
#######################################################
#                                                     #
#                        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 T0304TS168_3
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS168_3.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      -       -           -
LGA    P      28      -       -           -
LGA    C      29      V      35          4.502
LGA    F      30      Q      36           -
LGA    G      31      E      37           -
LGA    A      32      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    R      33      Y      43           #
LGA    L      34      L      44          0.707
LGA    V      35      A      45          1.646
LGA    Q      36      D      46          1.492
LGA    E      37      R      47          3.080
LGA    G      38      A      48          4.274
LGA    N      39      -       -           -
LGA    R      40      G      49          0.715
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      I      50          1.487
LGA    L      44      R      51          3.227
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      G      52          1.604
LGA    A      48      L      53           #
LGA    G      49      F      54          3.298
LGA    I      50      -       -           -
LGA    R      51      S      55          0.771
LGA    G      52      D      56          4.371
LGA    L      53      -       -           -
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      A      57          3.748
LGA    -       -      D      58           -
LGA    A      59      A      59          3.446
LGA    Y      60      Y      60          3.582
LGA    H      61      H      61          2.914
LGA    L      62      L      62          2.102
LGA    D      63      D      63          0.561
LGA    Q      64      Q      64          1.306
LGA    A      65      A      65          2.027
LGA    F      66      F      66          2.772
LGA    P      67      P      67          2.744
LGA    L      68      L      68          2.165
LGA    L      69      L      69          2.144
LGA    M      70      M      70          2.401
LGA    K      71      K      71          2.006
LGA    Q      72      Q      72          1.567
LGA    L      73      L      73          1.655
LGA    E      74      E      74          1.659
LGA    L      75      L      75          1.284
LGA    M      76      M      76          1.347
LGA    L      77      L      77          1.670
LGA    T      78      T      78          1.389
LGA    S      79      -       -           -
LGA    G      80      S      79          4.915
LGA    E      81      G      80          4.169
LGA    L      82      E      81          5.063
LGA    -       -      L      82           -
LGA    N      83      N      83          5.187
LGA    P      84      P      84           -
LGA    R      85      R      85          5.197
LGA    H      86      H      86          2.470
LGA    Q      87      Q      87          4.101
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      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    H      88      D     102           #
LGA    T      89      T     103          1.034
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    V      90      Y     109          3.009
LGA    T      91      V     110          3.605
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    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      Y     111           #
LGA    D     108      L     112          2.803
LGA    Y     109      A     113          1.771
LGA    V     110      V     114           #
LGA    Y     111      Y     115           -
LGA    L     112      P     116           -
LGA    A     113      T     117           -
LGA    V     114      P     118           -
LGA    Y     115      E     119           -
LGA    P     116      M     120           -
LGA    T     117      K     121           -
LGA    P     118      N     122           -
LGA    E     119      -       -           -
LGA    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    2.90    56.52     28.773     1.535

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.245412 * X  +  -0.304332 * Y  +   0.920410 * Z  +  47.098366
  Y_new =   0.227676 * X  +   0.904795 * Y  +   0.359875 * Z  +  19.887852
  Z_new =  -0.942304 * X  +   0.297873 * Y  +  -0.152758 * Z  +  48.416344 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.044655   -1.096938  [ DEG:   117.1501    -62.8499 ]
  Theta =   1.229447    1.912145  [ DEG:    70.4421    109.5579 ]
  Phi   =   2.393666   -0.747927  [ DEG:   137.1470    -42.8530 ]
 
# 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: T0304TS168_3                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS168_3.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   2.90   56.52  28.773
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS168_3
