11      V      26           -
LGA    D      12      T      27           -
LGA    D      13      P      28           -
LGA    N      14      C      29           -
LGA    H      15      F      30           -
LGA    D      16      G      31           -
LGA    R      17      A      32           -
LGA    P      18      R      33           -
LGA    W      19      L      34           -
LGA    W      20      -       -           -
LGA    G      21      -       -           -
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      V      35           #
LGA    P      28      Q      36          3.861
LGA    C      29      E      37          0.918
LGA    -       -      G      38           -
LGA    F      30      N      39          3.807
LGA    G      31      R      40          3.655
LGA    A      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      L      41          2.792
LGA    V      35      H      42          2.597
LGA    Q      36      Y      43          1.999
LGA    E      37      -       -           -
LGA    G      38      L      44           #
LGA    N      39      A      45          3.306
LGA    -       -      D      46           -
LGA    R      40      R      47          5.609
LGA    L      41      A      48           #
LGA    H      42      -       -           -
LGA    Y      43      G      49          2.999
LGA    L      44      I      50          3.183
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      R      51          2.040
LGA    G      49      G      52          3.188
LGA    I      50      L      53           #
LGA    R      51      -       -           -
LGA    G      52      F      54          4.483
LGA    L      53      S      55          2.492
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      D      56          4.861
LGA    A      57      A      57          4.437
LGA    D      58      D      58          3.301
LGA    A      59      A      59          2.005
LGA    Y      60      Y      60          2.063
LGA    H      61      H      61          0.954
LGA    L      62      L      62          1.369
LGA    D      63      D      63          1.518
LGA    Q      64      Q      64          2.645
LGA    A      65      A      65          3.590
LGA    F      66      F      66          3.185
LGA    P      67      P      67          2.938
LGA    L      68      L      68          3.158
LGA    L      69      L      69          2.762
LGA    M      70      M      70          1.908
LGA    K      71      K      71          1.943
LGA    Q      72      Q      72          2.031
LGA    L      73      L      73          1.361
LGA    E      74      E      74          0.511
LGA    L      75      L      75          0.911
LGA    M      76      M      76          0.894
LGA    L      77      L      77          0.443
LGA    T      78      T      78          0.359
LGA    S      79      S      79          1.376
LGA    G      80      G      80          5.752
LGA    E      81      -       -           -
LGA    L      82      -       -           -
LGA    N      83      -       -           -
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      E      81           #
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    Q      87      H      88          4.304
LGA    H      88      T      89          4.034
LGA    T      89      V      90           #
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    V      90      T     103          2.383
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    T      91      Y     109          2.784
LGA    L      92      V     110           #
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      -       -           -
LGA    L     112      -       -           -
LGA    A     113      Y     111          4.415
LGA    V     114      L     112          2.333
LGA    Y     115      A     113           #
LGA    P     116      V     114           -
LGA    T     117      Y     115           -
LGA    P     118      P     116           -
LGA    E     119      T     117           -
LGA    M     120      P     118           -
LGA    K     121      E     119           -
LGA    N     122      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  107    5.0     46    2.99    60.87     27.978     1.488

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.421104 * X  +  -0.701282 * Y  +   0.575217 * Z  +  43.748062
  Y_new =  -0.266533 * X  +   0.701866 * Y  +   0.660564 * Z  +  26.779644
  Z_new =  -0.866967 * X  +   0.124852 * Y  +  -0.482473 * Z  +  47.719009 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.888373   -0.253220  [ DEG:   165.4916    -14.5084 ]
  Theta =   1.049083    2.092509  [ DEG:    60.1081    119.8919 ]
  Phi   =  -2.577305    0.564287  [ DEG:  -147.6687     32.3313 ]
 
# 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: T0304TS393_4                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS393_4.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  107   5.0   46   2.99   60.87  27.978
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS393_4
