
#######################################################
#                                                     #
#                        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   19 (  151),  selected   19 , name T0348TS186_4
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS186_4.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    P      43      -       -           -
LGA    M      44      -       -           -
LGA    M      45      -       -           -
LGA    L      46      D       2          3.599
LGA    E      47      A       3          2.207
LGA    S      48      K       4          1.874
LGA    E      49      F       5          3.458
LGA    A      50      L       6          0.789
LGA    R      51      E       7          1.210
LGA    E      52      I       8          1.411
LGA    L      53      L       9          1.656
LGA    A      54      V      10          0.811
LGA    P      55      C      11          2.743
LGA    E      56      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    E      57      C      29          1.569
LGA    E      58      K      30          2.649
LGA    V      59      G      31          4.637
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      A      35           -
LGA    -       -      F      36           -
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    K      60      E      58          3.962
LGA    L      61      V      59           #
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   61    5.0     14    2.60     7.14     17.997     0.518

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.984354 * X  +  -0.157146 * Y  +   0.079704 * Z  +  32.686897
  Y_new =   0.017170 * X  +  -0.535734 * Y  +  -0.844212 * Z  + 124.144981
  Z_new =   0.175365 * X  +  -0.829635 * Y  +   0.530050 * Z  +  82.369232 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.002267    2.139326  [ DEG:   -57.4257    122.5743 ]
  Theta =  -0.176276   -2.965317  [ DEG:   -10.0999   -169.9001 ]
  Phi   =   3.124151   -0.017441  [ DEG:   179.0007     -0.9993 ]
 
# 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: T0348TS186_4                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS186_4.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   61   5.0   14   2.60    7.14  17.997
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS186_4
PFRMAT TS
TARGET T0348
MODEL  4
PARENT 1g3j_B
ATOM      1  N   PRO    43     -10.761  57.274  61.376  1.00  0.00
ATOM      2  CA  PRO    43      -9.632  56.315  61.559  1.00  0.00
ATOM      3  C   PRO    43      -9.047  55.899  60.216  1.00  0.00
ATOM      4  O   PRO    43      -9.726  55.944  59.190  1.00  0.00
ATOM      5  CB  PRO    43     -10.269  55.128  62.284  1.00  0.00
ATOM      6  CG  PRO    43     -11.467  55.704  62.962  1.00  0.00
ATOM      7  CD  PRO    43     -12.008  56.754  62.032  1.00  0.00
ATOM      8  N   MET    44      -7.775  55.511  60.229  1.00  0.00
ATOM      9  CA  MET    44      -7.086  55.080  59.018  1.00  0.00
ATOM     10  C   MET    44      -7.029  53.558  58.948  1.00  0.00
ATOM     11  O   MET    44      -7.121  52.875  59.972  1.00  0.00
ATOM     12  CB  MET    44      -5.655  55.619  58.995  1.00  0.00
ATOM     13  CG  MET    44      -5.563  57.133  58.897  1.00  0.00
ATOM     14  SD  MET    44      -3.865  57.733  58.965  1.00  0.00
ATOM     15  CE  MET    44      -3.338  57.453  57.277  1.00  0.00
ATOM     16  N   MET    45      -6.885  53.032  57.737  1.00  0.00
ATOM     17  CA  MET    45      -6.813  51.592  57.520  1.00  0.00
ATOM     18  C   MET    45      -5.476  51.072  58.056  1.00  0.00
ATOM     19  O   MET    45      -4.417  51.612  57.728  1.00  0.00
ATOM     20  CB  MET    45      -6.915  51.270  56.027  1.00  0.00
ATOM     21  CG  MET    45      -8.281  51.555  55.424  1.00  0.00
ATOM     22  SD  MET    45      -9.577  50.506  56.109  1.00  0.00
ATOM     23  CE  MET    45      -9.154  48.924  55.381  1.00  0.00
ATOM     24  N   LEU    46      -3.282  49.918  44.260  1.00  0.00
ATOM     25  CA  LEU    46      -3.268  49.290  45.574  1.00  0.00
ATOM     26  C   LEU    46      -1.914  49.482  46.235  1.00  0.00
ATOM     27  O   LEU    46      -0.897  49.609  45.558  1.00  0.00
