
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS168_1.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      V      35           -
LGA    G      21      Q      36           -
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      E      37          3.304
LGA    P      28      G      38          3.500
LGA    C      29      N      39           #
LGA    F      30      R      40          4.597
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      L      41          5.051
LGA    L      34      H      42          3.088
LGA    V      35      Y      43          3.852
LGA    Q      36      L      44          1.842
LGA    E      37      -       -           -
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      A      45          3.670
LGA    L      41      D      46           -
LGA    H      42      R      47           -
LGA    Y      43      A      48          4.569
LGA    L      44      G      49          1.910
LGA    A      45      I      50          2.731
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      R      51          1.039
LGA    G      49      G      52          4.544
LGA    I      50      L      53           #
LGA    R      51      F      54          4.227
LGA    G      52      S      55          3.578
LGA    L      53      D      56          4.044
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      A      57           #
LGA    D      58      D      58          4.316
LGA    A      59      A      59          2.688
LGA    Y      60      Y      60          3.238
LGA    H      61      H      61          1.821
LGA    L      62      L      62          0.765
LGA    D      63      D      63          1.480
LGA    Q      64      Q      64          2.188
LGA    A      65      A      65          2.317
LGA    F      66      F      66          2.543
LGA    P      67      P      67          2.272
LGA    L      68      L      68          1.991
LGA    L      69      L      69          1.922
LGA    M      70      M      70          1.623
LGA    K      71      K      71          1.201
LGA    Q      72      Q      72          1.084
LGA    L      73      L      73          0.967
LGA    E      74      E      74          0.369
LGA    L      75      L      75          0.364
LGA    M      76      M      76          0.659
LGA    L      77      L      77          0.644
LGA    T      78      T      78          0.559
LGA    S      79      S      79          3.869
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    L      82      G      80          4.003
LGA    N      83      -       -           -
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      -       -           -
LGA    Q      87      E      81          3.516
LGA    H      88      L      82          2.563
LGA    T      89      N      83          2.845
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
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    -       -      D     102           -
LGA    V      90      T     103          2.038
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    T      91      D     108          4.146
LGA    L      92      Y     109          1.644
LGA    Y      93      V     110           #
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      Y     111          4.925
LGA    T      98      L     112          1.584
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      -       -           -
LGA    V     114      A     113           #
LGA    Y     115      V     114           -
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     47    2.92    48.94     28.399     1.557

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.323271 * X  +  -0.747312 * Y  +   0.580535 * Z  +  45.743229
  Y_new =  -0.593476 * X  +   0.317728 * Y  +   0.739483 * Z  +  25.264782
  Z_new =  -0.737077 * X  +  -0.583587 * Y  +  -0.340799 * Z  +  48.582924 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.099348    1.042245  [ DEG:  -120.2838     59.7162 ]
  Theta =   0.828734    2.312858  [ DEG:    47.4830    132.5170 ]
  Phi   =  -1.072025    2.069568  [ DEG:   -61.4225    118.5775 ]
 
# 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_1                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS168_1.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   47   2.92   48.94  28.399
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS168_1
PFRMAT TS
TARGET T0304
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      48.177  18.812  76.567  1.00 25.00           C
ATOM      2  CA  SER     2      47.951  21.752  74.182  1.00 25.00           C
ATOM      3  CA  ASP     3      45.307  21.145  71.484  1.00 25.00           C
ATOM      4  CA  THR     4      43.098  18.423  72.795  1.00 25.00           C