PFRMAT TS
TARGET T0304
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      41.866  19.993  72.307  1.00 25.00           C
ATOM      2  CA  SER     2      40.274  23.371  73.134  1.00 25.00           C
ATOM      3  CA  ASP     3      37.761  25.115  70.894  1.00 25.00           C
ATOM      4  CA  THR     4      34.742  23.286  72.287  1.00 25.00           C
ATOM      5  CA  LEU     5      32.721  24.881  69.534  1.00 25.00           C
ATOM      6  CA  PRO     6      30.267  23.503  66.992  1.00 25.00           C
ATOM      7  CA  GLY     7      27.171  25.430  68.246  1.00 25.00           C
ATOM      8  CA  THR     8      27.641  27.439  65.016  1.00 25.00           C
ATOM      9  CA  THR     9      28.277  29.284  61.793  1.00 25.00           C
ATOM     10  CA  LEU    10      30.349  32.181  60.430  1.00 25.00           C
ATOM     11  CA  PRO    11      28.420  35.452  60.422  1.00 25.00           C
ATOM     12  CA  ASP    12      24.758  36.549  60.267  1.00 25.00           C
ATOM     13  CA  ASP    13      22.495  39.503  60.649  1.00 25.00           C
ATOM     14  CA  ASN    14      25.350  41.787  61.497  1.00 25.00           C
ATOM     15  CA  HIS    15      25.187  41.930  65.279  1.00 25.00           C
ATOM     16  CA  ASP    16      27.715  44.678  65.994  1.00 25.00           C
ATOM     17  CA  ARG    17      29.591  45.101  62.700  1.00 25.00           C
ATOM     18  CA  PRO    18      32.775  44.182  60.870  1.00 25.00           C
ATOM     19  CA  TRP    19      36.419  43.239  60.315  1.00 25.00           C
ATOM     20  CA  TRP    20      38.514  40.489  61.816  1.00 25.00           C
ATOM     21  CA  GLY    21      42.091  41.241  62.804  1.00 25.00           C
ATOM     22  CA  LEU    22      44.677  38.489  62.759  1.00 25.00           C
ATOM     23  CA  PRO    23      43.192  37.622  59.326  1.00 25.00           C
ATOM     24  CA  CYS    24      44.506  35.171  56.650  1.00 25.00           C
ATOM     25  CA  THR    25      46.255  33.010  59.304  1.00 25.00           C
ATOM     26  CA  VAL    26      46.154  30.287  56.608  1.00 25.00           C
ATOM     27  CA  THR    27      48.600  28.051  58.431  1.00 25.00           C
ATOM     28  CA  PRO    28      49.957  24.967  56.653  1.00 25.00           C
ATOM     29  CA  CYS    29      53.287  25.548  54.858  1.00 25.00           C
ATOM     30  CA  PHE    30      56.075  25.030  52.329  1.00 25.00           C
ATOM     31  CA  GLY    31      56.534  21.328  51.464  1.00 25.00           C
ATOM     32  CA  ALA    32      53.004  20.568  52.739  1.00 25.00           C
ATOM     33  CA  ARG    33      51.596  23.432  50.622  1.00 25.00           C
ATOM     34  CA  LEU    34      53.440  22.095  47.543  1.00 25.00           C
ATOM     35  CA  VAL    35      52.033  18.593  48.189  1.00 25.00           C
ATOM     36  CA  GLN    36      48.502  20.043  48.504  1.00 25.00           C
ATOM     37  CA  GLU    37      48.960  21.939  45.208  1.00 25.00           C
ATOM     38  CA  GLY    38      50.157  18.728  43.499  1.00 25.00           C
ATOM     39  CA  ASN    39      47.107  16.845  44.847  1.00 25.00           C
ATOM     40  CA  ARG    40      44.796  19.608  43.549  1.00 25.00           C
ATOM     41  CA  LEU    41      46.473  19.429  40.111  1.00 25.00           C
ATOM     42  CA  HIS    42      46.027  15.625  40.064  1.00 25.00           C
ATOM     43  CA  TYR    43      42.330  16.022  40.979  1.00 25.00           C
ATOM     44  CA  LEU    44      41.884  18.586  38.168  1.00 25.00           C
ATOM     45  CA  ALA    45      43.561  16.196  35.689  1.00 25.00           C
ATOM     46  CA  ASP    46      41.249  13.360  36.821  1.00 25.00           C
ATOM     47  CA  ARG    47      38.200  15.633  36.367  1.00 25.00           C
ATOM     48  CA  ALA    48      36.873  19.010  37.626  1.00 25.00           C
ATOM     49  CA  GLY    49      37.413  20.273  34.064  1.00 25.00           C
ATOM     50  CA  ILE    50      40.715  21.664  32.794  1.00 25.00           C
ATOM     51  CA  ARG    51      42.844  23.808  30.561  1.00 25.00           C
ATOM     52  CA  GLY    52      41.846  21.748  27.569  1.00 25.00           C
ATOM     53  CA  LEU    53      41.007  18.075  28.102  1.00 25.00           C
ATOM     54  CA  PHE    54      41.630  14.856  30.033  1.00 25.00           C
ATOM     55  CA  SER    55      43.250  11.685  28.838  1.00 25.00           C
ATOM     56  CA  ASP    56      46.920  10.681  28.277  1.00 25.00           C
ATOM     57  CA  ALA    57      49.151  13.386  26.736  1.00 25.00           C
ATOM     58  CA  ASP    58      46.592  16.073  27.687  1.00 25.00           C
ATOM     59  CA  ALA    59      46.476  14.727  31.272  1.00 25.00           C
ATOM     60  CA  TYR    60      50.301  14.802  31.449  1.00 25.00           C
