
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS393_2.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      -       -           -
LGA    W      20      -       -           -
LGA    G      21      -       -           -
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      L      34           #
LGA    P      28      V      35          1.826
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    C      29      L      41          2.583
LGA    F      30      H      42          3.233
LGA    G      31      -       -           -
LGA    A      32      Y      43          1.914
LGA    R      33      L      44          4.989
LGA    L      34      A      45           #
LGA    V      35      D      46           #
LGA    Q      36      R      47          4.508
LGA    E      37      A      48          5.096
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      G      49          2.412
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      I      50          2.988
LGA    L      44      R      51          3.488
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      G      52          2.188
LGA    G      49      L      53          2.049
LGA    I      50      F      54          1.254
LGA    R      51      S      55          1.874
LGA    G      52      -       -           -
LGA    L      53      -       -           -
LGA    F      54      D      56          5.046
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      A      57           #
LGA    Y      60      D      58           -
LGA    H      61      -       -           -
LGA    L      62      -       -           -
LGA    D      63      A      59          3.004
LGA    Q      64      Y      60          4.256
LGA    A      65      H      61          3.215
LGA    F      66      L      62          1.202
LGA    P      67      D      63          1.842
LGA    L      68      Q      64          2.394
LGA    L      69      A      65          1.423
LGA    M      70      F      66          2.403
LGA    K      71      P      67          2.401
LGA    Q      72      L      68          1.302
LGA    L      73      L      69          1.262
LGA    E      74      M      70          1.709
LGA    L      75      K      71          0.946
LGA    M      76      Q      72          0.237
LGA    L      77      L      73          0.957
LGA    T      78      E      74          0.359
LGA    S      79      L      75          3.602
LGA    G      80      M      76          1.654
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    E      81      E      81          1.360
LGA    L      82      L      82          0.927
LGA    N      83      N      83          1.621
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    P      84      H      86          2.043
LGA    R      85      Q      87          4.088
LGA    H      86      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    -       -      D     102           -
LGA    Q      87      T     103          1.527
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    H      88      Y     109          4.021
LGA    T      89      V     110           #
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    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      Y     111           #
LGA    A     113      L     112          3.877
LGA    V     114      A     113          3.536
LGA    Y     115      V     114          3.151
LGA    P     116      Y     115           #
LGA    T     117      P     116           -
LGA    P     118      T     117           -
LGA    E     119      P     118           -
LGA    M     120      E     119           -
LGA    K     121      M     120           -
LGA    N     122      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  107    5.0     43    2.77    11.63     27.317     1.499

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.138835 * X  +  -0.941549 * Y  +   0.306935 * Z  +  47.636852
  Y_new =  -0.563715 * X  +   0.329961 * Y  +   0.757199 * Z  +  17.936638
  Z_new =  -0.814217 * X  +  -0.067899 * Y  +  -0.576576 * Z  +  44.733017 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.024371    0.117222  [ DEG:  -173.2837      6.7163 ]
  Theta =   0.951380    2.190213  [ DEG:    54.5100    125.4900 ]
  Phi   =  -1.812276    1.329317  [ DEG:  -103.8358     76.1642 ]
 
# 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_2                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS393_2.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   43   2.77   11.63  27.317
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS393_2
PFRMAT TS
TARGET T0304
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      71.084  16.069  45.991  1.00 25.00           C
ATOM      2  CA  SER     2      69.701  16.367  49.490  1.00 25.00           C
