
#######################################################
#                                                     #
#                        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  126 (  126),  selected  126 , name T0372TS599_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS599_5-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    I       2      -       -           -
LGA    P       3      -       -           -
LGA    F       4      -       -           -
LGA    K       5      M       1          4.982
LGA    -       -      I       2           -
LGA    D       6      P       3          1.428
LGA    I       7      F       4           #
LGA    T       8      K       5          5.348
LGA    L       9      D       6           #
LGA    A      10      I       7           -
LGA    D      11      -       -           -
LGA    R      12      T       8          4.552
LGA    D      13      L       9          3.199
LGA    T      14      A      10          1.910
LGA    I      15      D      11          2.971
LGA    T      16      -       -           -
LGA    A      17      R      12          5.200
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    F      18      T      16           #
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    T      19      S      30           #
LGA    M      20      F      31          3.059
LGA    K      21      S      32          3.729
LGA    S      22      -       -           -
LGA    D      23      N      33          3.798
LGA    R      24      L      34          3.537
LGA    R      25      C      35           #
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    N      26      R      38           #
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    C      27      Y      41          4.099
LGA    D      28      D      42          4.616
LGA    L      29      T      43          5.391
LGA    S      30      Q      44           #
LGA    F      31      -       -           -
LGA    S      32      -       -           -
LGA    N      33      -       -           -
LGA    L      34      -       -           -
LGA    C      35      F      45          2.793
LGA    S      36      A      46          1.462
LGA    W      37      V      47          2.397
LGA    R      38      I      48          2.456
LGA    F      39      D      49          1.481
LGA    L      40      D      50          2.050
LGA    Y      41      F      51          2.427
LGA    D      42      L      52          1.838
LGA    T      43      V      53          1.096
LGA    Q      44      F      54          1.776
LGA    F      45      K      55          2.263
LGA    A      46      F      56          2.986
LGA    V      47      W      57          2.749
LGA    I      48      A      58          2.077
LGA    D      49      G      59          2.506
LGA    D      50      E      60          2.386
LGA    F      51      Q      61          1.811
LGA    L      52      L      62          2.235
LGA    V      53      A      63          1.798
LGA    F      54      Y      64          1.265
LGA    K      55      M      65          1.499
LGA    F      56      M      66          3.324
LGA    W      57      P      67          1.357
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    A      58      L      73          3.638
LGA    G      59      K      74           -
LGA    E      60      A      75           -
LGA    Q      61      V      76           -
LGA    L      62      L      77           #
LGA    A      63      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    Y      64      I      81           #
LGA    M      65      E      82           -
LGA    M      66      -       -           -
LGA    P      67      -       -           -
LGA    V      68      -       -           -
LGA    G      69      -       -           -
LGA    N      70      -       -           -
LGA    G      71      -       -           -
LGA    D      72      -       -           -
LGA    L      73      -       -           -
LGA    K      74      D      83           #
LGA    A      75      -       -           -
LGA    V      76      -       -           -
LGA    L      77      A      84          1.554
LGA    R      78      D      85          3.130
LGA    K      79      K      86          4.913
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    L      80      N      90           #
LGA    I      81      F      91           #
LGA    E      82      C      92           -
LGA    D      83      M      93           -
