
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0348TS550_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS550_2.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       3      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    K       4      L       9          2.740
LGA    F       5      V      10          3.775
LGA    L       6      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    E       7      G      16          4.978
LGA    I       8      P      17          2.495
LGA    L       9      L      18          4.632
LGA    V      10      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    C      11      C      29          0.978
LGA    P      12      K      30          1.756
LGA    L      13      G      31          1.812
LGA    C      14      D      32          1.581
LGA    K      15      R      33          3.148
LGA    G      16      -       -           -
LGA    P      17      -       -           -
LGA    L      18      -       -           -
LGA    V      19      -       -           -
LGA    F      20      -       -           -
LGA    E      26      L      34          0.312
LGA    L      27      A      35          2.212
LGA    I      28      F      36          1.652
LGA    C      29      P      37          1.015
LGA    K      30      I      38          2.575
LGA    G      31      K      39          0.878
LGA    D      32      -       -           -
LGA    R      33      D      40           #
LGA    L      34      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    A      35      M      44          4.270
LGA    F      36      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    P      37      A      50          2.483
LGA    I      38      R      51          3.343
LGA    K      39      E      52          3.041
LGA    D      40      L      53          1.746
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    G      41      E      58          2.821
LGA    I      42      V      59           -
LGA    P      43      K      60          2.973
LGA    M      44      L      61           #
LGA    M      45      E      62           -
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    E      49      -       -           -
LGA    A      50      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   61    5.0     23    2.76     8.70     25.826     0.805

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.637355 * X  +   0.738812 * Y  +  -0.218942 * Z  + -212.608154
  Y_new =  -0.555019 * X  +   0.637247 * Y  +   0.534668 * Z  +  83.876999
  Z_new =   0.534539 * X  +  -0.219256 * Y  +   0.816207 * Z  + -83.232254 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.262433    2.879160  [ DEG:   -15.0363    164.9637 ]
  Theta =  -0.563963   -2.577630  [ DEG:   -32.3127   -147.6873 ]
  Phi   =  -0.716456    2.425137  [ DEG:   -41.0499    138.9501 ]
 
# 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: T0348TS550_2                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS550_2.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   61   5.0   23   2.76    8.70  25.826
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS550_2
PFRMAT TS
TARGET T0348
MODEL 2
PARENT 1hr0_S
ATOM      1  N   ALA     3      15.942  35.560  57.016  1.00  0.00
ATOM      2  CA  ALA     3      15.513  35.428  58.401  1.00  0.00
ATOM      3  C   ALA     3      14.008  35.537  58.646  1.00  0.00
ATOM      4  O   ALA     3      13.574  35.625  59.791  1.00  0.00
ATOM      5  N   LYS     4      13.211  35.533  57.581  1.00  0.00
ATOM      6  CA  LYS     4      11.764  35.583  57.756  1.00  0.00
ATOM      7  C   LYS     4      11.497  34.324  58.549  1.00  0.00
