
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0349TS550_5
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS550_5.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    V      11      E       3          6.262
LGA    L      12      L       4          1.724
LGA    L      13      -       -           -
LGA    S      14      -       -           -
LGA    A      15      -       -           -
LGA    V      16      L       5          2.169
LGA    G      17      R       6          3.976
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      T       7          3.747
LGA    I      25      N       8          3.116
LGA    G      26      D       9           -
LGA    H      27      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    L      28      L      13          3.965
LGA    V      29      S      14          4.288
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    L      30      G      17          1.852
LGA    D      31      A      18          0.682
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    Q      32      D      21          2.345
LGA    N      33      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    M      34      H      27          3.891
LGA    S      35      L      28          3.415
LGA    -       -      V      29           -
LGA    I      36      L      30          1.120
LGA    -       -      D      31           -
LGA    -       -      Q      32           -
LGA    -       -      N      33           -
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      I      44           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    P      45      R      47          5.368
LGA    R      46      V      48           #
LGA    R      47      L      49          3.247
LGA    V      48      V      50          2.364
LGA    L      49      H      51          4.941
LGA    V      50      E      52          2.202
LGA    -       -      D      53           -
LGA    H      51      D      54          2.843
LGA    E      52      L      55          2.120
LGA    -       -      A      56           -
LGA    D      53      G      57          2.000
LGA    D      54      A      58          2.171
LGA    L      55      R      59          2.220
LGA    A      56      R      60          1.225
LGA    G      57      L      61          0.451
LGA    A      58      L      62          0.417
LGA    R      59      T      63          2.092
LGA    R      60      D      64          2.025
LGA    L      61      A      65          3.282
LGA    -       -      G      66           -
LGA    L      62      L      67          2.861
LGA    T      63      A      68           #
LGA    D      64      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   75    5.0     31    3.05    12.90     26.554     0.985

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.487290 * X  +  -0.328810 * Y  +   0.808970 * Z  +  34.173004
  Y_new =   0.744192 * X  +   0.641047 * Y  +  -0.187713 * Z  + -26.352520
  Z_new =  -0.456866 * X  +   0.693500 * Y  +   0.557073 * Z  + -23.343889 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.894060   -2.247533  [ DEG:    51.2259   -128.7741 ]
  Theta =   0.474469    2.667124  [ DEG:    27.1851    152.8149 ]