LGA    A      84      L      94           -
LGA    D      85      G      95           -
LGA    K      86      V      96           -
LGA    E      87      C      97           -
LGA    K      88      S      98           -
LGA    H      89      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    N      90      L     108          4.839
LGA    F      91      P     109           #
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    C      92      F     112           #
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    M      93      A     293          4.339
LGA    L      94      C     294          3.356
LGA    G      95      L     295           -
LGA    V      96      K     296           -
LGA    C      97      D     297           -
LGA    S      98      H     298           -
LGA    N      99      -       -           -
LGA    M     100      -       -           -
LGA    R     101      -       -           -
LGA    A     102      -       -           -
LGA    D     103      -       -           -
LGA    L     104      -       -           -
LGA    E     105      -       -           -
LGA    A     106      -       -           -
LGA    I     107      -       -           -
LGA    L     108      -       -           -
LGA    P     109      -       -           -
LGA    E     110      -       -           -
LGA    R     111      -       -           -
LGA    F     112      -       -           -
LGA    I     113      -       -           -
LGA    F     114      -       -           -
LGA    T     115      -       -           -
LGA    E     116      -       -           -
LGA    D     117      -       -           -
LGA    K     290      -       -           -
LGA    Y     291      -       -           -
LGA    M     292      -       -           -
LGA    A     293      -       -           -
LGA    C     294      -       -           -
LGA    L     295      -       -           -
LGA    K     296      -       -           -
LGA    D     297      -       -           -
LGA    H     298      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  126  126    5.0     45    3.18     6.67     23.392     1.373

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.989521 * X  +   0.051197 * Y  +   0.135007 * Z  +  23.047087
  Y_new =   0.143107 * X  +  -0.223470 * Y  +  -0.964148 * Z  +  50.005264
  Z_new =  -0.019191 * X  +   0.973365 * Y  +  -0.228455 * Z  + -13.557124 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.801330   -1.340263  [ DEG:   103.2086    -76.7914 ]
  Theta =   0.019193    3.122400  [ DEG:     1.0997    178.9003 ]
  Phi   =   0.143627   -2.997966  [ DEG:     8.2292   -171.7708 ]
 
# 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: T0372TS599_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS599_5-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  126  126   5.0   45   3.18    6.67  23.392
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS599_5-D1
PFRMAT TS                                                                       
TARGET T0372                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      40.922  70.950  -3.833  1.00  0.00              
ATOM      2  CA  ILE     2      43.010  67.802  -2.371  1.00  0.00              
ATOM      3  CA  PRO     3      43.265  64.644  -4.148  1.00  0.00              
ATOM      4  CA  PHE     4      45.753  62.235  -3.214  1.00  0.00              
ATOM      5  CA  LYS     5      46.049  59.003  -5.225  1.00  0.00              
ATOM      6  CA  ASP     6      48.225  56.610  -3.270  1.00  0.00              
ATOM      7  CA  ILE     7      49.453  58.380  -0.142  1.00  0.00              
ATOM      8  CA  THR     8      52.281  56.548   1.509  1.00  0.00              
ATOM      9  CA  LEU     9      52.429  56.511   5.277  1.00  0.00              
ATOM     10  CA  ALA    10      55.925  56.373   6.700  1.00  0.00              
ATOM     11  CA  ASP    11      56.555  54.308   9.700  1.00  0.00              
ATOM     12  CA  ARG    12      55.220  50.871   9.001  1.00  0.00              
ATOM     13  CA  ASP    13      54.365  50.055  12.600  1.00  0.00              
ATOM     14  CA  THR    14      52.308  53.289  12.818  1.00  0.00              
ATOM     15  CA  ILE    15      50.462  52.513   9.583  1.00  0.00              
ATOM     16  CA  THR    16      49.543  49.010  10.742  1.00  0.00              
ATOM     17  CA  ALA    17      48.262  50.398  13.865  1.00  0.00              