ATOM      5  CA  LEU     5      43.437  16.748  69.453  1.00 25.00           C
ATOM      6  CA  PRO     6      40.169  15.751  67.819  1.00 25.00           C
ATOM      7  CA  GLY     7      37.925  16.756  70.719  1.00 25.00           C
ATOM      8  CA  THR     8      36.430  19.269  68.267  1.00 25.00           C
ATOM      9  CA  THR     9      33.814  19.229  65.529  1.00 25.00           C
ATOM     10  CA  LEU    10      32.662  22.572  64.128  1.00 25.00           C
ATOM     11  CA  PRO    11      29.874  23.486  66.494  1.00 25.00           C
ATOM     12  CA  ASP    12      27.568  24.314  63.608  1.00 25.00           C
ATOM     13  CA  ASP    13      25.766  27.631  63.537  1.00 25.00           C
ATOM     14  CA  ASN    14      24.021  30.975  64.250  1.00 25.00           C
ATOM     15  CA  HIS    15      25.704  32.972  67.091  1.00 25.00           C
ATOM     16  CA  ASP    16      28.185  32.727  70.016  1.00 25.00           C
ATOM     17  CA  ARG    17      30.807  33.472  67.322  1.00 25.00           C
ATOM     18  CA  PRO    18      32.596  35.666  64.813  1.00 25.00           C
ATOM     19  CA  TRP    19      36.326  35.131  64.248  1.00 25.00           C
ATOM     20  CA  TRP    20      38.778  36.887  61.892  1.00 25.00           C
ATOM     21  CA  GLY    21      41.376  39.543  62.684  1.00 25.00           C
ATOM     22  CA  LEU    22      43.815  38.315  59.983  1.00 25.00           C
ATOM     23  CA  PRO    23      46.401  35.831  61.291  1.00 25.00           C
ATOM     24  CA  CYS    24      47.368  33.539  58.418  1.00 25.00           C
ATOM     25  CA  THR    25      49.020  30.792  60.377  1.00 25.00           C
ATOM     26  CA  VAL    26      48.629  28.377  57.512  1.00 25.00           C
ATOM     27  CA  THR    27      52.364  27.815  57.978  1.00 25.00           C
ATOM     28  CA  PRO    28      54.569  25.177  56.348  1.00 25.00           C
ATOM     29  CA  CYS    29      54.783  23.779  52.869  1.00 25.00           C
ATOM     30  CA  PHE    30      56.625  20.438  52.385  1.00 25.00           C
ATOM     31  CA  GLY    31      56.999  17.508  49.947  1.00 25.00           C
ATOM     32  CA  ALA    32      53.874  15.853  51.418  1.00 25.00           C
ATOM     33  CA  ARG    33      51.931  19.132  51.044  1.00 25.00           C
ATOM     34  CA  LEU    34      53.075  19.422  47.401  1.00 25.00           C
ATOM     35  CA  VAL    35      51.966  15.817  46.739  1.00 25.00           C
ATOM     36  CA  GLN    36      48.552  16.552  48.310  1.00 25.00           C
ATOM     37  CA  GLU    37      48.192  19.677  46.125  1.00 25.00           C
ATOM     38  CA  GLY    38      49.076  17.631  43.011  1.00 25.00           C
ATOM     39  CA  ASN    39      46.475  14.992  43.976  1.00 25.00           C
ATOM     40  CA  ARG    40      43.839  17.729  44.453  1.00 25.00           C
ATOM     41  CA  LEU    41      44.701  19.193  41.020  1.00 25.00           C
ATOM     42  CA  HIS    42      44.383  15.721  39.433  1.00 25.00           C
ATOM     43  CA  TYR    43      40.976  15.239  41.116  1.00 25.00           C
ATOM     44  CA  LEU    44      39.823  18.651  39.816  1.00 25.00           C
ATOM     45  CA  ALA    45      40.975  17.724  36.284  1.00 25.00           C
ATOM     46  CA  ASP    46      39.073  14.408  36.508  1.00 25.00           C
ATOM     47  CA  ARG    47      35.927  16.261  37.661  1.00 25.00           C
ATOM     48  CA  ALA    48      35.282  20.011  37.217  1.00 25.00           C
ATOM     49  CA  GLY    49      37.104  22.262  34.684  1.00 25.00           C
ATOM     50  CA  ILE    50      40.418  21.596  33.000  1.00 25.00           C
ATOM     51  CA  ARG    51      43.451  20.919  30.711  1.00 25.00           C
ATOM     52  CA  GLY    52      41.401  17.937  29.440  1.00 25.00           C
ATOM     53  CA  LEU    53      42.003  14.244  29.225  1.00 25.00           C
ATOM     54  CA  PHE    54      42.676  12.060  32.320  1.00 25.00           C
ATOM     55  CA  SER    55      45.443   9.465  32.055  1.00 25.00           C
ATOM     56  CA  ASP    56      47.663  10.084  29.028  1.00 25.00           C
ATOM     57  CA  ALA    57      50.291  12.421  27.511  1.00 25.00           C
ATOM     58  CA  ASP    58      47.917  15.398  27.924  1.00 25.00           C
ATOM     59  CA  ALA    59      47.301  14.432  31.578  1.00 25.00           C
ATOM     60  CA  TYR    60      51.076  14.196  32.178  1.00 25.00           C
ATOM     61  CA  HIS    61      51.568  17.648  30.596  1.00 25.00           C
ATOM     62  CA  LEU    62      48.809  19.091  32.827  1.00 25.00           C
ATOM     63  CA  ASP    63      50.463  17.542  35.915  1.00 25.00           C
