
#######################################################
#                                                     #
#                        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 T0304TS599_3
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS599_3.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    S       2      -       -           -
LGA    D       3      D      16          3.718
LGA    T       4      -       -           -
LGA    L       5      -       -           -
LGA    P       6      R      17           #
LGA    G       7      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    T       8      V      26           #
LGA    T       9      T      27          2.578
LGA    L      10      P      28          3.382
LGA    P      11      C      29           #
LGA    D      12      -       -           -
LGA    D      13      -       -           -
LGA    N      14      -       -           -
LGA    H      15      -       -           -
LGA    D      16      -       -           -
LGA    R      17      -       -           -
LGA    P      18      -       -           -
LGA    W      19      -       -           -
LGA    W      20      -       -           -
LGA    G      21      F      30           #
LGA    L      22      G      31           #
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      A      32           #
LGA    P      28      R      33           #
LGA    C      29      L      34           -
LGA    F      30      V      35           -
LGA    G      31      Q      36           -
LGA    A      32      E      37           -
LGA    R      33      G      38           -
LGA    L      34      N      39           -
LGA    V      35      R      40           -
LGA    Q      36      L      41           -
LGA    E      37      H      42           -
LGA    G      38      Y      43           -
LGA    N      39      L      44          3.336
LGA    R      40      A      45          2.556
LGA    L      41      D      46           #
LGA    H      42      R      47           #
LGA    Y      43      A      48           #
LGA    L      44      -       -           -
LGA    A      45      -       -           -
LGA    D      46      G      49          4.182
LGA    R      47      I      50          3.417
LGA    A      48      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    G      49      F      54          4.594
LGA    I      50      -       -           -
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      S      55           #
LGA    F      54      D      56          3.546
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      A      57          2.648
LGA    A      59      D      58           #
LGA    -       -      A      59           -
LGA    Y      60      Y      60          3.147
LGA    H      61      H      61          1.823
LGA    L      62      L      62          1.722
LGA    D      63      D      63          1.526
LGA    Q      64      Q      64          1.907
LGA    A      65      A      65          2.085
LGA    F      66      F      66          1.413
LGA    P      67      P      67          1.652
LGA    L      68      L      68          1.895
LGA    L      69      L      69          1.346
LGA    M      70      M      70          1.071
LGA    K      71      K      71          1.298
LGA    Q      72      Q      72          0.965
LGA    L      73      L      73          0.308
LGA    E      74      E      74          0.705
LGA    L      75      L      75          0.485
LGA    M      76      M      76          0.187
LGA    L      77      L      77          0.458
LGA    T      78      T      78          0.826
LGA    S      79      S      79          1.012
LGA    G      80      G      80          1.357
LGA    E      81      E      81          1.462
LGA    L      82      L      82          2.011
LGA    N      83      N      83          2.072
LGA    P      84      P      84          3.739
LGA    R      85      R      85          1.601