  Phi   =   0.991061   -2.150532  [ DEG:    56.7836   -123.2164 ]
 
# 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: T0349TS550_5                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS550_5.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   75   5.0   31   3.05   12.90  26.554
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS550_5
PFRMAT TS
TARGET T0349
MODEL 5
PARENT 1ubf_A
ATOM      1  N   VAL    11      10.464   4.368  -2.564  1.00  0.00
ATOM      2  CA  VAL    11      10.353   4.632  -1.142  1.00  0.00
ATOM      3  C   VAL    11       8.912   4.384  -0.712  1.00  0.00
ATOM      4  O   VAL    11       8.649   3.459   0.048  1.00  0.00
ATOM      5  N   LEU    12       7.986   5.208  -1.214  1.00  0.00
ATOM      6  CA  LEU    12       6.564   5.092  -0.877  1.00  0.00
ATOM      7  C   LEU    12       6.152   3.624  -0.884  1.00  0.00
ATOM      8  O   LEU    12       5.579   3.133   0.087  1.00  0.00
ATOM      9  N   LEU    13       6.447   2.928  -1.978  1.00  0.00
ATOM     10  CA  LEU    13       6.105   1.520  -2.066  1.00  0.00
ATOM     11  C   LEU    13       6.750   0.701  -0.968  1.00  0.00
ATOM     12  O   LEU    13       6.140  -0.220  -0.438  1.00  0.00
ATOM     13  N   SER    14       7.982   1.030  -0.612  1.00  0.00
ATOM     14  CA  SER    14       8.663   0.285   0.433  1.00  0.00
ATOM     15  C   SER    14       7.951   0.439   1.806  1.00  0.00
ATOM     16  O   SER    14       7.833  -0.536   2.564  1.00  0.00
ATOM     17  N   ALA    15       7.464   1.646   2.111  1.00  0.00
ATOM     18  CA  ALA    15       6.764   1.927   3.374  1.00  0.00
ATOM     19  C   ALA    15       5.485   1.132   3.531  1.00  0.00
ATOM     20  O   ALA    15       5.173   0.657   4.620  1.00  0.00
ATOM     21  N   VAL    16       4.734   1.008   2.443  1.00  0.00
ATOM     22  CA  VAL    16       3.489   0.253   2.458  1.00  0.00
ATOM     23  C   VAL    16       3.771  -1.176   2.923  1.00  0.00
ATOM     24  O   VAL    16       3.185  -1.658   3.904  1.00  0.00
ATOM     25  N   GLY    17       4.682  -1.844   2.225  1.00  0.00
ATOM     26  CA  GLY    17       5.033  -3.193   2.586  1.00  0.00
ATOM     27  C   GLY    17       5.339  -3.233   4.066  1.00  0.00
ATOM     28  O   GLY    17       4.727  -3.993   4.800  1.00  0.00
ATOM     29  N   ALA    18       6.275  -2.406   4.506  1.00  0.00
ATOM     30  CA  ALA    18       6.629  -2.362   5.915  1.00  0.00
ATOM     31  C   ALA    18       5.459  -1.828   6.744  1.00  0.00
ATOM     32  O   ALA    18       5.274  -2.224   7.901  1.00  0.00
ATOM     33  N   LEU    19       4.672  -0.933   6.148  1.00  0.00
ATOM     34  CA  LEU    19       3.542  -0.336   6.840  1.00  0.00
ATOM     35  C   LEU    19       2.476  -1.336   7.242  1.00  0.00
ATOM     36  O   LEU    19       1.773  -1.142   8.237  1.00  0.00
ATOM     37  N   LEU    20       2.365  -2.416   6.476  1.00  0.00
ATOM     38  CA  LEU    20       1.373  -3.448   6.746  1.00  0.00
ATOM     39  C   LEU    20       1.901  -4.690   7.478  1.00  0.00
ATOM     40  O   LEU    20       1.202  -5.291   8.292  1.00  0.00
ATOM     41  N   ASP    21       3.135  -5.074   7.189  1.00  0.00
