
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0311AL381_1-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311AL381_1-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R       8           -
LGA    -       -      P       9           -
LGA    -       -      G      10           -
LGA    -       -      D      11           -
LGA    -       -      I      12           -
LGA    I      13      I      13          0.831
LGA    Q      14      Q      14          0.945
LGA    E      15      E      15          0.649
LGA    S      16      S      16          0.842
LGA    L      17      L      17          1.311
LGA    D      18      D      18          1.316
LGA    E      19      E      19          1.090
LGA    L      20      L      20          1.328
LGA    N      21      N      21          1.232
LGA    V      22      V      22          1.064
LGA    S      23      S      23          0.734
LGA    L      24      L      24          0.747
LGA    R      25      R      25          0.374
LGA    E      26      E      26          0.397
LGA    F      27      F      27          1.079
LGA    A      28      A      28          0.750
LGA    R      29      R      29          0.849
LGA    A      30      A      30          1.129
LGA    M      31      M      31          1.486
LGA    E      32      E      32          1.253
LGA    I      33      I      33          0.561
LGA    A      34      A      34          0.811
LGA    P      35      P      35          1.141
LGA    S      36      S      36          1.048
LGA    T      37      T      37          1.022
LGA    A      38      A      38          1.205
LGA    S      39      S      39          1.013
LGA    R      40      R      40          0.765
LGA    L      41      L      41          1.174
LGA    L      42      L      42          1.228
LGA    T      43      T      43          0.849
LGA    G      44      G      44          0.950
LGA    K      45      K      45          0.713
LGA    A      46      A      46          1.936
LGA    A      47      A      47          0.933
LGA    L      48      L      48          2.790
LGA    T      49      T      49          2.310
LGA    P      50      P      50          0.844
LGA    E      51      E      51          0.939
LGA    M      52      M      52          1.721
LGA    A      53      A      53          1.559
LGA    I      54      I      54          0.681
LGA    K      55      K      55          0.746
LGA    L      56      L      56          1.065
LGA    S      57      S      57          1.262
LGA    V      58      V      58          1.164
LGA    V      59      V      59          1.406
LGA    I      60      I      60          0.877
LGA    G      61      G      61          2.125
LGA    S      62      S      62          2.200
LGA    S      63      S      63          2.957
LGA    P      64      P      64          3.514
LGA    -       -      Q      65           -
LGA    Q      65      M      66          1.020
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   64    5.0     53    1.35    98.11     78.392     3.644

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.477088 * X  +   0.631768 * Y  +   0.610947 * Z  +  40.634335
  Y_new =  -0.367167 * X  +   0.488309 * Y  +  -0.791671 * Z  +  13.936828
  Z_new =  -0.798483 * X  +  -0.602017 * Y  +  -0.001002 * Z  +  24.806648 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.572461    1.569132  [ DEG:   -90.0954     89.9046 ]
  Theta =   0.924771    2.216822  [ DEG:    52.9855    127.0145 ]
  Phi   =  -2.485665    0.655928  [ DEG:  -142.4181     37.5819 ]
 
# 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: T0311AL381_1-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311AL381_1-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   64   5.0   53   1.35   98.11  78.392
REMARK  ---------------------------------------------------------- 
MOLECULE T0311AL381_1-D1
REMARK Aligment from pdb entry: 1utxA
ATOM      1  N   ILE    13      33.925   2.765  13.333  1.00  0.00              
ATOM      2  CA  ILE    13      32.541   2.305  13.257  1.00  0.00              
ATOM      3  C   ILE    13      31.892   2.205  14.646  1.00  0.00              
ATOM      4  O   ILE    13      30.778   2.638  14.814  1.00  0.00              