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    H      86      T     103          3.376
LGA    -       -      L     104           -
LGA    Q      87      S     105           #
LGA    H      88      S     106           #
LGA    T      89      C     107          3.678
LGA    V      90      D     108          5.186
LGA    T      91      Y     109          5.691
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      V     110           #
LGA    L     112      Y     111          4.697
LGA    A     113      L     112          2.729
LGA    V     114      A     113          3.078
LGA    Y     115      V     114           #
LGA    P     116      Y     115           -
LGA    -       -      P     116           -
LGA    T     117      T     117           #
LGA    P     118      P     118           -
LGA    E     119      E     119           -
LGA    M     120      M     120           -
LGA    K     121      K     121           -
LGA    N     122      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  107    5.0     43    2.71    65.12     28.972     1.533

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.688027 * X  +  -0.413592 * Y  +   0.596288 * Z  +  43.644447
  Y_new =   0.571965 * X  +  -0.814779 * Y  +   0.094823 * Z  +  23.311960
  Z_new =   0.446625 * X  +   0.406297 * Y  +   0.797150 * Z  +  42.798908 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.471367   -2.670226  [ DEG:    27.0073   -152.9927 ]
  Theta =  -0.462990   -2.678603  [ DEG:   -26.5274   -153.4726 ]
  Phi   =   2.448049   -0.693544  [ DEG:   140.2628    -39.7371 ]
 
# 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: T0304TS599_3                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_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   43   2.71   65.12  28.972
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_3
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      23.967  18.037  45.185  1.00  0.00              
ATOM      2  CA  SER     2      22.218  15.971  42.561  1.00  0.00              
ATOM      3  CA  ASP     3      26.339  15.290  43.007  1.00  0.00              
ATOM      4  CA  THR     4      23.997  15.368  40.266  1.00  0.00              
ATOM      5  CA  LEU     5      24.759  18.881  38.947  1.00  0.00              
ATOM      6  CA  PRO     6      28.487  19.119  38.362  1.00  0.00              
ATOM      7  CA  GLY     7      28.437  20.486  34.815  1.00  0.00              
ATOM      8  CA  THR     8      30.796  23.401  35.052  1.00  0.00              
ATOM      9  CA  THR     9      33.644  23.149  32.610  1.00  0.00              
ATOM     10  CA  LEU    10      36.728  25.237  32.948  1.00  0.00              
ATOM     11  CA  PRO    11      37.260  28.186  30.656  1.00  0.00              
ATOM     12  CA  ASP    12      39.394  27.938  27.613  1.00  0.00              
ATOM     13  CA  ASP    13      42.562  29.830  28.269  1.00  0.00              
ATOM     14  CA  ASN    14      41.562  33.336  27.211  1.00  0.00              
ATOM     15  CA  HIS    15      43.220  35.127  30.117  1.00  0.00              
ATOM     16  CA  ASP    16      40.336  36.712  31.932  1.00  0.00              
ATOM     17  CA  ARG    17      39.871  34.571  34.992  1.00  0.00              
ATOM     18  CA  PRO    18      37.093  32.245  33.758  1.00  0.00              
ATOM     19  CA  TRP    19      38.322  28.934  35.175  1.00  0.00              
ATOM     20  CA  TRP    20      35.160  27.425  36.458  1.00  0.00              
ATOM     21  CA  GLY    21      36.233  24.087  37.802  1.00  0.00              
ATOM     22  CA  LEU    22      33.135  22.309  38.992  1.00  0.00              
ATOM     23  CA  PRO    23      33.060  20.605  42.330  1.00  0.00              
ATOM     24  CA  CYS    24      29.875  21.806  44.099  1.00  0.00              
ATOM     25  CA  THR    25      30.954  22.933  47.616  1.00  0.00              
ATOM     26  CA  VAL    26      34.286  21.216  47.974  1.00  0.00              