ATOM     28  CB  LEU    46      -3.542  47.790  45.454  1.00  0.00
ATOM     29  CG  LEU    46      -4.935  47.392  44.961  1.00  0.00
ATOM     30  CD1 LEU    46      -5.026  45.887  44.766  1.00  0.00
ATOM     31  CD2 LEU    46      -5.999  47.807  45.967  1.00  0.00
ATOM     32  N   GLU    47      -1.907  49.504  47.561  1.00  0.00
ATOM     33  CA  GLU    47      -0.662  49.652  48.297  1.00  0.00
ATOM     34  C   GLU    47       0.077  48.316  48.355  1.00  0.00
ATOM     35  O   GLU    47      -0.536  47.269  48.569  1.00  0.00
ATOM     36  CB  GLU    47      -0.938  50.120  49.727  1.00  0.00
ATOM     37  CG  GLU    47      -1.548  51.508  49.819  1.00  0.00
ATOM     38  CD  GLU    47      -1.775  51.952  51.251  1.00  0.00
ATOM     39  OE1 GLU    47      -1.491  51.156  52.171  1.00  0.00
ATOM     40  OE2 GLU    47      -2.237  53.094  51.453  1.00  0.00
ATOM     41  N   SER    48       1.385  48.360  48.116  1.00  0.00
ATOM     42  CA  SER    48       2.231  47.170  48.183  1.00  0.00
ATOM     43  C   SER    48       2.226  46.710  49.635  1.00  0.00
ATOM     44  O   SER    48       2.038  47.525  50.536  1.00  0.00
ATOM     45  CB  SER    48       3.656  47.500  47.734  1.00  0.00
ATOM     46  OG  SER    48       4.288  48.380  48.647  1.00  0.00
ATOM     47  N   GLU    49       2.438  45.415  49.861  1.00  0.00
ATOM     48  CA  GLU    49       2.456  44.871  51.219  1.00  0.00
ATOM     49  C   GLU    49       3.421  43.707  51.381  1.00  0.00
ATOM     50  O   GLU    49       3.528  42.853  50.506  1.00  0.00
ATOM     51  CB  GLU    49       1.070  44.383  51.627  1.00  0.00
ATOM     52  CG  GLU    49       0.025  45.454  51.757  1.00  0.00
ATOM     53  CD  GLU    49      -1.312  44.881  52.148  1.00  0.00
ATOM     54  OE1 GLU    49      -1.381  44.199  53.193  1.00  0.00
ATOM     55  OE2 GLU    49      -2.288  45.101  51.406  1.00  0.00
ATOM     56  N   ALA    50       4.047  43.645  52.552  1.00  0.00
ATOM     57  CA  ALA    50       5.005  42.591  52.881  1.00  0.00
ATOM     58  C   ALA    50       4.313  41.358  53.441  1.00  0.00
ATOM     59  O   ALA    50       3.320  41.469  54.156  1.00  0.00
ATOM     60  CB  ALA    50       5.997  43.084  53.924  1.00  0.00
ATOM     61  N   ARG    51       4.821  40.182  53.080  1.00  0.00
ATOM     62  CA  ARG    51       4.295  38.921  53.589  1.00  0.00
ATOM     63  C   ARG    51       5.339  38.486  54.612  1.00  0.00
ATOM     64  O   ARG    51       6.493  38.224  54.259  1.00  0.00
ATOM     65  CB  ARG    51       4.150  37.905  52.455  1.00  0.00
ATOM     66  CG  ARG    51       3.153  38.311  51.381  1.00  0.00
ATOM     67  CD  ARG    51       3.128  37.306  50.241  1.00  0.00
ATOM     68  NE  ARG    51       2.208  37.706  49.179  1.00  0.00
ATOM     69  CZ  ARG    51       1.966  36.984  48.090  1.00  0.00
ATOM     70  NH1 ARG    51       1.114  37.428  47.176  1.00  0.00
ATOM     71  NH2 ARG    51       2.577  35.819  47.918  1.00  0.00
ATOM     72  N   GLU    52       4.941  38.446  55.882  1.00  0.00
ATOM     73  CA  GLU    52       5.856  38.081  56.958  1.00  0.00
ATOM     74  C   GLU    52       6.137  36.584  57.004  1.00  0.00
ATOM     75  O   GLU    52       5.331  35.813  57.524  1.00  0.00
ATOM     76  CB  GLU    52       5.272  38.478  58.315  1.00  0.00
ATOM     77  CG  GLU    52       6.214  38.252  59.486  1.00  0.00
ATOM     78  CD  GLU    52       5.558  38.530  60.824  1.00  0.00
ATOM     79  OE1 GLU    52       4.393  38.982  60.832  1.00  0.00
ATOM     80  OE2 GLU    52       6.208  38.296  61.864  1.00  0.00
ATOM     81  N   LEU    53       7.266  36.172  56.434  1.00  0.00
ATOM     82  CA  LEU    53       7.651  34.766  56.448  1.00  0.00
ATOM     83  C   LEU    53       8.590  34.557  57.629  1.00  0.00
ATOM     84  O   LEU    53       9.507  35.352  57.845  1.00  0.00
ATOM     85  CB  LEU    53       8.361  34.392  55.146  1.00  0.00
ATOM     86  CG  LEU    53       7.549  34.556  53.859  1.00  0.00
ATOM     87  CD1 LEU    53       8.398  34.223  52.642  1.00  0.00
ATOM     88  CD2 LEU    53       6.341  33.631  53.865  1.00  0.00
ATOM     89  N   ALA    54       8.359  33.498  58.395  1.00  0.00