ATOM     42  CA  ASP    21       3.699  -6.249   7.825  1.00  0.00
ATOM     43  C   ASP    21       4.052  -5.937   9.271  1.00  0.00
ATOM     44  O   ASP    21       4.495  -6.804  10.018  1.00  0.00
ATOM     45  N   GLY    22       3.527  -5.425   7.554  1.00  0.00
ATOM     46  CA  GLY    22       2.272  -4.748   7.213  1.00  0.00
ATOM     47  C   GLY    22       1.895  -4.875   5.761  1.00  0.00
ATOM     48  O   GLY    22       2.548  -4.310   4.877  1.00  0.00
ATOM     49  N   ALA    23       0.766  -5.527   5.538  1.00  0.00
ATOM     50  CA  ALA    23       0.289  -5.708   4.194  1.00  0.00
ATOM     51  C   ALA    23      -1.086  -5.100   4.002  1.00  0.00
ATOM     52  O   ALA    23      -1.948  -5.173   4.897  1.00  0.00
ATOM     53  N   ASP    24      -1.234  -4.413   2.864  1.00  0.00
ATOM     54  CA  ASP    24      -2.488  -3.793   2.503  1.00  0.00
ATOM     55  C   ASP    24      -3.222  -4.650   1.495  1.00  0.00
ATOM     56  O   ASP    24      -2.765  -4.831   0.361  1.00  0.00
ATOM     57  N   ILE    25      -4.361  -5.175   1.935  1.00  0.00
ATOM     58  CA  ILE    25      -5.228  -6.005   1.112  1.00  0.00
ATOM     59  C   ILE    25      -6.588  -5.330   1.168  1.00  0.00
ATOM     60  O   ILE    25      -7.023  -4.930   2.246  1.00  0.00
ATOM     61  N   GLY    26      -7.219  -5.144   0.009  1.00  0.00
ATOM     62  CA  GLY    26      -8.541  -4.509  -0.077  1.00  0.00
ATOM     63  C   GLY    26      -8.554  -3.083   0.473  1.00  0.00
ATOM     64  O   GLY    26      -8.642  -2.865   1.686  1.00  0.00
ATOM     65  N   HIS    27      -7.941  -2.321  -0.108  1.00  0.00
ATOM     66  CA  HIS    27      -7.993  -0.913   0.280  1.00  0.00
ATOM     67  C   HIS    27      -7.086  -0.559   1.446  1.00  0.00
ATOM     68  O   HIS    27      -7.484  -0.615   2.614  1.00  0.00
ATOM     69  N   LEU    28      -5.856  -0.190   1.114  1.00  0.00
ATOM     70  CA  LEU    28      -4.887   0.209   2.115  1.00  0.00
ATOM     71  C   LEU    28      -5.431   1.438   2.838  1.00  0.00
ATOM     72  O   LEU    28      -5.897   2.392   2.210  1.00  0.00
ATOM     73  N   VAL    29      -5.390   1.386   4.165  1.00  0.00
ATOM     74  CA  VAL    29      -5.874   2.478   4.999  1.00  0.00
ATOM     75  C   VAL    29      -5.030   2.653   6.270  1.00  0.00
ATOM     76  O   VAL    29      -4.934   1.747   7.097  1.00  0.00
ATOM     77  N   LEU    30      -4.415   3.828   6.399  1.00  0.00
ATOM     78  CA  LEU    30      -3.572   4.178   7.540  1.00  0.00
ATOM     79  C   LEU    30      -4.424   4.755   8.663  1.00  0.00
ATOM     80  O   LEU    30      -4.776   5.939   8.647  1.00  0.00
ATOM     81  N   ASP    31      -4.648   5.588   9.105  1.00  0.00
ATOM     82  CA  ASP    31      -5.893   6.044   9.715  1.00  0.00
ATOM     83  C   ASP    31      -6.398   6.616   8.436  1.00  0.00
ATOM     84  O   ASP    31      -5.658   6.689   7.488  1.00  0.00
ATOM     85  N   GLN    32      -7.688   6.743   8.175  1.00  0.00
ATOM     86  CA  GLN    32      -7.445   7.489   6.945  1.00  0.00
ATOM     87  C   GLN    32      -7.014   6.483   5.892  1.00  0.00
ATOM     88  O   GLN    32      -6.019   5.785   6.083  1.00  0.00
ATOM     89  N   ASN    33      -7.754   6.392   4.789  1.00  0.00