PFRMAT TS
TARGET T0304
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      47.795  -3.693  56.066  1.00 25.00           C
ATOM      2  CA  SER     2      46.772  -0.043  56.572  1.00 25.00           C
ATOM      3  CA  ASP     3      45.538   2.280  59.371  1.00 25.00           C
ATOM      4  CA  THR     4      43.627   1.887  62.652  1.00 25.00           C
ATOM      5  CA  LEU     5      40.112   3.296  62.982  1.00 25.00           C
ATOM      6  CA  PRO     6      38.190   3.441  59.756  1.00 25.00           C
ATOM      7  CA  GLY     7      34.593   4.543  59.583  1.00 25.00           C
ATOM      8  CA  THR     8      34.234   6.826  62.606  1.00 25.00           C
ATOM      9  CA  THR     9      35.179  10.373  61.605  1.00 25.00           C
ATOM     10  CA  LEU    10      34.847  12.340  64.787  1.00 25.00           C
ATOM     11  CA  PRO    11      32.116  14.515  66.400  1.00 25.00           C
ATOM     12  CA  ASP    12      29.441  15.269  69.036  1.00 25.00           C
ATOM     13  CA  ASP    13      31.840  15.746  72.006  1.00 25.00           C
ATOM     14  CA  ASN    14      35.422  16.123  73.137  1.00 25.00           C
ATOM     15  CA  HIS    15      33.927  18.742  75.547  1.00 25.00           C
ATOM     16  CA  ASP    16      37.444  20.247  75.827  1.00 25.00           C
ATOM     17  CA  ARG    17      40.069  17.575  75.948  1.00 25.00           C
ATOM     18  CA  PRO    18      43.846  17.214  75.315  1.00 25.00           C
ATOM     19  CA  TRP    19      45.753  17.403  72.031  1.00 25.00           C
ATOM     20  CA  TRP    20      49.046  15.924  70.826  1.00 25.00           C
ATOM     21  CA  GLY    21      50.344  18.138  68.096  1.00 25.00           C
ATOM     22  CA  LEU    22      52.533  18.831  65.086  1.00 25.00           C
ATOM     23  CA  PRO    23      50.405  21.986  64.645  1.00 25.00           C
ATOM     24  CA  CYS    24      49.065  21.475  61.103  1.00 25.00           C
ATOM     25  CA  THR    25      48.224  25.243  61.168  1.00 25.00           C
ATOM     26  CA  VAL    26      46.097  25.274  58.005  1.00 25.00           C
ATOM     27  CA  THR    27      43.592  22.678  56.793  1.00 25.00           C
ATOM     28  CA  PRO    28      46.137  21.263  54.379  1.00 25.00           C
ATOM     29  CA  CYS    29      48.913  18.773  53.561  1.00 25.00           C
ATOM     30  CA  PHE    30      48.271  15.141  54.434  1.00 25.00           C
ATOM     31  CA  GLY    31      49.073  12.692  51.601  1.00 25.00           C
ATOM     32  CA  ALA    32      45.353  11.851  51.242  1.00 25.00           C
ATOM     33  CA  ARG    33      44.499  15.582  51.100  1.00 25.00           C
ATOM     34  CA  LEU    34      47.170  16.115  48.407  1.00 25.00           C
ATOM     35  CA  VAL    35      45.753  13.189  46.385  1.00 25.00           C
ATOM     36  CA  GLN    36      42.229  14.661  46.679  1.00 25.00           C
ATOM     37  CA  GLU    37      43.526  18.065  45.500  1.00 25.00           C
ATOM     38  CA  GLY    38      45.255  16.401  42.515  1.00 25.00           C
ATOM     39  CA  ASN    39      42.013  14.564  41.631  1.00 25.00           C
ATOM     40  CA  ARG    40      40.067  17.856  41.822  1.00 25.00           C
ATOM     41  CA  LEU    41      42.640  19.539  39.540  1.00 25.00           C
ATOM     42  CA  HIS    42      42.349  16.651  37.041  1.00 25.00           C
ATOM     43  CA  TYR    43      38.532  16.961  37.091  1.00 25.00           C
ATOM     44  CA  LEU    44      38.805  20.730  36.472  1.00 25.00           C
ATOM     45  CA  ALA    45      41.183  20.101  33.536  1.00 25.00           C
ATOM     46  CA  ASP    46      38.740  17.539  32.075  1.00 25.00           C
ATOM     47  CA  ARG    47      35.866  20.047  32.418  1.00 25.00           C
ATOM     48  CA  ALA    48      37.949  22.879  30.922  1.00 25.00           C
ATOM     49  CA  GLY    49      40.467  21.032  28.667  1.00 25.00           C
ATOM     50  CA  ILE    50      43.989  19.516  28.828  1.00 25.00           C
ATOM     51  CA  ARG    51      42.636  17.112  26.194  1.00 25.00           C
ATOM     52  CA  GLY    52      40.718  14.400  28.126  1.00 25.00           C
ATOM     53  CA  LEU    53      41.872  10.804  27.669  1.00 25.00           C
ATOM     54  CA  PHE    54      42.843  10.983  31.349  1.00 25.00           C
ATOM     55  CA  SER    55      45.150   8.059  30.729  1.00 25.00           C
ATOM     56  CA  ASP    56      48.050   8.964  28.508  1.00 25.00           C
ATOM     57  CA  ALA    57      50.949  11.092  27.193  1.00 25.00           C
ATOM     58  CA  ASP    58      48.666  14.164  27.060  1.00 25.00           C
ATOM     59  CA  ALA    59      47.533  13.507  30.659  1.00 25.00           C
ATOM     60  CA  TYR    60      51.182  13.202  31.779  1.00 25.00           C
ATOM     61  CA  HIS    61      52.020  16.504  30.029  1.00 25.00           C
