
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0353TS550_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS550_1.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    H      19      M       1           -
LGA    -       -      Q       2           -
LGA    F      20      I       3           #
LGA    D      21      H       4          1.866
LGA    V      22      V       5          2.570
LGA    -       -      Y       6           -
LGA    -       -      D       7           -
LGA    -       -      T       8           -
LGA    -       -      Y       9           -
LGA    -       -      V      10           -
LGA    -       -      K      11           -
LGA    -       -      A      12           -
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    K      30      H      16          4.884
LGA    K      31      V      17          4.618
LGA    A      32      -       -           -
LGA    I      33      -       -           -
LGA    E      34      M      18          2.716
LGA    F      35      H      19          4.935
LGA    A      36      F      20          2.002
LGA    K      37      D      21          4.462
LGA    Q      38      -       -           -
LGA    W      39      V      22          1.060
LGA    L      40      F      23          4.868
LGA    S      41      -       -           -
LGA    S      42      T      24           #
LGA    E      54      D      25          4.084
LGA    -       -      V      26           -
LGA    C      55      R      27          3.663
LGA    R      56      D      28          3.964
LGA    -       -      D      29           -
LGA    -       -      K      30           -
LGA    F      57      K      31          1.598
LGA    C      58      A      32          4.498
LGA    H      59      I      33          3.532
LGA    S      60      E      34          0.463
LGA    Q      61      F      35          3.846
LGA    -       -      A      36           -
LGA    -       -      K      37           -
LGA    -       -      Q      38           -
LGA    -       -      W      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    -       -      E      46           -
LGA    -       -      G      47           -
LGA    -       -      A      48           -
LGA    -       -      T      49           -
LGA    -       -      V      50           -
LGA    -       -      T      51           -
LGA    D      65      S      52          2.442
LGA    E      66      E      53          1.746
LGA    V      67      E      54          2.937
LGA    I      68      C      55          2.827
LGA    E      69      R      56          3.434
LGA    A      70      -       -           -
LGA    I      71      -       -           -
LGA    K      72      F      57          4.338
LGA    Q      73      -       -           -
LGA    N      74      -       -           -
LGA    G      75      -       -           -
LGA    Y      76      -       -           -
LGA    F      77      -       -           -
LGA    I      78      C      58          1.099
LGA    Y      79      H      59          2.424
LGA    K      80      S      60           #
LGA    M      81      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   85    5.0     26    3.37     7.69     17.224     0.749

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.848811 * X  +  -0.510387 * Y  +  -0.137933 * Z  +  43.306751
  Y_new =  -0.262509 * X  +   0.180395 * Y  +   0.947917 * Z  +  -8.493344
  Z_new =  -0.458922 * X  +   0.840811 * Y  +  -0.287102 * Z  + -24.115152 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.899842   -1.241751  [ DEG:   108.8529    -71.1471 ]
  Theta =   0.476782    2.664811  [ DEG:    27.3176    152.6824 ]
  Phi   =  -2.841656    0.299936  [ DEG:  -162.8149     17.1851 ]
 