ATOM     90  CA  ASN    33      -7.384   5.448   3.744  1.00  0.00
ATOM     91  C   ASN    33      -6.354   6.073   2.815  1.00  0.00
ATOM     92  O   ASN    33      -6.090   7.277   2.879  1.00  0.00
ATOM     93  N   MET    34      -5.775   5.244   1.949  1.00  0.00
ATOM     94  CA  MET    34      -4.769   5.698   1.002  1.00  0.00
ATOM     95  C   MET    34      -5.297   5.478  -0.413  1.00  0.00
ATOM     96  O   MET    34      -5.216   6.359  -1.268  1.00  0.00
ATOM     97  N   SER    35      -5.838   4.290  -0.654  1.00  0.00
ATOM     98  CA  SER    35      -6.371   3.980  -1.970  1.00  0.00
ATOM     99  C   SER    35      -6.530   2.491  -2.204  1.00  0.00
ATOM    100  O   SER    35      -6.183   1.673  -1.347  1.00  0.00
ATOM    101  N   ILE    36      -7.069   2.138  -3.367  1.00  0.00
ATOM    102  CA  ILE    36      -7.268   0.740  -3.732  1.00  0.00
ATOM    103  C   ILE    36      -6.187   0.338  -4.728  1.00  0.00
ATOM    104  O   ILE    36      -6.084   0.924  -5.802  1.00  0.00
ATOM    105  N   PRO    45       0.460   4.005  -3.352  1.00  0.00
ATOM    106  CA  PRO    45       1.891   4.207  -3.507  1.00  0.00
ATOM    107  C   PRO    45       2.025   5.647  -3.978  1.00  0.00
ATOM    108  O   PRO    45       2.924   6.371  -3.545  1.00  0.00
ATOM    109  N   ARG    46       1.109   6.059  -4.856  1.00  0.00
ATOM    110  CA  ARG    46       1.102   7.424  -5.368  1.00  0.00
ATOM    111  C   ARG    46       0.508   8.349  -4.318  1.00  0.00
ATOM    112  O   ARG    46       0.702   9.563  -4.367  1.00  0.00
ATOM    113  N   ARG    47      -0.218   7.771  -3.367  1.00  0.00
ATOM    114  CA  ARG    47      -0.793   8.563  -2.291  1.00  0.00
ATOM    115  C   ARG    47       0.354   8.961  -1.368  1.00  0.00
ATOM    116  O   ARG    47       0.437  10.097  -0.895  1.00  0.00
ATOM    117  N   VAL    48       1.245   8.018  -1.105  1.00  0.00
ATOM    118  CA  VAL    48       2.388   8.318  -0.269  1.00  0.00
ATOM    119  C   VAL    48       3.307   9.244  -1.053  1.00  0.00
ATOM    120  O   VAL    48       3.809  10.227  -0.514  1.00  0.00
ATOM    121  N   LEU    49       3.498   8.937  -2.334  1.00  0.00
ATOM    122  CA  LEU    49       4.366   9.723  -3.212  1.00  0.00
ATOM    123  C   LEU    49       4.046  11.217  -3.262  1.00  0.00
ATOM    124  O   LEU    49       4.948  12.040  -3.421  1.00  0.00
ATOM    125  N   VAL    50       2.768  11.567  -3.130  1.00  0.00
ATOM    126  CA  VAL    50       2.349  12.970  -3.154  1.00  0.00
ATOM    127  C   VAL    50       2.045  13.529  -1.763  1.00  0.00
ATOM    128  O   VAL    50       1.704  14.706  -1.613  1.00  0.00
ATOM    129  N   HIS    51       2.165  12.683  -0.762  1.00  0.00
ATOM    130  CA  HIS    51       1.902  13.100   0.608  1.00  0.00
ATOM    131  C   HIS    51       3.072  12.697   1.486  1.00  0.00
ATOM    132  O   HIS    51       3.028  11.680   2.169  1.00  0.00
ATOM    133  N   GLU    52       4.148  13.489   1.452  1.00  0.00
ATOM    134  CA  GLU    52       5.358  13.242   2.232  1.00  0.00
ATOM    135  C   GLU    52       5.001  13.317   3.706  1.00  0.00
ATOM    136  O   GLU    52       5.515  12.560   4.530  1.00  0.00
ATOM    137  N   ASP    53       4.111  14.253   4.015  1.00  0.00