ATOM     62  CA  LEU    62      49.052  18.201  31.755  1.00 25.00           C
ATOM     63  CA  ASP    63      50.217  16.848  35.143  1.00 25.00           C
ATOM     64  CA  GLN    64      53.754  18.160  34.478  1.00 25.00           C
ATOM     65  CA  ALA    65      52.333  21.595  33.558  1.00 25.00           C
ATOM     66  CA  PHE    66      50.263  21.630  36.780  1.00 25.00           C
ATOM     67  CA  PRO    67      53.375  20.721  38.819  1.00 25.00           C
ATOM     68  CA  LEU    68      55.337  23.541  37.126  1.00 25.00           C
ATOM     69  CA  LEU    69      52.515  26.009  37.913  1.00 25.00           C
ATOM     70  CA  MET    70      52.506  24.870  41.570  1.00 25.00           C
ATOM     71  CA  LYS    71      56.303  25.336  41.750  1.00 25.00           C
ATOM     72  CA  GLN    72      55.967  28.852  40.269  1.00 25.00           C
ATOM     73  CA  LEU    73      53.259  29.704  42.839  1.00 25.00           C
ATOM     74  CA  GLU    74      55.508  28.431  45.666  1.00 25.00           C
ATOM     75  CA  LEU    75      58.408  30.560  44.351  1.00 25.00           C
ATOM     76  CA  MET    76      56.123  33.631  44.218  1.00 25.00           C
ATOM     77  CA  LEU    77      54.991  32.974  47.817  1.00 25.00           C
ATOM     78  CA  THR    78      58.640  32.670  48.937  1.00 25.00           C
ATOM     79  CA  SER    79      59.676  31.573  52.414  1.00 25.00           C
ATOM     80  CA  GLY    80      61.138  35.045  52.589  1.00 25.00           C
ATOM     81  CA  GLU    81      57.931  37.014  53.369  1.00 25.00           C
ATOM     82  CA  LEU    82      54.789  37.641  51.256  1.00 25.00           C
ATOM     83  CA  ASN    83      53.081  40.900  52.222  1.00 25.00           C
ATOM     84  CA  PRO    84      51.589  41.579  55.685  1.00 25.00           C
ATOM     85  CA  ARG    85      48.091  42.080  54.259  1.00 25.00           C
ATOM     86  CA  HIS    86      48.033  40.483  50.839  1.00 25.00           C
ATOM     87  CA  GLN    87      46.547  37.156  52.090  1.00 25.00           C
ATOM     88  CA  HIS    88      45.667  33.461  52.069  1.00 25.00           C
ATOM     89  CA  THR    89      45.833  32.220  48.473  1.00 25.00           C
ATOM     90  CA  VAL    90      45.132  28.604  49.606  1.00 25.00           C
ATOM     91  CA  THR    91      47.436  25.978  51.128  1.00 25.00           C
ATOM     92  CA  LEU    92      49.355  22.764  50.552  1.00 25.00           C
ATOM     93  CA  TYR    93      52.627  21.653  48.995  1.00 25.00           C
ATOM     94  CA  ALA    94      55.265  20.565  46.499  1.00 25.00           C
ATOM     95  CA  LYS    95      56.557  17.739  44.343  1.00 25.00           C
ATOM     96  CA  GLY    96      53.505  16.848  42.237  1.00 25.00           C
ATOM     97  CA  LEU    97      50.022  18.098  41.485  1.00 25.00           C
ATOM     98  CA  THR    98      47.122  20.607  41.119  1.00 25.00           C
ATOM     99  CA  CYS    99      44.592  22.443  43.264  1.00 25.00           C
ATOM    100  CA  LYS   100      41.428  22.354  45.441  1.00 25.00           C
ATOM    101  CA  ALA   101      43.030  24.080  48.480  1.00 25.00           C
ATOM    102  CA  ASP   102      39.484  25.188  49.136  1.00 25.00           C
ATOM    103  CA  THR   103      35.808  24.246  49.662  1.00 25.00           C
ATOM    104  CA  LEU   104      36.149  21.455  47.150  1.00 25.00           C
ATOM    105  CA  SER   105      34.274  23.124  44.316  1.00 25.00           C
ATOM    106  CA  SER   106      35.591  26.710  44.294  1.00 25.00           C
ATOM    107  CA  CYS   107      39.392  26.704  43.778  1.00 25.00           C
ATOM    108  CA  ASP   108      42.259  27.798  41.486  1.00 25.00           C
ATOM    109  CA  TYR   109      44.433  25.935  38.978  1.00 25.00           C
ATOM    110  CA  VAL   110      47.711  27.036  40.601  1.00 25.00           C
ATOM    111  CA  TYR   111      48.163  27.533  44.403  1.00 25.00           C
ATOM    112  CA  LEU   112      48.895  23.908  45.358  1.00 25.00           C
ATOM    113  CA  ALA   113      49.705  20.190  45.720  1.00 25.00           C
ATOM    114  CA  VAL   114      51.588  17.090  46.865  1.00 25.00           C
ATOM    115  CA  TYR   115      53.362  14.773  49.304  1.00 25.00           C
ATOM    116  CA  PRO   116      56.657  15.192  51.097  1.00 25.00           C
ATOM    117  CA  THR   117      59.637  14.340  53.225  1.00 25.00           C
ATOM    118  CA  PRO   118      63.232  13.786  54.493  1.00 25.00           C
ATOM    119  CA  GLU   119      65.830  11.944  56.496  1.00 25.00           C
ATOM    120  CA  MET   120      65.294  10.310  59.884  1.00 25.00           C
ATOM    121  CA  LYS   121      65.518  11.489  63.510  1.00 25.00           C
ATOM    122  CA  ASN   122      63.571  11.516  66.803  1.00 25.00           C
TER
END