# 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: T0353TS550_1                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS550_1.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   85   5.0   26   3.37    7.69  17.224
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS550_1
PFRMAT TS
TARGET T0353
MODEL 1
PARENT 1b6a
ATOM      1  N   HIS    19       0.605   9.209  -8.247  1.00  0.00
ATOM      2  CA  HIS    19       1.789   8.399  -8.006  1.00  0.00
ATOM      3  C   HIS    19       2.465   8.678  -6.671  1.00  0.00
ATOM      4  O   HIS    19       2.509   9.835  -6.222  1.00  0.00
ATOM      5  N   PHE    20       2.796   7.609  -5.924  1.00  0.00
ATOM      6  CA  PHE    20       3.389   7.723  -4.592  1.00  0.00
ATOM      7  C   PHE    20       4.476   6.672  -4.454  1.00  0.00
ATOM      8  O   PHE    20       4.438   5.663  -5.156  1.00  0.00
ATOM      9  N   ASP    21       5.444   6.836  -3.554  1.00  0.00
ATOM     10  CA  ASP    21       6.450   5.783  -3.373  1.00  0.00
ATOM     11  C   ASP    21       7.087   5.988  -1.999  1.00  0.00
ATOM     12  O   ASP    21       7.403   7.118  -1.625  1.00  0.00
ATOM     13  N   VAL    22       7.273   4.900  -1.275  1.00  0.00
ATOM     14  CA  VAL    22       7.989   4.976   0.003  1.00  0.00
ATOM     15  C   VAL    22       9.375   5.540  -0.201  1.00  0.00
ATOM     16  O   VAL    22      10.069   5.250  -1.178  1.00  0.00
ATOM     17  N   LYS    30      -4.763   3.873  13.641  1.00  0.00
ATOM     18  CA  LYS    30      -5.113   2.579  13.051  1.00  0.00
ATOM     19  C   LYS    30      -5.179   2.550  11.540  1.00  0.00
ATOM     20  O   LYS    30      -4.683   1.603  10.880  1.00  0.00
ATOM     21  N   LYS    31      -5.803   3.539  10.903  1.00  0.00
ATOM     22  CA  LYS    31      -5.925   3.524   9.444  1.00  0.00
ATOM     23  C   LYS    31      -4.582   3.810   8.797  1.00  0.00
ATOM     24  O   LYS    31      -4.292   3.175   7.770  1.00  0.00
ATOM     25  N   ALA    32      -3.760   4.660   9.396  1.00  0.00
ATOM     26  CA  ALA    32      -2.420   4.948   8.874  1.00  0.00
ATOM     27  C   ALA    32      -1.498   3.749   9.029  1.00  0.00
ATOM     28  O   ALA    32      -0.790   3.427   8.054  1.00  0.00
ATOM     29  N   ILE    33      -1.550   3.076  10.188  1.00  0.00
ATOM     30  CA  ILE    33      -0.784   1.845  10.379  1.00  0.00
ATOM     31  C   ILE    33      -1.207   0.783   9.383  1.00  0.00
ATOM     32  O   ILE    33      -0.312   0.145   8.764  1.00  0.00
ATOM     33  N   GLU    34      -2.513   0.592   9.183  1.00  0.00
ATOM     34  CA  GLU    34      -2.926  -0.420   8.200  1.00  0.00
ATOM     35  C   GLU    34      -2.453  -0.100   6.787  1.00  0.00
ATOM     36  O   GLU    34      -1.923  -0.985   6.080  1.00  0.00
ATOM     37  N   PHE    35      -2.591   1.155   6.349  1.00  0.00
ATOM     38  CA  PHE    35      -2.171   1.513   5.000  1.00  0.00
ATOM     39  C   PHE    35      -0.672   1.311   4.837  1.00  0.00
ATOM     40  O   PHE    35      -0.214   0.786   3.819  1.00  0.00
ATOM     41  N   ALA    36       0.148   1.709   5.825  1.00  0.00
ATOM     42  CA  ALA    36       1.577   1.462   5.709  1.00  0.00
ATOM     43  C   ALA    36       1.895  -0.037   5.629  1.00  0.00
ATOM     44  O   ALA    36       2.743  -0.409   4.809  1.00  0.00
ATOM     45  N   LYS    37       1.143  -0.862   6.371  1.00  0.00
ATOM     46  CA  LYS    37       1.364  -2.313   6.217  1.00  0.00
ATOM     47  C   LYS    37       0.995  -2.789   4.822  1.00  0.00
ATOM     48  O   LYS    37       1.788  -3.584   4.274  1.00  0.00
ATOM     49  N   GLN    38      -0.105  -2.309   4.247  1.00  0.00
ATOM     50  CA  GLN    38      -0.477  -2.654   2.880  1.00  0.00
ATOM     51  C   GLN    38       0.624  -2.262   1.906  1.00  0.00
ATOM     52  O   GLN    38       1.001  -3.056   1.014  1.00  0.00
ATOM     53  N   TRP    39       1.199  -1.077   2.087  1.00  0.00
ATOM     54  CA  TRP    39       2.242  -0.604   1.165  1.00  0.00