ATOM     61  CA  HIS    61      50.314  18.414  30.178  1.00 25.00           C
ATOM     62  CA  LEU    62      47.712  19.378  32.816  1.00 25.00           C
ATOM     63  CA  ASP    63      49.827  17.724  35.545  1.00 25.00           C
ATOM     64  CA  GLN    64      52.922  19.627  34.333  1.00 25.00           C
ATOM     65  CA  ALA    65      50.957  22.913  34.399  1.00 25.00           C
ATOM     66  CA  PHE    66      49.771  22.162  37.961  1.00 25.00           C
ATOM     67  CA  PRO    67      53.374  21.430  39.033  1.00 25.00           C
ATOM     68  CA  LEU    68      54.535  24.729  37.472  1.00 25.00           C
ATOM     69  CA  LEU    69      51.755  26.608  39.317  1.00 25.00           C
ATOM     70  CA  MET    70      52.786  24.950  42.612  1.00 25.00           C
ATOM     71  CA  LYS    71      56.434  25.939  41.996  1.00 25.00           C
ATOM     72  CA  GLN    72      55.362  29.547  41.290  1.00 25.00           C
ATOM     73  CA  LEU    73      53.312  29.598  44.525  1.00 25.00           C
ATOM     74  CA  GLU    74      56.322  28.265  46.482  1.00 25.00           C
ATOM     75  CA  LEU    75      58.553  30.970  44.941  1.00 25.00           C
ATOM     76  CA  MET    76      55.993  33.656  45.893  1.00 25.00           C
ATOM     77  CA  LEU    77      55.878  32.311  49.477  1.00 25.00           C
ATOM     78  CA  THR    78      59.703  32.385  49.654  1.00 25.00           C
ATOM     79  CA  SER    79      59.349  36.159  49.103  1.00 25.00           C
ATOM     80  CA  GLY    80      61.336  37.072  45.937  1.00 25.00           C
ATOM     81  CA  GLU    81      59.013  39.727  44.592  1.00 25.00           C
ATOM     82  CA  LEU    82      56.610  40.811  47.411  1.00 25.00           C
ATOM     83  CA  ASN    83      56.530  44.077  45.403  1.00 25.00           C
ATOM     84  CA  PRO    84      54.152  45.835  47.706  1.00 25.00           C
ATOM     85  CA  ARG    85      51.619  45.216  44.879  1.00 25.00           C
ATOM     86  CA  HIS    86      51.706  41.599  43.711  1.00 25.00           C
ATOM     87  CA  GLN    87      50.202  39.334  46.372  1.00 25.00           C
ATOM     88  CA  HIS    88      47.153  37.157  46.343  1.00 25.00           C
ATOM     89  CA  THR    89      46.215  34.153  48.448  1.00 25.00           C
ATOM     90  CA  VAL    90      44.186  30.934  48.895  1.00 25.00           C
ATOM     91  CA  THR    91      43.865  27.755  50.991  1.00 25.00           C
ATOM     92  CA  LEU    92      45.590  24.443  51.974  1.00 25.00           C
ATOM     93  CA  TYR    93      43.732  22.633  54.768  1.00 25.00           C
ATOM     94  CA  ALA    94      40.728  23.044  52.467  1.00 25.00           C
ATOM     95  CA  LYS    95      38.159  25.625  51.444  1.00 25.00           C
ATOM     96  CA  GLY    96      36.649  24.976  47.997  1.00 25.00           C
ATOM     97  CA  LEU    97      39.065  25.127  45.082  1.00 25.00           C
ATOM     98  CA  THR    98      39.314  22.684  42.154  1.00 25.00           C
ATOM     99  CA  CYS    99      38.984  19.370  44.089  1.00 25.00           C
ATOM    100  CA  LYS   100      38.316  15.797  45.325  1.00 25.00           C
ATOM    101  CA  ALA   101      38.828  16.978  48.916  1.00 25.00           C
ATOM    102  CA  ASP   102      36.187  19.767  49.037  1.00 25.00           C
ATOM    103  CA  THR   103      36.564  19.616  52.819  1.00 25.00           C
ATOM    104  CA  LEU   104      39.483  17.526  54.098  1.00 25.00           C
ATOM    105  CA  SER   105      37.750  14.182  54.354  1.00 25.00           C
ATOM    106  CA  SER   106      40.286  12.725  51.986  1.00 25.00           C
ATOM    107  CA  CYS   107      40.271  12.222  48.230  1.00 25.00           C
ATOM    108  CA  ASP   108      43.450  14.242  48.405  1.00 25.00           C
ATOM    109  CA  TYR   109      45.230  16.555  50.906  1.00 25.00           C
ATOM    110  CA  VAL   110      43.558  19.240  48.732  1.00 25.00           C
ATOM    111  CA  TYR   111      43.030  22.653  47.137  1.00 25.00           C
ATOM    112  CA  LEU   112      45.320  25.646  46.440  1.00 25.00           C
ATOM    113  CA  ALA   113      46.308  26.159  42.795  1.00 25.00           C
ATOM    114  CA  VAL   114      44.291  29.346  42.961  1.00 25.00           C
ATOM    115  CA  TYR   115      42.439  32.705  42.595  1.00 25.00           C
ATOM    116  CA  PRO   116      39.176  33.013  44.514  1.00 25.00           C
ATOM    117  CA  THR   117      36.162  34.440  42.676  1.00 25.00           C
ATOM    118  CA  PRO   118      34.128  37.640  41.985  1.00 25.00           C
ATOM    119  CA  GLU   119      31.802  39.322  39.479  1.00 25.00           C
ATOM    120  CA  MET   120      30.803  41.542  42.378  1.00 25.00           C
ATOM    121  CA  LYS   121      31.976  45.120  41.937  1.00 25.00           C
ATOM    122  CA  ASN   122      32.540  46.066  45.540  1.00 25.00           C
TER
END