ATOM      8  O   LYS     4      10.770  34.327  59.539  1.00  0.00
ATOM      9  N   PHE     5      12.119  33.244  58.085  1.00  0.00
ATOM     10  CA  PHE     5      11.980  31.940  58.701  1.00  0.00
ATOM     11  C   PHE     5      13.193  31.558  59.534  1.00  0.00
ATOM     12  O   PHE     5      13.079  30.790  60.488  1.00  0.00
ATOM     13  N   LEU     6      14.356  32.097  59.185  1.00  0.00
ATOM     14  CA  LEU     6      15.557  31.765  59.933  1.00  0.00
ATOM     15  C   LEU     6      15.314  31.987  61.413  1.00  0.00
ATOM     16  O   LEU     6      15.553  31.094  62.224  1.00  0.00
ATOM     17  N   GLU     7      14.821  33.172  61.762  1.00  0.00
ATOM     18  CA  GLU     7      14.553  33.488  63.154  1.00  0.00
ATOM     19  C   GLU     7      13.127  33.121  63.541  1.00  0.00
ATOM     20  O   GLU     7      12.690  33.389  64.658  1.00  0.00
ATOM     21  N   ILE     8      12.404  32.509  62.611  1.00  0.00
ATOM     22  CA  ILE     8      11.038  32.074  62.875  1.00  0.00
ATOM     23  C   ILE     8      11.040  30.558  62.993  1.00  0.00
ATOM     24  O   ILE     8      10.055  29.959  63.427  1.00  0.00
ATOM     25  N   LEU     9      12.146  29.945  62.579  1.00  0.00
ATOM     26  CA  LEU     9      12.285  28.498  62.642  1.00  0.00
ATOM     27  C   LEU     9      12.915  28.133  63.968  1.00  0.00
ATOM     28  O   LEU     9      12.490  27.189  64.629  1.00  0.00
ATOM     29  N   VAL    10      11.332  28.519  63.396  1.00  0.00
ATOM     30  CA  VAL    10      10.105  27.718  63.432  1.00  0.00
ATOM     31  C   VAL    10      10.241  26.458  62.574  1.00  0.00
ATOM     32  O   VAL    10       9.611  25.428  62.858  1.00  0.00
ATOM     33  N   CYS    11      11.045  26.537  61.516  1.00  0.00
ATOM     34  CA  CYS    11      11.210  25.394  60.618  1.00  0.00
ATOM     35  C   CYS    11      11.890  24.223  61.301  1.00  0.00
ATOM     36  O   CYS    11      11.691  23.061  60.919  1.00  0.00
ATOM     37  N   PRO    12      12.696  24.534  62.316  1.00  0.00
ATOM     38  CA  PRO    12      13.430  23.530  63.075  1.00  0.00
ATOM     39  C   PRO    12      12.665  23.080  64.297  1.00  0.00
ATOM     40  O   PRO    12      12.972  22.047  64.850  1.00  0.00
ATOM     41  N   LEU    13      11.678  23.860  64.722  1.00  0.00
ATOM     42  CA  LEU    13      10.912  23.514  65.913  1.00  0.00
ATOM     43  C   LEU    13       9.583  22.762  65.730  1.00  0.00
ATOM     44  O   LEU    13       8.971  22.358  66.731  1.00  0.00
ATOM     45  N   CYS    14       9.123  22.606  64.486  1.00  0.00
ATOM     46  CA  CYS    14       7.871  21.892  64.172  1.00  0.00
ATOM     47  C   CYS    14       8.223  20.988  63.021  1.00  0.00
ATOM     48  O   CYS    14       9.141  21.284  62.264  1.00  0.00
ATOM     49  N   LYS    15       7.500  19.881  62.860  1.00  0.00
ATOM     50  CA  LYS    15       7.899  19.056  61.722  1.00  0.00
ATOM     51  C   LYS    15       7.351  19.572  60.390  1.00  0.00
ATOM     52  O   LYS    15       7.893  19.264  59.355  1.00  0.00
ATOM     53  N   GLY    16       6.311  20.398  60.419  1.00  0.00
ATOM     54  CA  GLY    16       5.733  20.905  59.160  1.00  0.00
ATOM     55  C   GLY    16       4.776  22.062  59.411  1.00  0.00
ATOM     56  O   GLY    16       4.653  22.528  60.545  1.00  0.00
ATOM     57  N   PRO    17       4.129  22.543  58.343  1.00  0.00
ATOM     58  CA  PRO    17       3.132  23.598  58.478  1.00  0.00
ATOM     59  C   PRO    17       3.408  25.070  58.192  1.00  0.00
ATOM     60  O   PRO    17       2.464  25.860  58.133  1.00  0.00
ATOM     61  N   LEU    18       5.211  25.632  58.336  1.00  0.00
ATOM     62  CA  LEU    18       5.525  27.040  58.146  1.00  0.00