ATOM     55  C   TRP    39       3.470  -1.486   1.304  1.00  0.00
ATOM     56  O   TRP    39       4.066  -1.888   0.320  1.00  0.00
ATOM     57  N   LEU    40       3.853  -1.789   2.552  1.00  0.00
ATOM     58  CA  LEU    40       5.082  -2.566   2.755  1.00  0.00
ATOM     59  C   LEU    40       4.912  -3.970   2.193  1.00  0.00
ATOM     60  O   LEU    40       5.875  -4.506   1.619  1.00  0.00
ATOM     61  N   SER    41       3.727  -4.568   2.345  1.00  0.00
ATOM     62  CA  SER    41       3.498  -5.914   1.836  1.00  0.00
ATOM     63  C   SER    41       3.430  -5.977   0.310  1.00  0.00
ATOM     64  O   SER    41       3.924  -6.948  -0.277  1.00  0.00
ATOM     65  N   SER    42       2.863  -4.977  -0.344  1.00  0.00
ATOM     66  CA  SER    42       2.515  -5.099  -1.756  1.00  0.00
ATOM     67  C   SER    42       3.513  -4.378  -2.641  1.00  0.00
ATOM     68  O   SER    42       3.667  -4.791  -3.805  1.00  0.00
ATOM     69  N   GLU    54       3.708   3.171  -6.441  1.00  0.00
ATOM     70  CA  GLU    54       2.336   2.688  -6.600  1.00  0.00
ATOM     71  C   GLU    54       1.439   3.873  -6.906  1.00  0.00
ATOM     72  O   GLU    54       1.860   5.011  -6.995  1.00  0.00
ATOM     73  N   CYS    55       0.168   3.549  -7.190  1.00  0.00
ATOM     74  CA  CYS    55      -0.805   4.625  -7.400  1.00  0.00
ATOM     75  C   CYS    55      -2.090   4.349  -6.631  1.00  0.00
ATOM     76  O   CYS    55      -2.271   3.253  -6.080  1.00  0.00
ATOM     77  N   ARG    56      -2.984   5.345  -6.648  1.00  0.00
ATOM     78  CA  ARG    56      -4.248   5.178  -5.918  1.00  0.00
ATOM     79  C   ARG    56      -5.092   4.066  -6.507  1.00  0.00
ATOM     80  O   ARG    56      -5.686   3.265  -5.756  1.00  0.00
ATOM     81  N   PHE    57      -5.099   3.865  -7.833  1.00  0.00
ATOM     82  CA  PHE    57      -5.847   2.732  -8.383  1.00  0.00
ATOM     83  C   PHE    57      -5.372   1.394  -7.852  1.00  0.00
ATOM     84  O   PHE    57      -6.131   0.425  -7.729  1.00  0.00
ATOM     85  N   CYS    58      -4.064   1.255  -7.603  1.00  0.00
ATOM     86  CA  CYS    58      -3.517   0.017  -7.073  1.00  0.00
ATOM     87  C   CYS    58      -3.903  -0.243  -5.618  1.00  0.00
ATOM     88  O   CYS    58      -3.857  -1.400  -5.191  1.00  0.00
ATOM     89  N   HIS    59      -4.215   0.818  -4.856  1.00  0.00
ATOM     90  CA  HIS    59      -4.766   0.577  -3.524  1.00  0.00
ATOM     91  C   HIS    59      -6.232   0.176  -3.632  1.00  0.00
ATOM     92  O   HIS    59      -6.649  -0.710  -2.882  1.00  0.00
ATOM     93  N   SER    60      -6.962   0.801  -4.545  1.00  0.00
ATOM     94  CA  SER    60      -8.375   0.445  -4.744  1.00  0.00
ATOM     95  C   SER    60      -8.512  -1.026  -5.099  1.00  0.00
ATOM     96  O   SER    60      -9.414  -1.715  -4.601  1.00  0.00
ATOM     97  N   GLN    61      -7.636  -1.550  -5.960  1.00  0.00
ATOM     98  CA  GLN    61      -7.752  -2.926  -6.417  1.00  0.00
ATOM     99  C   GLN    61      -7.447  -3.929  -5.308  1.00  0.00
ATOM    100  O   GLN    61      -7.900  -5.069  -5.370  1.00  0.00
ATOM    101  N   ASP    65      -7.371   8.026   1.976  1.00  0.00
ATOM    102  CA  ASP    65      -6.679   9.213   1.471  1.00  0.00
ATOM    103  C   ASP    65      -6.081  10.008   2.618  1.00  0.00
ATOM    104  O   ASP    65      -4.954  10.508   2.498  1.00  0.00
ATOM    105  N   GLU    66      -6.804  10.078   3.761  1.00  0.00
ATOM    106  CA  GLU    66      -6.189  10.750   4.898  1.00  0.00
ATOM    107  C   GLU    66      -5.000   9.966   5.444  1.00  0.00
ATOM    108  O   GLU    66      -4.006  10.605   5.822  1.00  0.00
ATOM    109  N   VAL    67      -5.095   8.627   5.495  1.00  0.00
ATOM    110  CA  VAL    67      -3.910   7.853   5.911  1.00  0.00
ATOM    111  C   VAL    67      -2.730   8.076   4.978  1.00  0.00