ATOM     90  CA  ALA    54       9.186  33.200  59.560  1.00  0.00
ATOM     91  C   ALA    54       9.146  31.713  59.873  1.00  0.00
ATOM     92  O   ALA    54       8.815  31.311  60.988  1.00  0.00
ATOM     93  CB  ALA    54       8.683  33.962  60.777  1.00  0.00
ATOM     94  N   PRO    55       9.510  30.901  58.884  1.00  0.00
ATOM     95  CA  PRO    55       9.507  29.453  59.038  1.00  0.00
ATOM     96  C   PRO    55      10.887  28.880  59.371  1.00  0.00
ATOM     97  O   PRO    55      11.781  28.837  58.524  1.00  0.00
ATOM     98  CB  PRO    55       9.024  28.938  57.680  1.00  0.00
ATOM     99  CG  PRO    55       9.467  29.979  56.707  1.00  0.00
ATOM    100  CD  PRO    55       9.534  31.268  57.478  1.00  0.00
ATOM    101  N   GLU    56      11.045  28.460  60.623  1.00  0.00
ATOM    102  CA  GLU    56      12.282  27.854  61.106  1.00  0.00
ATOM    103  C   GLU    56      12.181  26.379  60.748  1.00  0.00
ATOM    104  O   GLU    56      13.108  25.789  60.195  1.00  0.00
ATOM    105  CB  GLU    56      12.387  28.008  62.627  1.00  0.00
ATOM    106  CG  GLU    56      13.653  27.420  63.232  1.00  0.00
ATOM    107  CD  GLU    56      13.722  27.573  64.746  1.00  0.00
ATOM    108  OE1 GLU    56      12.667  27.532  65.419  1.00  0.00
ATOM    109  OE2 GLU    56      14.846  27.724  65.266  1.00  0.00
ATOM    110  N   GLU    57      11.024  25.816  61.092  1.00  0.00
ATOM    111  CA  GLU    57      10.674  24.427  60.838  1.00  0.00
ATOM    112  C   GLU    57      11.688  23.321  60.610  1.00  0.00
ATOM    113  O   GLU    57      12.536  23.391  59.718  1.00  0.00
ATOM    114  CB  GLU    57       9.827  24.311  59.570  1.00  0.00
ATOM    115  CG  GLU    57       9.354  22.899  59.266  1.00  0.00
ATOM    116  CD  GLU    57       8.471  22.832  58.035  1.00  0.00
ATOM    117  OE1 GLU    57       8.218  23.894  57.427  1.00  0.00
ATOM    118  OE2 GLU    57       8.034  21.719  57.677  1.00  0.00
ATOM    119  N   GLU    58      11.546  22.266  61.406  1.00  0.00
ATOM    120  CA  GLU    58      12.375  21.065  61.327  1.00  0.00
ATOM    121  C   GLU    58      13.867  21.110  61.631  1.00  0.00
ATOM    122  O   GLU    58      14.651  21.735  60.916  1.00  0.00
ATOM    123  CB  GLU    58      12.169  20.368  59.975  1.00  0.00
ATOM    124  CG  GLU    58      11.256  19.150  60.016  1.00  0.00
ATOM    125  CD  GLU    58       9.808  19.496  60.306  1.00  0.00
ATOM    126  OE1 GLU    58       9.501  19.869  61.460  1.00  0.00
ATOM    127  OE2 GLU    58       8.976  19.391  59.378  1.00  0.00
ATOM    128  N   VAL    59      14.236  20.420  62.706  1.00  0.00
ATOM    129  CA  VAL    59      15.627  20.265  63.116  1.00  0.00
ATOM    130  C   VAL    59      15.747  18.758  63.072  1.00  0.00
ATOM    131  O   VAL    59      15.090  18.059  63.843  1.00  0.00
ATOM    132  CB  VAL    59      15.871  20.853  64.519  1.00  0.00
ATOM    133  CG1 VAL    59      17.320  20.656  64.935  1.00  0.00
ATOM    134  CG2 VAL    59      15.566  22.343  64.532  1.00  0.00
ATOM    135  N   LYS    60      16.524  18.259  62.120  1.00  0.00
ATOM    136  CA  LYS    60      16.713  16.827  61.971  1.00  0.00
ATOM    137  C   LYS    60      17.370  16.219  63.215  1.00  0.00
ATOM    138  O   LYS    60      18.554  15.877  63.217  1.00  0.00
ATOM    139  CB  LYS    60      17.610  16.528  60.769  1.00  0.00
ATOM    140  CG  LYS    60      16.983  16.866  59.427  1.00  0.00
ATOM    141  CD  LYS    60      17.914  16.514  58.278  1.00  0.00
ATOM    142  CE  LYS    60      17.295  16.873  56.936  1.00  0.00
ATOM    143  NZ  LYS    60      18.202  16.545  55.801  1.00  0.00
ATOM    144  N   LEU    61      16.577  16.120  64.281  1.00  0.00
ATOM    145  CA  LEU    61      17.008  15.567  65.563  1.00  0.00
ATOM    146  C   LEU    61      16.806  14.049  65.599  1.00  0.00
ATOM    147  O   LEU    61      16.347  13.486  64.579  1.00  0.00
ATOM    148  CB  LEU    61      16.205  16.184  66.710  1.00  0.00
ATOM    149  CG  LEU    61      16.273  17.706  66.843  1.00  0.00
ATOM    150  CD1 LEU    61      15.400  18.184  67.994  1.00  0.00
ATOM    151  CD2 LEU    61      17.700  18.160  67.107  1.00  0.00
TER
END