ATOM    138  CA  ASP    53       3.620  14.477   5.369  1.00  0.00
ATOM    139  C   ASP    53       3.282  13.170   6.088  1.00  0.00
ATOM    140  O   ASP    53       3.967  12.781   7.034  1.00  0.00
ATOM    141  N   ASP    54       2.224  12.500   5.636  1.00  0.00
ATOM    142  CA  ASP    54       1.806  11.240   6.240  1.00  0.00
ATOM    143  C   ASP    54       2.943  10.222   6.082  1.00  0.00
ATOM    144  O   ASP    54       3.309   9.543   7.041  1.00  0.00
ATOM    145  N   LEU    55       3.515  10.160   4.879  1.00  0.00
ATOM    146  CA  LEU    55       4.622   9.262   4.543  1.00  0.00
ATOM    147  C   LEU    55       5.693   9.227   5.634  1.00  0.00
ATOM    148  O   LEU    55       6.013   8.157   6.169  1.00  0.00
ATOM    149  N   ALA    56       6.272  10.387   5.933  1.00  0.00
ATOM    150  CA  ALA    56       7.289  10.462   6.971  1.00  0.00
ATOM    151  C   ALA    56       6.771   9.714   8.188  1.00  0.00
ATOM    152  O   ALA    56       7.395   8.760   8.647  1.00  0.00
ATOM    153  N   GLY    57       5.602  10.127   8.677  1.00  0.00
ATOM    154  CA  GLY    57       4.995   9.506   9.850  1.00  0.00
ATOM    155  C   GLY    57       5.079   7.972   9.837  1.00  0.00
ATOM    156  O   GLY    57       5.511   7.370  10.828  1.00  0.00
ATOM    157  N   ALA    58       4.666   7.340   8.734  1.00  0.00
ATOM    158  CA  ALA    58       4.751   5.883   8.644  1.00  0.00
ATOM    159  C   ALA    58       6.226   5.532   8.794  1.00  0.00
ATOM    160  O   ALA    58       6.587   4.769   9.686  1.00  0.00
ATOM    161  N   ARG    59       7.079   6.095   7.941  1.00  0.00
ATOM    162  CA  ARG    59       8.511   5.817   8.039  1.00  0.00
ATOM    163  C   ARG    59       9.049   6.059   9.440  1.00  0.00
ATOM    164  O   ARG    59       9.905   5.322   9.932  1.00  0.00
ATOM    165  N   ARG    60       8.553   7.115  10.067  1.00  0.00
ATOM    166  CA  ARG    60       8.982   7.473  11.407  1.00  0.00
ATOM    167  C   ARG    60       8.624   6.323  12.347  1.00  0.00
ATOM    168  O   ARG    60       9.506   5.694  12.943  1.00  0.00
ATOM    169  N   LEU    61       7.327   6.033  12.453  1.00  0.00
ATOM    170  CA  LEU    61       6.840   4.953  13.313  1.00  0.00
ATOM    171  C   LEU    61       7.492   3.601  13.037  1.00  0.00
ATOM    172  O   LEU    61       7.738   2.814  13.960  1.00  0.00
ATOM    173  N   LEU    62       7.760   3.330  11.765  1.00  0.00
ATOM    174  CA  LEU    62       8.374   2.068  11.388  1.00  0.00
ATOM    175  C   LEU    62       9.786   1.977  11.982  1.00  0.00
ATOM    176  O   LEU    62      10.178   0.927  12.493  1.00  0.00
ATOM    177  N   THR    63      10.553   3.066  11.935  1.00  0.00
ATOM    178  CA  THR    63      11.896   3.019  12.512  1.00  0.00
ATOM    179  C   THR    63      11.883   2.920  14.031  1.00  0.00
ATOM    180  O   THR    63      12.717   2.227  14.607  1.00  0.00
ATOM    181  N   ASP    64      10.966   3.607  14.704  1.00  0.00
ATOM    182  CA  ASP    64      10.932   3.466  16.157  1.00  0.00
ATOM    183  C   ASP    64      10.630   2.024  16.492  1.00  0.00
ATOM    184  O   ASP    64      11.425   1.340  17.149  1.00  0.00
TER
END