ATOM      3  CA  ASP     3      66.941  14.057  50.669  1.00 25.00           C
ATOM      4  CA  THR     4      67.653  10.594  49.270  1.00 25.00           C
ATOM      5  CA  LEU     5      64.775   8.107  48.982  1.00 25.00           C
ATOM      6  CA  PRO     6      63.960   5.378  46.487  1.00 25.00           C
ATOM      7  CA  GLY     7      64.802   2.675  49.026  1.00 25.00           C
ATOM      8  CA  THR     8      62.467   4.336  51.473  1.00 25.00           C
ATOM      9  CA  THR     9      59.296   3.913  53.500  1.00 25.00           C
ATOM     10  CA  LEU    10      57.155   4.427  56.567  1.00 25.00           C
ATOM     11  CA  PRO    11      56.550   2.044  59.516  1.00 25.00           C
ATOM     12  CA  ASP    12      56.917  -1.639  60.606  1.00 25.00           C
ATOM     13  CA  ASP    13      54.229  -2.210  63.294  1.00 25.00           C
ATOM     14  CA  ASN    14      54.569   1.520  64.113  1.00 25.00           C
ATOM     15  CA  HIS    15      57.828   0.515  65.751  1.00 25.00           C
ATOM     16  CA  ASP    16      58.009   4.066  67.119  1.00 25.00           C
ATOM     17  CA  ARG    17      59.505   7.132  68.857  1.00 25.00           C
ATOM     18  CA  PRO    18      57.224   9.205  66.638  1.00 25.00           C
ATOM     19  CA  TRP    19      54.996  12.333  66.588  1.00 25.00           C
ATOM     20  CA  TRP    20      56.651  14.971  64.379  1.00 25.00           C
ATOM     21  CA  GLY    21      56.896  18.699  65.082  1.00 25.00           C
ATOM     22  CA  LEU    22      56.122  19.095  61.427  1.00 25.00           C
ATOM     23  CA  PRO    23      53.086  21.316  61.621  1.00 25.00           C
ATOM     24  CA  CYS    24      52.072  21.445  57.955  1.00 25.00           C
ATOM     25  CA  THR    25      48.522  20.946  59.231  1.00 25.00           C
ATOM     26  CA  VAL    26      45.855  19.860  56.821  1.00 25.00           C
ATOM     27  CA  THR    27      46.622  23.195  55.064  1.00 25.00           C
ATOM     28  CA  PRO    28      49.065  21.404  52.720  1.00 25.00           C
ATOM     29  CA  CYS    29      51.794  21.795  50.035  1.00 25.00           C
ATOM     30  CA  PHE    30      53.670  19.753  47.473  1.00 25.00           C
ATOM     31  CA  GLY    31      52.162  16.236  47.630  1.00 25.00           C
ATOM     32  CA  ALA    32      48.800  17.701  48.736  1.00 25.00           C
ATOM     33  CA  ARG    33      48.909  20.203  45.839  1.00 25.00           C
ATOM     34  CA  LEU    34      49.665  17.363  43.383  1.00 25.00           C
ATOM     35  CA  VAL    35      46.727  15.341  44.777  1.00 25.00           C
ATOM     36  CA  GLN    36      44.423  18.377  44.393  1.00 25.00           C
ATOM     37  CA  GLU    37      45.595  18.839  40.776  1.00 25.00           C
ATOM     38  CA  GLY    38      44.924  15.137  40.060  1.00 25.00           C
ATOM     39  CA  ASN    39      41.419  15.455  41.570  1.00 25.00           C
ATOM     40  CA  ARG    40      40.740  18.540  39.405  1.00 25.00           C
ATOM     41  CA  LEU    41      41.914  16.645  36.291  1.00 25.00           C
ATOM     42  CA  HIS    42      39.618  13.712  37.181  1.00 25.00           C
ATOM     43  CA  TYR    43      36.674  16.120  37.630  1.00 25.00           C
ATOM     44  CA  LEU    44      37.426  17.711  34.228  1.00 25.00           C
ATOM     45  CA  ALA    45      37.541  14.244  32.605  1.00 25.00           C
ATOM     46  CA  ASP    46      34.183  13.351  34.215  1.00 25.00           C
ATOM     47  CA  ARG    47      32.666  16.622  32.923  1.00 25.00           C
ATOM     48  CA  ALA    48      33.704  20.016  31.404  1.00 25.00           C
ATOM     49  CA  GLY    49      36.438  18.364  29.282  1.00 25.00           C
ATOM     50  CA  ILE    50      40.078  18.751  30.090  1.00 25.00           C
ATOM     51  CA  ARG    51      42.202  18.678  26.883  1.00 25.00           C
ATOM     52  CA  GLY    52      39.583  16.789  24.875  1.00 25.00           C
ATOM     53  CA  LEU    53      40.954  13.354  23.982  1.00 25.00           C
ATOM     54  CA  PHE    54      40.265  12.194  27.477  1.00 25.00           C
ATOM     55  CA  SER    55      40.609   8.510  26.680  1.00 25.00           C
ATOM     56  CA  ASP    56      43.515   6.094  26.050  1.00 25.00           C
ATOM     57  CA  ALA    57      47.338   6.081  26.269  1.00 25.00           C
ATOM     58  CA  ASP    58      47.468   9.546  24.643  1.00 25.00           C
ATOM     59  CA  ALA    59      44.866  10.841  27.137  1.00 25.00           C
ATOM     60  CA  TYR    60      46.907   9.412  30.046  1.00 25.00           C
ATOM     61  CA  HIS    61      50.066  11.099  28.691  1.00 25.00           C
ATOM     62  CA  LEU    62      48.195  14.427  28.400  1.00 25.00           C