ATOM     18  CA  PHE    18      46.164  52.987  12.108  1.00  0.00              
ATOM     19  CA  THR    19      44.590  50.272   9.992  1.00  0.00              
ATOM     20  CA  MET    20      43.913  48.183  13.121  1.00  0.00              
ATOM     21  CA  LYS    21      42.092  51.017  14.732  1.00  0.00              
ATOM     22  CA  SER    22      39.768  51.677  11.884  1.00  0.00              
ATOM     23  CA  ASP    23      38.976  48.028  11.046  1.00  0.00              
ATOM     24  CA  ARG    24      39.958  48.210   7.464  1.00  0.00              
ATOM     25  CA  ARG    25      41.844  45.550   5.660  1.00  0.00              
ATOM     26  CA  ASN    26      43.905  46.738   3.024  1.00  0.00              
ATOM     27  CA  CYS    27      44.721  44.320   0.518  1.00  0.00              
ATOM     28  CA  ASP    28      46.880  46.039  -2.029  1.00  0.00              
ATOM     29  CA  LEU    29      48.791  48.166   0.329  1.00  0.00              
ATOM     30  CA  SER    30      52.464  47.844   0.913  1.00  0.00              
ATOM     31  CA  PHE    31      54.199  51.167   0.724  1.00  0.00              
ATOM     32  CA  SER    32      54.383  51.527   4.467  1.00  0.00              
ATOM     33  CA  ASN    33      50.578  51.662   4.770  1.00  0.00              
ATOM     34  CA  LEU    34      48.825  52.633   1.657  1.00  0.00              
ATOM     35  CA  CYS    35      46.111  55.220   2.007  1.00  0.00              
ATOM     36  CA  SER    36      43.997  56.427  -0.953  1.00  0.00              
ATOM     37  CA  TRP    37      42.282  59.771  -0.903  1.00  0.00              
ATOM     38  CA  ARG    38      40.153  61.040  -3.819  1.00  0.00              
ATOM     39  CA  PHE    39      38.179  64.115  -2.844  1.00  0.00              
ATOM     40  CA  LEU    40      38.302  63.587   0.917  1.00  0.00              
ATOM     41  CA  TYR    41      36.465  60.297   0.960  1.00  0.00              
ATOM     42  CA  ASP    42      38.360  57.736   2.906  1.00  0.00              
ATOM     43  CA  THR    43      38.916  54.549   1.039  1.00  0.00              
ATOM     44  CA  GLN    44      38.717  51.202   2.830  1.00  0.00              
ATOM     45  CA  PHE    45      39.612  47.976   0.976  1.00  0.00              
ATOM     46  CA  ALA    46      38.536  44.656   2.362  1.00  0.00              
ATOM     47  CA  VAL    47      39.824  41.420   0.830  1.00  0.00              
ATOM     48  CA  ILE    48      37.897  38.234   1.434  1.00  0.00              
ATOM     49  CA  ASP    49      38.897  34.971  -0.190  1.00  0.00              
ATOM     50  CA  ASP    50      38.085  35.861  -3.723  1.00  0.00              
ATOM     51  CA  PHE    51      35.902  38.862  -3.202  1.00  0.00              
ATOM     52  CA  LEU    52      36.984  42.272  -3.155  1.00  0.00              
ATOM     53  CA  VAL    53      35.111  44.902  -1.105  1.00  0.00              
ATOM     54  CA  PHE    54      35.660  48.512  -1.644  1.00  0.00              
ATOM     55  CA  LYS    55      34.356  51.054   0.809  1.00  0.00              
ATOM     56  CA  PHE    56      34.213  54.769  -0.180  1.00  0.00              
ATOM     57  CA  TRP    57      33.214  57.375   2.287  1.00  0.00              
ATOM     58  CA  ALA    58      31.671  60.538   0.953  1.00  0.00              
ATOM     59  CA  GLY    59      28.758  61.942   2.976  1.00  0.00              
ATOM     60  CA  GLU    60      26.366  59.130   2.270  1.00  0.00              
ATOM     61  CA  GLN    61      28.553  56.103   2.201  1.00  0.00              
ATOM     62  CA  LEU    62      29.298  54.404  -0.989  1.00  0.00              
ATOM     63  CA  ALA    63      30.056  50.703  -1.039  1.00  0.00              
ATOM     64  CA  TYR    64      31.698  49.111  -4.045  1.00  0.00              
ATOM     65  CA  MET    65      31.681  45.331  -4.400  1.00  0.00              
ATOM     66  CA  MET    66      34.116  43.725  -6.708  1.00  0.00              
ATOM     67  CA  PRO    67      33.961  40.040  -7.573  1.00  0.00              
ATOM     68  CA  VAL    68      37.287  38.437  -7.264  1.00  0.00              
ATOM     69  CA  GLY    69      39.674  36.865  -9.657  1.00  0.00              
ATOM     70  CA  ASN    70      43.146  37.839  -8.632  1.00  0.00              
ATOM     71  CA  GLY    71      44.327  40.066 -11.369  1.00  0.00              
ATOM     72  CA  ASP    72      41.169  42.018 -12.061  1.00  0.00              