ATOM      5  N   GLN    14      32.577   1.598  15.616  1.00  0.00              
ATOM      6  CA  GLN    14      32.037   1.466  16.970  1.00  0.00              
ATOM      7  C   GLN    14      31.575   2.819  17.516  1.00  0.00              
ATOM      8  O   GLN    14      30.436   2.950  17.954  1.00  0.00              
ATOM      9  N   GLU    15      32.442   3.828  17.439  1.00  0.00              
ATOM     10  CA  GLU    15      32.150   5.114  18.051  1.00  0.00              
ATOM     11  C   GLU    15      30.987   5.824  17.365  1.00  0.00              
ATOM     12  O   GLU    15      30.121   6.402  18.038  1.00  0.00              
ATOM     13  N   SER    16      30.953   5.762  16.033  1.00  0.00              
ATOM     14  CA  SER    16      29.895   6.419  15.274  1.00  0.00              
ATOM     15  C   SER    16      28.560   5.720  15.522  1.00  0.00              
ATOM     16  O   SER    16      27.545   6.366  15.748  1.00  0.00              
ATOM     17  N   LEU    17      28.574   4.401  15.467  1.00  0.00              
ATOM     18  CA  LEU    17      27.382   3.606  15.724  1.00  0.00              
ATOM     19  C   LEU    17      26.818   3.893  17.125  1.00  0.00              
ATOM     20  O   LEU    17      25.619   4.133  17.294  1.00  0.00              
ATOM     21  N   ASP    18      27.687   3.865  18.119  1.00  0.00              
ATOM     22  CA  ASP    18      27.274   4.091  19.504  1.00  0.00              
ATOM     23  C   ASP    18      26.755   5.496  19.709  1.00  0.00              
ATOM     24  O   ASP    18      25.754   5.677  20.381  1.00  0.00              
ATOM     25  N   GLU    19      27.416   6.469  19.106  1.00  0.00              
ATOM     26  CA  GLU    19      26.987   7.859  19.191  1.00  0.00              
ATOM     27  C   GLU    19      25.571   8.046  18.670  1.00  0.00              
ATOM     28  O   GLU    19      24.793   8.799  19.252  1.00  0.00              
ATOM     29  N   LEU    20      25.236   7.349  17.583  1.00  0.00              
ATOM     30  CA  LEU    20      23.913   7.400  16.996  1.00  0.00              
ATOM     31  C   LEU    20      22.887   6.535  17.746  1.00  0.00              
ATOM     32  O   LEU    20      21.740   6.482  17.348  1.00  0.00              
ATOM     33  N   ASN    21      23.303   5.854  18.828  1.00  0.00              
ATOM     34  CA  ASN    21      22.429   4.995  19.644  1.00  0.00              
ATOM     35  C   ASN    21      21.872   3.783  18.882  1.00  0.00              
ATOM     36  O   ASN    21      20.768   3.313  19.133  1.00  0.00              
ATOM     37  N   VAL    22      22.671   3.266  17.963  1.00  0.00              
ATOM     38  CA  VAL    22      22.294   2.113  17.149  1.00  0.00              
ATOM     39  C   VAL    22      22.990   0.904  17.730  1.00  0.00              
ATOM     40  O   VAL    22      24.201   0.931  17.872  1.00  0.00              
ATOM     41  N   SER    23      22.253  -0.157  18.058  1.00  0.00              
ATOM     42  CA  SER    23      22.912  -1.374  18.567  1.00  0.00              
ATOM     43  C   SER    23      23.507  -2.163  17.417  1.00  0.00              
ATOM     44  O   SER    23      23.169  -1.933  16.263  1.00  0.00              
ATOM     45  N   LEU    24      24.371  -3.121  17.733  1.00  0.00              
ATOM     46  CA  LEU    24      24.943  -3.979  16.701  1.00  0.00              
ATOM     47  C   LEU    24      23.863  -4.737  15.937  1.00  0.00              
ATOM     48  O   LEU    24      23.930  -4.802  14.713  1.00  0.00              
ATOM     49  N   ARG    25      22.869  -5.310  16.628  1.00  0.00              
ATOM     50  CA  ARG    25      21.810  -6.054  15.945  1.00  0.00              
ATOM     51  C   ARG    25      20.978  -5.125  15.085  1.00  0.00              
ATOM     52  O   ARG    25      20.508  -5.515  14.032  1.00  0.00              
ATOM     53  N   GLU    26      20.774  -3.903  15.542  1.00  0.00              
ATOM     54  CA  GLU    26      20.014  -2.920  14.750  1.00  0.00              
ATOM     55  C   GLU    26      20.710  -2.611  13.415  1.00  0.00              
ATOM     56  O   GLU    26      20.079  -2.616  12.343  1.00  0.00              