ATOM     63  CA  ASP    63      46.951  14.070  32.005  1.00 25.00           C
ATOM     64  CA  GLN    64      50.521  13.350  33.192  1.00 25.00           C
ATOM     65  CA  ALA    65      51.791  16.444  31.324  1.00 25.00           C
ATOM     66  CA  PHE    66      49.046  18.575  32.935  1.00 25.00           C
ATOM     67  CA  PRO    67      49.995  17.227  36.392  1.00 25.00           C
ATOM     68  CA  LEU    68      53.677  18.050  35.729  1.00 25.00           C
ATOM     69  CA  LEU    69      52.715  21.596  34.651  1.00 25.00           C
ATOM     70  CA  MET    70      50.634  22.027  37.837  1.00 25.00           C
ATOM     71  CA  LYS    71      53.584  20.816  39.958  1.00 25.00           C
ATOM     72  CA  GLN    72      55.907  23.291  38.184  1.00 25.00           C
ATOM     73  CA  LEU    73      53.415  26.128  38.828  1.00 25.00           C
ATOM     74  CA  GLU    74      53.225  25.153  42.526  1.00 25.00           C
ATOM     75  CA  LEU    75      57.048  25.141  42.746  1.00 25.00           C
ATOM     76  CA  MET    76      57.177  28.606  41.120  1.00 25.00           C
ATOM     77  CA  LEU    77      54.575  29.900  43.614  1.00 25.00           C
ATOM     78  CA  THR    78      56.615  28.471  46.522  1.00 25.00           C
ATOM     79  CA  SER    79      56.962  32.157  47.471  1.00 25.00           C
ATOM     80  CA  GLY    80      57.300  34.336  44.302  1.00 25.00           C
ATOM     81  CA  GLU    81      54.403  36.420  45.643  1.00 25.00           C
ATOM     82  CA  LEU    82      51.961  35.515  48.418  1.00 25.00           C
ATOM     83  CA  ASN    83      51.819  37.621  51.558  1.00 25.00           C
ATOM     84  CA  PRO    84      48.445  39.359  51.974  1.00 25.00           C
ATOM     85  CA  ARG    85      45.075  37.915  52.934  1.00 25.00           C
ATOM     86  CA  HIS    86      46.933  34.647  53.621  1.00 25.00           C
ATOM     87  CA  GLN    87      45.871  32.063  50.971  1.00 25.00           C
ATOM     88  CA  HIS    88      44.255  29.111  49.123  1.00 25.00           C
ATOM     89  CA  THR    89      42.601  25.974  50.526  1.00 25.00           C
ATOM     90  CA  VAL    90      41.486  22.425  49.561  1.00 25.00           C
ATOM     91  CA  THR    91      43.889  19.487  49.816  1.00 25.00           C
ATOM     92  CA  LEU    92      43.858  15.676  49.724  1.00 25.00           C
ATOM     93  CA  TYR    93      43.415  12.412  47.881  1.00 25.00           C
ATOM     94  CA  ALA    94      40.899  12.305  45.084  1.00 25.00           C
ATOM     95  CA  LYS    95      41.005   8.571  45.722  1.00 25.00           C
ATOM     96  CA  GLY    96      44.531   7.239  45.584  1.00 25.00           C
ATOM     97  CA  LEU    97      45.207   9.936  42.930  1.00 25.00           C
ATOM     98  CA  THR    98      48.752  10.604  44.242  1.00 25.00           C
ATOM     99  CA  CYS    99      48.423  11.572  47.906  1.00 25.00           C
ATOM    100  CA  LYS   100      47.467  11.686  51.616  1.00 25.00           C
ATOM    101  CA  ALA   101      43.735  11.318  52.296  1.00 25.00           C
ATOM    102  CA  ASP   102      40.103  10.635  51.525  1.00 25.00           C
ATOM    103  CA  THR   103      36.475  10.708  50.226  1.00 25.00           C
ATOM    104  CA  LEU   104      33.306  12.223  48.783  1.00 25.00           C
ATOM    105  CA  SER   105      31.096  15.073  50.005  1.00 25.00           C
ATOM    106  CA  SER   106      31.516  16.291  46.372  1.00 25.00           C
ATOM    107  CA  CYS   107      35.195  16.361  45.380  1.00 25.00           C
ATOM    108  CA  ASP   108      35.800  16.795  49.093  1.00 25.00           C
ATOM    109  CA  TYR   109      38.838  14.570  48.657  1.00 25.00           C
ATOM    110  CA  VAL   110      40.111  17.321  46.379  1.00 25.00           C
ATOM    111  CA  TYR   111      39.929  20.843  45.012  1.00 25.00           C
ATOM    112  CA  LEU   112      42.131  22.683  42.499  1.00 25.00           C
ATOM    113  CA  ALA   113      45.840  23.371  42.683  1.00 25.00           C
ATOM    114  CA  VAL   114      45.992  25.037  39.213  1.00 25.00           C
ATOM    115  CA  TYR   115      46.084  28.110  36.997  1.00 25.00           C
ATOM    116  CA  PRO   116      42.518  28.871  38.206  1.00 25.00           C
ATOM    117  CA  THR   117      39.447  31.177  38.397  1.00 25.00           C
ATOM    118  CA  PRO   118      37.352  34.248  37.765  1.00 25.00           C
ATOM    119  CA  GLU   119      35.717  37.385  36.291  1.00 25.00           C
ATOM    120  CA  MET   120      32.613  37.892  38.372  1.00 25.00           C
ATOM    121  CA  LYS   121      30.695  37.974  41.636  1.00 25.00           C
ATOM    122  CA  ASN   122      31.676  35.860  44.654  1.00 25.00           C
TER
END