ATOM     73  CA  LEU    73      39.067  43.722  -9.502  1.00  0.00              
ATOM     74  CA  LYS    74      40.934  46.939  -9.238  1.00  0.00              
ATOM     75  CA  ALA    75      41.046  47.578 -12.961  1.00  0.00              
ATOM     76  CA  VAL    76      37.399  46.949 -13.514  1.00  0.00              
ATOM     77  CA  LEU    77      36.259  49.149 -10.695  1.00  0.00              
ATOM     78  CA  ARG    78      38.438  51.978 -11.739  1.00  0.00              
ATOM     79  CA  LYS    79      37.137  51.866 -15.308  1.00  0.00              
ATOM     80  CA  LEU    80      33.508  51.863 -14.328  1.00  0.00              
ATOM     81  CA  ILE    81      34.014  54.869 -12.023  1.00  0.00              
ATOM     82  CA  GLU    82      35.658  56.740 -14.730  1.00  0.00              
ATOM     83  CA  ASP    83      33.075  56.117 -17.188  1.00  0.00              
ATOM     84  CA  ALA    84      30.351  57.318 -14.907  1.00  0.00              
ATOM     85  CA  ASP    85      32.145  60.500 -14.409  1.00  0.00              
ATOM     86  CA  LYS    86      32.362  61.406 -17.965  1.00  0.00              
ATOM     87  CA  GLU    87      28.726  60.826 -18.524  1.00  0.00              
ATOM     88  CA  LYS    88      27.751  62.742 -15.454  1.00  0.00              
ATOM     89  CA  HIS    89      26.294  59.865 -13.469  1.00  0.00              
ATOM     90  CA  ASN    90      26.770  59.555  -9.753  1.00  0.00              
ATOM     91  CA  PHE    91      27.944  56.057  -9.205  1.00  0.00              
ATOM     92  CA  CYS    92      28.070  54.263  -5.956  1.00  0.00              
ATOM     93  CA  MET    93      27.838  50.473  -5.945  1.00  0.00              
ATOM     94  CA  LEU    94      26.371  48.719  -2.919  1.00  0.00              
ATOM     95  CA  GLY    95      26.882  45.067  -2.342  1.00  0.00              
ATOM     96  CA  VAL    96      24.042  43.319  -0.675  1.00  0.00              
ATOM     97  CA  CYS    97      24.698  41.123   2.332  1.00  0.00              
ATOM     98  CA  SER    98      23.426  37.626   2.504  1.00  0.00              
ATOM     99  CA  ASN    99      20.736  38.593   5.074  1.00  0.00              
ATOM    100  CA  MET   100      19.295  41.095   2.627  1.00  0.00              
ATOM    101  CA  ARG   101      19.171  38.613  -0.222  1.00  0.00              
ATOM    102  CA  ALA   102      17.314  36.142   1.955  1.00  0.00              
ATOM    103  CA  ASP   103      14.792  38.816   2.924  1.00  0.00              
ATOM    104  CA  LEU   104      14.217  39.867  -0.671  1.00  0.00              
ATOM    105  CA  GLU   105      13.636  36.283  -1.806  1.00  0.00              
ATOM    106  CA  ALA   106      11.097  35.840   0.954  1.00  0.00              
ATOM    107  CA  ILE   107       9.248  39.051  -0.038  1.00  0.00              
ATOM    108  CA  LEU   108       9.246  38.260  -3.717  1.00  0.00              
ATOM    109  CA  PRO   109       8.067  34.692  -3.426  1.00  0.00              
ATOM    110  CA  GLU   110       4.791  35.368  -1.566  1.00  0.00              
ATOM    111  CA  ARG   111       3.506  38.022  -3.911  1.00  0.00              
ATOM    112  CA  PHE   112       4.439  41.192  -2.173  1.00  0.00              
ATOM    113  CA  ILE   113       4.556  44.517  -3.796  1.00  0.00              
ATOM    114  CA  PHE   114       6.827  47.109  -2.229  1.00  0.00              
ATOM    115  CA  THR   115       7.179  50.604  -3.574  1.00  0.00              
ATOM    116  CA  GLU   116      10.330  52.562  -2.745  1.00  0.00              
ATOM    117  CA  ASP   117      10.261  56.240  -2.121  1.00  0.00              
ATOM    290  CA  LYS   290      18.034  40.626  -6.168  1.00  0.00              
ATOM    291  CA  TYR   291      19.056  42.835  -3.294  1.00  0.00              
ATOM    292  CA  MET   292      17.478  46.237  -3.631  1.00  0.00              
ATOM    293  CA  ALA   293      18.846  49.335  -2.037  1.00  0.00              
ATOM    294  CA  CYS   294      17.153  52.718  -2.195  1.00  0.00              
ATOM    295  CA  LEU   295      19.384  55.672  -1.537  1.00  0.00              
ATOM    296  CA  LYS   296      17.927  58.715   0.062  1.00  0.00              
ATOM    297  CA  ASP   297      18.738  61.361  -2.588  1.00  0.00              
ATOM    298  CA  HIS   298      18.139  59.069  -5.530  1.00  0.00              
TER                                                                             
END