ATOM     57  N   PHE    27      22.012  -2.349  13.484  1.00  0.00              
ATOM     58  CA  PHE    27      22.791  -2.065  12.279  1.00  0.00              
ATOM     59  C   PHE    27      22.840  -3.263  11.344  1.00  0.00              
ATOM     60  O   PHE    27      22.683  -3.110  10.145  1.00  0.00              
ATOM     61  N   ALA    28      23.056  -4.452  11.899  1.00  0.00              
ATOM     62  CA  ALA    28      23.116  -5.699  11.130  1.00  0.00              
ATOM     63  C   ALA    28      21.809  -5.917  10.336  1.00  0.00              
ATOM     64  O   ALA    28      21.827  -6.271   9.151  1.00  0.00              
ATOM     65  N   ARG    29      20.683  -5.707  11.010  1.00  0.00              
ATOM     66  CA  ARG    29      19.374  -5.837  10.393  1.00  0.00              
ATOM     67  C   ARG    29      19.201  -4.838   9.235  1.00  0.00              
ATOM     68  O   ARG    29      18.762  -5.213   8.159  1.00  0.00              
ATOM     69  N   ALA    30      19.603  -3.580   9.438  1.00  0.00              
ATOM     70  CA  ALA    30      19.470  -2.565   8.391  1.00  0.00              
ATOM     71  C   ALA    30      20.333  -2.915   7.166  1.00  0.00              
ATOM     72  O   ALA    30      19.901  -2.760   6.007  1.00  0.00              
ATOM     73  N   MET    31      21.531  -3.415   7.422  1.00  0.00              
ATOM     74  CA  MET    31      22.494  -3.694   6.364  1.00  0.00              
ATOM     75  C   MET    31      22.345  -5.094   5.788  1.00  0.00              
ATOM     76  O   MET    31      23.054  -5.452   4.848  1.00  0.00              
ATOM     77  N   GLU    32      21.438  -5.876   6.357  1.00  0.00              
ATOM     78  CA  GLU    32      21.261  -7.273   5.978  1.00  0.00              
ATOM     79  C   GLU    32      22.556  -8.087   6.047  1.00  0.00              
ATOM     80  O   GLU    32      22.907  -8.802   5.105  1.00  0.00              
ATOM     81  N   ILE    33      23.289  -7.935   7.156  1.00  0.00              
ATOM     82  CA  ILE    33      24.418  -8.789   7.475  1.00  0.00              
ATOM     83  C   ILE    33      24.253  -9.319   8.901  1.00  0.00              
ATOM     84  O   ILE    33      23.327  -8.932   9.620  1.00  0.00              
ATOM     85  N   ALA    34      25.162 -10.186   9.320  1.00  0.00              
ATOM     86  CA  ALA    34      25.119 -10.740  10.659  1.00  0.00              
ATOM     87  C   ALA    34      25.680  -9.771  11.683  1.00  0.00              
ATOM     88  O   ALA    34      26.515  -8.931  11.373  1.00  0.00              
ATOM     89  N   PRO    35      25.219  -9.899  12.919  1.00  0.00              
ATOM     90  CA  PRO    35      25.801  -9.155  14.013  1.00  0.00              
ATOM     91  C   PRO    35      27.287  -9.464  14.153  1.00  0.00              
ATOM     92  O   PRO    35      28.065  -8.569  14.423  1.00  0.00              
ATOM     93  N   SER    36      27.669 -10.728  13.950  1.00  0.00              
ATOM     94  CA  SER    36      29.078 -11.151  14.001  1.00  0.00              
ATOM     95  C   SER    36      29.924 -10.347  13.023  1.00  0.00              
ATOM     96  O   SER    36      31.038  -9.970  13.331  1.00  0.00              
ATOM     97  N   THR    37      29.394 -10.085  11.837  1.00  0.00              
ATOM     98  CA  THR    37      30.107  -9.248  10.869  1.00  0.00              
ATOM     99  C   THR    37      30.376  -7.839  11.383  1.00  0.00              
ATOM    100  O   THR    37      31.483  -7.342  11.246  1.00  0.00              
ATOM    101  N   ALA    38      29.356  -7.199  11.949  1.00  0.00              
ATOM    102  CA  ALA    38      29.506  -5.854  12.485  1.00  0.00              
ATOM    103  C   ALA    38      30.530  -5.881  13.625  1.00  0.00              
ATOM    104  O   ALA    38      31.444  -5.051  13.666  1.00  0.00              
ATOM    105  N   SER    39      30.400  -6.851  14.528  1.00  0.00              
ATOM    106  CA  SER    39      31.287  -6.941  15.676  1.00  0.00              
ATOM    107  C   SER    39      32.744  -7.183  15.237  1.00  0.00              
ATOM    108  O   SER    39      33.658  -6.569  15.770  1.00  0.00              