ATOM     63  C   LEU    18       5.328  27.340  56.672  1.00  0.00
ATOM     64  O   LEU    18       5.626  26.501  55.823  1.00  0.00
ATOM     65  N   VAL    19       4.828  28.528  56.364  1.00  0.00
ATOM     66  CA  VAL    19       4.622  28.901  54.974  1.00  0.00
ATOM     67  C   VAL    19       5.531  30.070  54.631  1.00  0.00
ATOM     68  O   VAL    19       5.303  31.194  55.077  1.00  0.00
ATOM     69  N   PHE    20       6.569  29.799  53.848  1.00  0.00
ATOM     70  CA  PHE    20       7.496  30.850  53.467  1.00  0.00
ATOM     71  C   PHE    20       7.504  31.089  51.964  1.00  0.00
ATOM     72  O   PHE    20       7.287  30.171  51.173  1.00  0.00
ATOM     73  N   GLU    26       9.016  21.493  58.702  1.00  0.00
ATOM     74  CA  GLU    26       8.223  21.346  57.495  1.00  0.00
ATOM     75  C   GLU    26       7.856  22.711  56.963  1.00  0.00
ATOM     76  O   GLU    26       6.939  23.361  57.463  1.00  0.00
ATOM     77  N   LEU    27       8.581  23.144  55.944  1.00  0.00
ATOM     78  CA  LEU    27       8.319  24.435  55.346  1.00  0.00
ATOM     79  C   LEU    27       7.596  24.262  54.020  1.00  0.00
ATOM     80  O   LEU    27       8.092  23.589  53.113  1.00  0.00
ATOM     81  N   ILE    28       6.419  24.864  53.914  1.00  0.00
ATOM     82  CA  ILE    28       5.641  24.796  52.690  1.00  0.00
ATOM     83  C   ILE    28       6.076  25.984  51.840  1.00  0.00
ATOM     84  O   ILE    28       5.781  27.137  52.166  1.00  0.00
ATOM     85  N   CYS    29       6.799  25.694  50.761  1.00  0.00
ATOM     86  CA  CYS    29       7.295  26.737  49.871  1.00  0.00
ATOM     87  C   CYS    29       6.292  27.070  48.763  1.00  0.00
ATOM     88  O   CYS    29       5.532  26.212  48.302  1.00  0.00
ATOM     89  N   LYS    30       6.306  28.333  48.352  1.00  0.00
ATOM     90  CA  LYS    30       5.411  28.851  47.324  1.00  0.00
ATOM     91  C   LYS    30       5.953  28.529  45.925  1.00  0.00
ATOM     92  O   LYS    30       7.157  28.618  45.687  1.00  0.00
ATOM     93  N   GLY    31       5.936  28.300  45.004  1.00  0.00
ATOM     94  CA  GLY    31       6.032  28.995  43.724  1.00  0.00
ATOM     95  C   GLY    31       5.046  28.385  42.727  1.00  0.00
ATOM     96  O   GLY    31       5.183  28.583  41.523  1.00  0.00
ATOM     97  N   ASP    32       4.053  27.651  43.230  1.00  0.00
ATOM     98  CA  ASP    32       3.067  26.999  42.370  1.00  0.00
ATOM     99  C   ASP    32       1.683  26.855  43.011  1.00  0.00
ATOM    100  O   ASP    32       0.971  25.884  42.750  1.00  0.00
ATOM    101  N   ARG    33       1.305  27.812  43.853  1.00  0.00
ATOM    102  CA  ARG    33       0.008  27.755  44.497  1.00  0.00
ATOM    103  C   ARG    33      -0.096  26.869  45.727  1.00  0.00
ATOM    104  O   ARG    33      -0.781  27.228  46.694  1.00  0.00
ATOM    105  N   LEU    34       0.570  25.714  45.710  1.00  0.00
ATOM    106  CA  LEU    34       0.512  24.788  46.843  1.00  0.00
ATOM    107  C   LEU    34       0.956  25.435  48.130  1.00  0.00
ATOM    108  O   LEU    34       0.445  25.111  49.195  1.00  0.00
ATOM    109  N   ALA    35       1.499  26.575  48.170  1.00  0.00
ATOM    110  CA  ALA    35       2.445  26.424  49.271  1.00  0.00
ATOM    111  C   ALA    35       2.599  24.930  49.473  1.00  0.00
ATOM    112  O   ALA    35       1.836  24.313  50.220  1.00  0.00
ATOM    113  N   PHE    36       3.573  24.345  48.783  1.00  0.00
ATOM    114  CA  PHE    36       3.807  22.912  48.884  1.00  0.00
ATOM    115  C   PHE    36       4.592  22.549  50.129  1.00  0.00
ATOM    116  O   PHE    36       5.739  22.955  50.303  1.00  0.00
ATOM    117  N   PRO    37       3.971  21.778  51.026  1.00  0.00