ATOM     64  CA  GLN    64      53.834  19.042  34.893  1.00 25.00           C
ATOM     65  CA  ALA    65      52.196  22.475  34.441  1.00 25.00           C
ATOM     66  CA  PHE    66      50.581  22.187  37.901  1.00 25.00           C
ATOM     67  CA  PRO    67      53.967  21.260  39.432  1.00 25.00           C
ATOM     68  CA  LEU    68      55.594  24.275  37.722  1.00 25.00           C
ATOM     69  CA  LEU    69      52.831  26.560  39.066  1.00 25.00           C
ATOM     70  CA  MET    70      53.350  25.156  42.591  1.00 25.00           C
ATOM     71  CA  LYS    71      57.120  25.763  42.304  1.00 25.00           C
ATOM     72  CA  GLN    72      56.478  29.361  41.160  1.00 25.00           C
ATOM     73  CA  LEU    73      54.118  29.910  44.125  1.00 25.00           C
ATOM     74  CA  GLU    74      56.766  28.526  46.521  1.00 25.00           C
ATOM     75  CA  LEU    75      59.394  30.864  45.004  1.00 25.00           C
ATOM     76  CA  MET    76      57.020  33.840  45.417  1.00 25.00           C
ATOM     77  CA  LEU    77      56.404  32.873  49.071  1.00 25.00           C
ATOM     78  CA  THR    78      60.179  32.638  49.671  1.00 25.00           C
ATOM     79  CA  SER    79      62.957  33.525  47.319  1.00 25.00           C
ATOM     80  CA  GLY    80      62.680  35.807  44.312  1.00 25.00           C
ATOM     81  CA  GLU    81      62.028  39.107  46.144  1.00 25.00           C
ATOM     82  CA  LEU    82      59.008  40.288  48.167  1.00 25.00           C
ATOM     83  CA  ASN    83      59.214  44.018  49.144  1.00 25.00           C
ATOM     84  CA  PRO    84      58.488  45.621  45.761  1.00 25.00           C
ATOM     85  CA  ARG    85      55.160  44.707  44.157  1.00 25.00           C
ATOM     86  CA  HIS    86      55.060  40.925  44.179  1.00 25.00           C
ATOM     87  CA  GLN    87      53.297  40.557  47.546  1.00 25.00           C
ATOM     88  CA  HIS    88      51.102  37.471  47.431  1.00 25.00           C
ATOM     89  CA  THR    89      49.652  34.518  49.374  1.00 25.00           C
ATOM     90  CA  VAL    90      47.290  32.025  51.117  1.00 25.00           C
ATOM     91  CA  THR    91      48.965  28.829  52.428  1.00 25.00           C
ATOM     92  CA  LEU    92      46.194  27.161  50.408  1.00 25.00           C
ATOM     93  CA  TYR    93      43.561  25.228  52.431  1.00 25.00           C
ATOM     94  CA  ALA    94      41.575  25.160  49.187  1.00 25.00           C
ATOM     95  CA  LYS    95      37.781  25.501  49.082  1.00 25.00           C
ATOM     96  CA  GLY    96      38.077  26.305  45.405  1.00 25.00           C
ATOM     97  CA  LEU    97      40.950  25.631  43.069  1.00 25.00           C
ATOM     98  CA  THR    98      44.737  25.617  43.183  1.00 25.00           C
ATOM     99  CA  CYS    99      44.678  23.267  46.131  1.00 25.00           C
ATOM    100  CA  LYS   100      45.253  21.252  49.353  1.00 25.00           C
ATOM    101  CA  ALA   101      41.614  20.084  49.001  1.00 25.00           C
ATOM    102  CA  ASP   102      39.401  20.851  52.000  1.00 25.00           C
ATOM    103  CA  THR   103      37.769  17.388  51.842  1.00 25.00           C
ATOM    104  CA  LEU   104      40.385  15.146  50.215  1.00 25.00           C
ATOM    105  CA  SER   105      41.727  13.147  53.124  1.00 25.00           C
ATOM    106  CA  SER   106      45.239  13.284  51.542  1.00 25.00           C
ATOM    107  CA  CYS   107      44.912  16.985  52.329  1.00 25.00           C
ATOM    108  CA  ASP   108      47.051  19.639  54.026  1.00 25.00           C
ATOM    109  CA  TYR   109      50.313  21.204  55.358  1.00 25.00           C
ATOM    110  CA  VAL   110      49.793  23.466  52.335  1.00 25.00           C
ATOM    111  CA  TYR   111      50.892  23.793  48.726  1.00 25.00           C
ATOM    112  CA  LEU   112      48.968  25.536  45.965  1.00 25.00           C
ATOM    113  CA  ALA   113      48.964  28.760  43.970  1.00 25.00           C
ATOM    114  CA  VAL   114      46.173  30.857  42.517  1.00 25.00           C
ATOM    115  CA  TYR   115      44.865  34.254  41.378  1.00 25.00           C
ATOM    116  CA  PRO   116      41.741  33.889  43.468  1.00 25.00           C
ATOM    117  CA  THR   117      38.618  35.717  44.790  1.00 25.00           C
ATOM    118  CA  PRO   118      35.658  37.725  43.534  1.00 25.00           C
ATOM    119  CA  GLU   119      34.975  41.503  43.426  1.00 25.00           C
ATOM    120  CA  MET   120      32.586  44.210  44.749  1.00 25.00           C
ATOM    121  CA  LYS   121      31.737  44.605  48.402  1.00 25.00           C
ATOM    122  CA  ASN   122      33.738  42.951  51.190  1.00 25.00           C
TER
END