ATOM    109  N   ARG    40      32.925  -8.036  14.226  1.00  0.00              
ATOM    110  CA  ARG    40      34.222  -8.329  13.655  1.00  0.00              
ATOM    111  C   ARG    40      34.925  -7.107  13.103  1.00  0.00              
ATOM    112  O   ARG    40      36.115  -6.940  13.316  1.00  0.00              
ATOM    113  N   LEU    41      34.191  -6.249  12.404  1.00  0.00              
ATOM    114  CA  LEU    41      34.751  -5.018  11.895  1.00  0.00              
ATOM    115  C   LEU    41      35.208  -4.148  13.057  1.00  0.00              
ATOM    116  O   LEU    41      36.319  -3.613  13.045  1.00  0.00              
ATOM    117  N   LEU    42      34.351  -4.023  14.064  1.00  0.00              
ATOM    118  CA  LEU    42      34.649  -3.174  15.218  1.00  0.00              
ATOM    119  C   LEU    42      35.802  -3.703  16.072  1.00  0.00              
ATOM    120  O   LEU    42      36.518  -2.922  16.685  1.00  0.00              
ATOM    121  N   THR    43      35.987  -5.010  16.110  1.00  0.00              
ATOM    122  CA  THR    43      37.109  -5.608  16.848  1.00  0.00              
ATOM    123  C   THR    43      38.363  -5.737  15.955  1.00  0.00              
ATOM    124  O   THR    43      39.348  -6.348  16.354  1.00  0.00              
ATOM    125  N   GLY    44      38.319  -5.150  14.755  1.00  0.00              
ATOM    126  CA  GLY    44      39.463  -5.115  13.842  1.00  0.00              
ATOM    127  C   GLY    44      39.963  -6.504  13.456  1.00  0.00              
ATOM    128  O   GLY    44      41.163  -6.717  13.276  1.00  0.00              
ATOM    129  N   LYS    45      39.057  -7.456  13.349  1.00  0.00              
ATOM    130  CA  LYS    45      39.430  -8.777  12.902  1.00  0.00              
ATOM    131  C   LYS    45      39.636  -8.767  11.383  1.00  0.00              
ATOM    132  O   LYS    45      40.338  -9.621  10.850  1.00  0.00              
ATOM    133  N   ALA    46      39.018  -7.805  10.695  1.00  0.00              
ATOM    134  CA  ALA    46      39.107  -7.692   9.235  1.00  0.00              
ATOM    135  C   ALA    46      38.373  -6.467   8.701  1.00  0.00              
ATOM    136  O   ALA    46      37.503  -5.890   9.362  1.00  0.00              
ATOM    137  N   ALA    47      38.697  -6.116   7.462  1.00  0.00              
ATOM    138  CA  ALA    47      37.984  -5.054   6.784  1.00  0.00              
ATOM    139  C   ALA    47      36.779  -5.591   6.005  1.00  0.00              
ATOM    140  O   ALA    47      36.791  -6.700   5.469  1.00  0.00              
ATOM    141  N   LEU    48      35.744  -4.780   5.933  1.00  0.00              
ATOM    142  CA  LEU    48      34.595  -5.093   5.086  1.00  0.00              
ATOM    143  C   LEU    48      34.937  -5.011   3.596  1.00  0.00              
ATOM    144  O   LEU    48      35.901  -4.358   3.213  1.00  0.00              
ATOM    145  N   THR    49      34.111  -5.647   2.777  1.00  0.00              
ATOM    146  CA  THR    49      34.128  -5.459   1.336  1.00  0.00              
ATOM    147  C   THR    49      33.853  -3.993   1.009  1.00  0.00              
ATOM    148  O   THR    49      33.300  -3.238   1.826  1.00  0.00              
ATOM    149  N   PRO    50      34.233  -3.585  -0.193  1.00  0.00              
ATOM    150  CA  PRO    50      33.900  -2.259  -0.667  1.00  0.00              
ATOM    151  C   PRO    50      32.401  -2.024  -0.598  1.00  0.00              
ATOM    152  O   PRO    50      31.955  -0.980  -0.115  1.00  0.00              
ATOM    153  N   GLU    51      31.616  -2.992  -1.063  1.00  0.00              
ATOM    154  CA  GLU    51      30.159  -2.796  -1.072  1.00  0.00              
ATOM    155  C   GLU    51      29.586  -2.582   0.335  1.00  0.00              
ATOM    156  O   GLU    51      28.735  -1.728   0.540  1.00  0.00              
ATOM    157  N   MET    52      30.050  -3.351   1.308  1.00  0.00              
ATOM    158  CA  MET    52      29.542  -3.217   2.673  1.00  0.00              
ATOM    159  C   MET    52      29.973  -1.886   3.291  1.00  0.00              
ATOM    160  O   MET    52      29.164  -1.217   3.964  1.00  0.00              