ATOM    118  CA  PRO    37       4.635  21.365  52.259  1.00  0.00
ATOM    119  C   PRO    37       5.872  20.508  51.964  1.00  0.00
ATOM    120  O   PRO    37       5.803  19.528  51.218  1.00  0.00
ATOM    121  N   ILE    38       7.001  20.885  52.550  1.00  0.00
ATOM    122  CA  ILE    38       8.241  20.146  52.353  1.00  0.00
ATOM    123  C   ILE    38       8.837  19.711  53.688  1.00  0.00
ATOM    124  O   ILE    38       9.106  20.546  54.553  1.00  0.00
ATOM    125  N   LYS    39       9.030  18.405  53.859  1.00  0.00
ATOM    126  CA  LYS    39       9.626  17.888  55.085  1.00  0.00
ATOM    127  C   LYS    39      11.138  17.980  54.907  1.00  0.00
ATOM    128  O   LYS    39      11.743  17.198  54.169  1.00  0.00
ATOM    129  N   ASP    40      11.098  16.311  54.820  1.00  0.00
ATOM    130  CA  ASP    40      12.007  15.365  55.463  1.00  0.00
ATOM    131  C   ASP    40      13.413  15.524  54.919  1.00  0.00
ATOM    132  O   ASP    40      13.623  15.497  53.700  1.00  0.00
ATOM    133  N   GLY    41      14.363  15.664  55.843  1.00  0.00
ATOM    134  CA  GLY    41      15.780  15.845  55.537  1.00  0.00
ATOM    135  C   GLY    41      16.015  16.597  54.230  1.00  0.00
ATOM    136  O   GLY    41      16.233  15.992  53.174  1.00  0.00
ATOM    137  N   ILE    42      15.956  17.926  54.317  1.00  0.00
ATOM    138  CA  ILE    42      16.157  18.799  53.162  1.00  0.00
ATOM    139  C   ILE    42      17.651  18.919  52.851  1.00  0.00
ATOM    140  O   ILE    42      18.059  19.008  51.693  1.00  0.00
ATOM    141  N   PRO    43      18.459  18.927  53.906  1.00  0.00
ATOM    142  CA  PRO    43      19.892  19.021  53.734  1.00  0.00
ATOM    143  C   PRO    43      20.320  20.200  52.893  1.00  0.00
ATOM    144  O   PRO    43      19.898  21.326  53.135  1.00  0.00
ATOM    145  N   MET    44      21.149  19.926  51.891  1.00  0.00
ATOM    146  CA  MET    44      21.700  20.942  50.998  1.00  0.00
ATOM    147  C   MET    44      20.753  21.573  49.980  1.00  0.00
ATOM    148  O   MET    44      21.021  22.675  49.500  1.00  0.00
ATOM    149  N   MET    45      19.665  20.886  49.637  1.00  0.00
ATOM    150  CA  MET    45      18.753  21.405  48.624  1.00  0.00
ATOM    151  C   MET    45      17.929  22.612  49.005  1.00  0.00
ATOM    152  O   MET    45      17.037  22.549  49.855  1.00  0.00
ATOM    153  N   LEU    46      18.231  23.716  48.336  1.00  0.00
ATOM    154  CA  LEU    46      17.541  24.962  48.590  1.00  0.00
ATOM    155  C   LEU    46      16.020  24.757  48.570  1.00  0.00
ATOM    156  O   LEU    46      15.459  24.215  47.611  1.00  0.00
ATOM    157  N   GLU    47      15.487  25.281  49.669  1.00  0.00
ATOM    158  CA  GLU    47      14.028  25.142  49.708  1.00  0.00
ATOM    159  C   GLU    47      13.317  25.043  48.364  1.00  0.00
ATOM    160  O   GLU    47      12.733  24.009  48.043  1.00  0.00
ATOM    161  N   SER    48      13.346  26.129  47.597  1.00  0.00
ATOM    162  CA  SER    48      12.708  26.145  46.293  1.00  0.00
ATOM    163  C   SER    48      13.034  24.936  45.436  1.00  0.00
ATOM    164  O   SER    48      12.238  24.534  44.583  1.00  0.00
ATOM    165  N   GLU    49      14.212  24.357  45.653  1.00  0.00
ATOM    166  CA  GLU    49      14.623  23.182  44.906  1.00  0.00
ATOM    167  C   GLU    49      13.694  22.020  45.212  1.00  0.00
ATOM    168  O   GLU    49      13.768  20.979  44.568  1.00  0.00
ATOM    169  N   ALA    50      12.819  22.195  46.194  1.00  0.00
ATOM    170  CA  ALA    50      11.908  21.128  46.579  1.00  0.00
ATOM    171  C   ALA    50      10.462  21.473  46.292  1.00  0.00
ATOM    172  O   ALA    50       9.546  20.720  46.627  1.00  0.00
TER
END