ATOM    112  O   VAL    67      -1.595   8.240   5.454  1.00  0.00
ATOM    113  N   ILE    68      -2.993   8.167   3.677  1.00  0.00
ATOM    114  CA  ILE    68      -1.950   8.401   2.691  1.00  0.00
ATOM    115  C   ILE    68      -1.349   9.793   2.835  1.00  0.00
ATOM    116  O   ILE    68      -0.126   9.925   2.854  1.00  0.00
ATOM    117  N   GLU    69      -2.205  10.787   3.121  1.00  0.00
ATOM    118  CA  GLU    69      -1.687  12.132   3.395  1.00  0.00
ATOM    119  C   GLU    69      -0.806  12.134   4.630  1.00  0.00
ATOM    120  O   GLU    69       0.261  12.745   4.695  1.00  0.00
ATOM    121  N   ALA    70      -1.235  11.403   5.680  1.00  0.00
ATOM    122  CA  ALA    70      -0.439  11.278   6.881  1.00  0.00
ATOM    123  C   ALA    70       0.942  10.677   6.644  1.00  0.00
ATOM    124  O   ALA    70       1.942  11.176   7.166  1.00  0.00
ATOM    125  N   ILE    71       1.006   9.614   5.819  1.00  0.00
ATOM    126  CA  ILE    71       2.307   9.041   5.507  1.00  0.00
ATOM    127  C   ILE    71       3.177   9.977   4.668  1.00  0.00
ATOM    128  O   ILE    71       4.393   9.944   4.839  1.00  0.00
ATOM    129  N   LYS    72       2.573  10.801   3.827  1.00  0.00
ATOM    130  CA  LYS    72       3.332  11.806   3.094  1.00  0.00
ATOM    131  C   LYS    72       3.826  12.913   4.024  1.00  0.00
ATOM    132  O   LYS    72       4.980  13.300   3.943  1.00  0.00
ATOM    133  N   GLN    73       2.977  13.373   4.942  1.00  0.00
ATOM    134  CA  GLN    73       3.349  14.426   5.875  1.00  0.00
ATOM    135  C   GLN    73       4.414  13.956   6.855  1.00  0.00
ATOM    136  O   GLN    73       5.273  14.740   7.275  1.00  0.00
ATOM    137  N   ASN    74       3.972  13.694   8.015  1.00  0.00
ATOM    138  CA  ASN    74       4.823  13.401   9.163  1.00  0.00
ATOM    139  C   ASN    74       5.623  12.114   9.014  1.00  0.00
ATOM    140  O   ASN    74       5.097  11.078   8.595  1.00  0.00
ATOM    141  N   GLY    75       6.899  12.193   9.373  1.00  0.00
ATOM    142  CA  GLY    75       7.775  11.040   9.292  1.00  0.00
ATOM    143  C   GLY    75       8.279  10.765   7.890  1.00  0.00
ATOM    144  O   GLY    75       9.202   9.974   7.706  1.00  0.00
ATOM    145  N   TYR    76       7.676  11.412   6.898  1.00  0.00
ATOM    146  CA  TYR    76       8.075  11.210   5.512  1.00  0.00
ATOM    147  C   TYR    76       7.982   9.731   5.138  1.00  0.00
ATOM    148  O   TYR    76       8.879   9.178   4.492  1.00  0.00
ATOM    149  N   PHE    77       6.892   9.087   5.539  1.00  0.00
ATOM    150  CA  PHE    77       6.709   7.675   5.237  1.00  0.00
ATOM    151  C   PHE    77       6.306   7.422   3.796  1.00  0.00
ATOM    152  O   PHE    77       6.160   6.278   3.368  1.00  0.00
ATOM    153  N   ILE    78       6.203   8.327   2.931  1.00  0.00
ATOM    154  CA  ILE    78       5.862   8.208   1.518  1.00  0.00
ATOM    155  C   ILE    78       6.038   9.570   0.868  1.00  0.00
ATOM    156  O   ILE    78       5.766  10.620   1.468  1.00  0.00
ATOM    157  N   TYR    79       6.491   9.599  -0.386  1.00  0.00
ATOM    158  CA  TYR    79       6.560  10.836  -1.143  1.00  0.00
ATOM    159  C   TYR    79       5.534  10.804  -2.278  1.00  0.00
ATOM    160  O   TYR    79       5.414   9.787  -2.966  1.00  0.00
ATOM    161  N   LYS    80       4.832  11.885  -2.467  1.00  0.00
ATOM    162  CA  LYS    80       3.956  12.064  -3.622  1.00  0.00
ATOM    163  C   LYS    80       4.768  12.536  -4.827  1.00  0.00
ATOM    164  O   LYS    80       5.754  13.249  -4.708  1.00  0.00
ATOM    165  N   MET    81       4.352  12.077  -5.999  1.00  0.00
ATOM    166  CA  MET    81       4.983  12.464  -7.270  1.00  0.00
ATOM    167  C   MET    81       3.889  12.931  -8.216  1.00  0.00
ATOM    168  O   MET    81       3.396  12.162  -9.029  1.00  0.00
TER
END