ATOM    161  N   ALA    53      31.226  -1.495   3.062  1.00  0.00              
ATOM    162  CA  ALA    53      31.710  -0.177   3.480  1.00  0.00              
ATOM    163  C   ALA    53      30.811   0.926   2.936  1.00  0.00              
ATOM    164  O   ALA    53      30.434   1.851   3.670  1.00  0.00              
ATOM    165  N   ILE    54      30.447   0.823   1.658  1.00  0.00              
ATOM    166  CA  ILE    54      29.605   1.847   1.025  1.00  0.00              
ATOM    167  C   ILE    54      28.193   1.880   1.622  1.00  0.00              
ATOM    168  O   ILE    54      27.629   2.949   1.802  1.00  0.00              
ATOM    169  N   LYS    55      27.647   0.714   1.951  1.00  0.00              
ATOM    170  CA  LYS    55      26.323   0.634   2.574  1.00  0.00              
ATOM    171  C   LYS    55      26.357   1.240   3.962  1.00  0.00              
ATOM    172  O   LYS    55      25.450   1.955   4.346  1.00  0.00              
ATOM    173  N   LEU    56      27.422   0.948   4.702  1.00  0.00              
ATOM    174  CA  LEU    56      27.613   1.519   6.042  1.00  0.00              
ATOM    175  C   LEU    56      27.617   3.040   5.949  1.00  0.00              
ATOM    176  O   LEU    56      26.927   3.691   6.722  1.00  0.00              
ATOM    177  N   SER    57      28.396   3.609   5.032  1.00  0.00              
ATOM    178  CA  SER    57      28.519   5.063   4.908  1.00  0.00              
ATOM    179  C   SER    57      27.200   5.698   4.492  1.00  0.00              
ATOM    180  O   SER    57      26.834   6.812   4.928  1.00  0.00              
ATOM    181  N   VAL    58      26.500   4.991   3.629  1.00  0.00              
ATOM    182  CA  VAL    58      25.231   5.462   3.115  1.00  0.00              
ATOM    183  C   VAL    58      24.238   5.616   4.276  1.00  0.00              
ATOM    184  O   VAL    58      23.674   6.698   4.497  1.00  0.00              
ATOM    185  N   VAL    59      24.046   4.551   5.029  1.00  0.00              
ATOM    186  CA  VAL    59      23.018   4.554   6.067  1.00  0.00              
ATOM    187  C   VAL    59      23.433   5.379   7.275  1.00  0.00              
ATOM    188  O   VAL    59      22.600   6.053   7.882  1.00  0.00              
ATOM    189  N   ILE    60      24.729   5.372   7.593  1.00  0.00              
ATOM    190  CA  ILE    60      25.215   6.211   8.679  1.00  0.00              
ATOM    191  C   ILE    60      25.371   7.690   8.300  1.00  0.00              
ATOM    192  O   ILE    60      25.767   8.497   9.139  1.00  0.00              
ATOM    193  N   GLY    61      25.038   8.046   7.063  1.00  0.00              
ATOM    194  CA  GLY    61      25.075   9.427   6.596  1.00  0.00              
ATOM    195  C   GLY    61      26.351  10.141   7.023  1.00  0.00              
ATOM    196  O   GLY    61      26.336  11.247   7.580  1.00  0.00              
ATOM    197  N   SER    62      27.465   9.455   6.772  1.00  0.00              
ATOM    198  CA  SER    62      28.790   9.913   7.165  1.00  0.00              
ATOM    199  C   SER    62      29.737   9.636   5.994  1.00  0.00              
ATOM    200  O   SER    62      29.683   8.534   5.427  1.00  0.00              
ATOM    201  N   SER    63      30.600  10.595   5.622  1.00  0.00              
ATOM    202  CA  SER    63      31.585  10.327   4.568  1.00  0.00              
ATOM    203  C   SER    63      32.334   9.067   4.917  1.00  0.00              
ATOM    204  O   SER    63      32.731   8.880   6.074  1.00  0.00              
ATOM    205  N   PRO    64      32.479   8.198   3.932  1.00  0.00              
ATOM    206  CA  PRO    64      33.110   6.908   4.117  1.00  0.00              
ATOM    207  C   PRO    64      34.480   7.044   4.769  1.00  0.00              
ATOM    208  O   PRO    64      34.839   6.249   5.620  1.00  0.00              
ATOM    209  N   GLN    65      35.234   8.069   4.395  1.00  0.00              
ATOM    210  CA  GLN    65      36.579   8.224   4.929  1.00  0.00              
ATOM    211  C   GLN    65      36.638   8.699   6.368  1.00  0.00              
ATOM    212  O   GLN    65      37.663   8.545   7.005  1.00  0.00              
END