ATOM     27  CA  THR    27      35.578  20.652  51.535  1.00  0.00              
ATOM     28  CA  PRO    28      38.996  19.002  51.597  1.00  0.00              
ATOM     29  CA  CYS    29      38.252  16.202  54.092  1.00  0.00              
ATOM     30  CA  PHE    30      35.477  14.981  51.763  1.00  0.00              
ATOM     31  CA  GLY    31      37.056  15.300  48.380  1.00  0.00              
ATOM     32  CA  ALA    32      36.684  11.676  47.397  1.00  0.00              
ATOM     33  CA  ARG    33      38.198  10.643  50.696  1.00  0.00              
ATOM     34  CA  LEU    34      41.220  12.912  50.015  1.00  0.00              
ATOM     35  CA  VAL    35      41.749  11.477  46.502  1.00  0.00              
ATOM     36  CA  GLN    36      41.328   7.959  47.783  1.00  0.00              
ATOM     37  CA  GLU    37      43.895   8.430  50.599  1.00  0.00              
ATOM     38  CA  GLY    38      46.662  10.186  48.732  1.00  0.00              
ATOM     39  CA  ASN    39      46.029  13.733  50.043  1.00  0.00              
ATOM     40  CA  ARG    40      46.843  15.884  47.041  1.00  0.00              
ATOM     41  CA  LEU    41      44.529  18.704  46.055  1.00  0.00              
ATOM     42  CA  HIS    42      46.042  19.637  42.642  1.00  0.00              
ATOM     43  CA  TYR    43      44.196  22.431  40.909  1.00  0.00              
ATOM     44  CA  LEU    44      45.638  22.155  37.377  1.00  0.00              
ATOM     45  CA  ALA    45      46.000  18.386  37.304  1.00  0.00              
ATOM     46  CA  ASP    46      42.326  17.564  38.042  1.00  0.00              
ATOM     47  CA  ARG    47      40.753  20.253  35.834  1.00  0.00              
ATOM     48  CA  ALA    48      42.907  19.319  32.817  1.00  0.00              
ATOM     49  CA  GLY    49      42.496  15.538  33.103  1.00  0.00              
ATOM     50  CA  ILE    50      46.122  14.433  33.863  1.00  0.00              
ATOM     51  CA  ARG    51      45.187  11.399  35.885  1.00  0.00              
ATOM     52  CA  GLY    52      42.800   9.788  33.479  1.00  0.00              
ATOM     53  CA  LEU    53      40.314  10.726  30.818  1.00  0.00              
ATOM     54  CA  PHE    54      42.603  12.635  28.479  1.00  0.00              
ATOM     55  CA  SER    55      44.975  10.998  26.085  1.00  0.00              
ATOM     56  CA  ASP    56      48.452   9.903  27.114  1.00  0.00              
ATOM     57  CA  ALA    57      50.148  12.892  25.390  1.00  0.00              
ATOM     58  CA  ASP    58      47.832  15.323  27.081  1.00  0.00              
ATOM     59  CA  ALA    59      48.487  13.693  30.512  1.00  0.00              
ATOM     60  CA  TYR    60      52.261  14.149  30.035  1.00  0.00              
ATOM     61  CA  HIS    61      51.737  17.813  29.072  1.00  0.00              
ATOM     62  CA  LEU    62      49.525  18.473  32.155  1.00  0.00              
ATOM     63  CA  ASP    63      52.046  16.851  34.542  1.00  0.00              
ATOM     64  CA  GLN    64      54.774  19.162  33.200  1.00  0.00              
ATOM     65  CA  ALA    65      52.460  22.166  33.721  1.00  0.00              
ATOM     66  CA  PHE    66      51.501  21.273  37.325  1.00  0.00              
ATOM     67  CA  PRO    67      55.083  20.790  38.533  1.00  0.00              
ATOM     68  CA  LEU    68      56.063  24.120  36.970  1.00  0.00              
ATOM     69  CA  LEU    69      53.113  25.922  38.621  1.00  0.00              
ATOM     70  CA  MET    70      53.828  24.513  42.027  1.00  0.00              
ATOM     71  CA  LYS    71      57.492  25.526  41.687  1.00  0.00              
ATOM     72  CA  GLN    72      56.535  29.084  40.791  1.00  0.00              
ATOM     73  CA  LEU    73      54.185  29.260  43.807  1.00  0.00              
ATOM     74  CA  GLU    74      56.915  27.916  46.095  1.00  0.00              
ATOM     75  CA  LEU    75      59.370  30.509  44.772  1.00  0.00              
ATOM     76  CA  MET    76      56.837  33.281  45.435  1.00  0.00              
ATOM     77  CA  LEU    77      56.221  32.040  48.963  1.00  0.00              
ATOM     78  CA  THR    78      59.881  31.867  49.922  1.00  0.00              
ATOM     79  CA  SER    79      60.551  35.319  48.473  1.00  0.00              
ATOM     80  CA  GLY    80      57.855  37.247  50.142  1.00  0.00              
ATOM     81  CA  GLU    81      55.771  38.008  47.109  1.00  0.00              
ATOM     82  CA  LEU    82      52.623  36.760  48.698  1.00  0.00              
ATOM     83  CA  ASN    83      51.510  38.015  52.063  1.00  0.00              
ATOM     84  CA  PRO    84      51.275  36.265  55.393  1.00  0.00              
ATOM     85  CA  ARG    85      47.603  35.418  55.266  1.00  0.00              
ATOM     86  CA  HIS    86      47.899  33.938  51.759  1.00  0.00              
ATOM     87  CA  GLN    87      50.908  31.633  52.261  1.00  0.00              
ATOM     88  CA  HIS    88      49.391  29.586  55.033  1.00  0.00              
ATOM     89  CA  THR    89      45.735  29.375  53.852  1.00  0.00              
ATOM     90  CA  VAL    90      44.573  27.080  51.089  1.00  0.00              
ATOM     91  CA  THR    91      41.862  28.264  48.739  1.00  0.00              
ATOM     92  CA  LEU    92      39.739  25.801  46.887  1.00  0.00              
ATOM     93  CA  TYR    93      37.873  27.023  43.899  1.00  0.00              
ATOM     94  CA  ALA    94      34.968  24.913  42.515  1.00  0.00              
ATOM     95  CA  LYS    95      32.170  26.351  44.617  1.00  0.00              
ATOM     96  CA  GLY    96      33.888  28.147  47.366  1.00  0.00              
ATOM     97  CA  LEU    97      36.206  26.101  49.534  1.00  0.00              
ATOM     98  CA  THR    98      38.385  27.738  52.102  1.00  0.00              
ATOM     99  CA  CYS    99      41.009  25.692  53.867  1.00  0.00              
ATOM    100  CA  LYS   100      42.793  27.180  56.772  1.00  0.00              
ATOM    101  CA  ALA   101      46.418  26.167  57.029  1.00  0.00              
ATOM    102  CA  ASP   102      46.038  24.849  60.508  1.00  0.00              
ATOM    103  CA  THR   103      42.703  23.026  60.554  1.00  0.00              
ATOM    104  CA  LEU   104      42.762  21.152  57.222  1.00  0.00              
ATOM    105  CA  SER   105      46.338  20.107  57.711  1.00  0.00              
ATOM    106  CA  SER   106      45.740  18.796  61.279  1.00  0.00              
ATOM    107  CA  CYS   107      42.724  16.744  60.246  1.00  0.00              
ATOM    108  CA  ASP   108      43.883  15.255  56.983  1.00  0.00              
ATOM    109  CA  TYR   109      42.330  17.579  54.468  1.00  0.00              
ATOM    110  CA  VAL   110      43.712  18.502  51.083  1.00  0.00              
ATOM    111  CA  TYR   111      43.638  22.148  49.907  1.00  0.00              
ATOM    112  CA  LEU   112      43.639  23.067  46.257  1.00  0.00              
ATOM    113  CA  ALA   113      44.756  26.448  45.244  1.00  0.00              
ATOM    114  CA  VAL   114      43.252  28.050  42.095  1.00  0.00              
ATOM    115  CA  TYR   115      44.715  31.344  41.047  1.00  0.00              
ATOM    116  CA  PRO   116      43.640  33.987  38.624  1.00  0.00              
ATOM    117  CA  THR   117      46.293  34.504  36.004  1.00  0.00              
ATOM    118  CA  PRO   118      46.718  38.249  36.061  1.00  0.00              
ATOM    119  CA  GLU   119      50.536  38.361  35.751  1.00  0.00              
ATOM    120  CA  MET   120      50.933  35.434  38.760  1.00  0.00              
ATOM    121  CA  LYS   121      49.502  33.100  41.681  1.00  0.00              
ATOM    122  CA  ASN   122      48.469  29.608  40.139  1.00  0.00              
TER                                                                             
END
