
#######################################################
#                                                     #
#                        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   51 (  204),  selected   51 , name T0311AL509_1-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311AL509_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           -
LGA    -       -      Q      14           -
LGA    -       -      E      15           -
LGA    -       -      S      16           -
LGA    R       8      L      17          1.813
LGA    P       9      D      18          1.650
LGA    G      10      E      19          1.733
LGA    D      11      L      20          1.991
LGA    I      12      N      21          1.688
LGA    I      13      V      22          1.334
LGA    Q      14      S      23          0.914
LGA    E      15      L      24          0.857
LGA    S      16      R      25          0.357
LGA    L      17      E      26          0.347
LGA    D      18      F      27          1.004
LGA    E      19      A      28          0.684
LGA    L      20      R      29          0.793
LGA    N      21      A      30          3.683
LGA    -       -      M      31           -
LGA    V      22      E      32          1.478
LGA    S      23      I      33          0.796
LGA    L      24      A      34          0.956
LGA    R      25      P      35          1.289
LGA    E      26      S      36          1.094
LGA    F      27      T      37          0.891
LGA    A      28      A      38          1.169
LGA    A      30      S      39          1.051
LGA    M      31      R      40          0.561
LGA    E      32      L      41          1.040
LGA    I      33      L      42          1.300
LGA    A      34      T      43          0.892
LGA    P      35      G      44          0.883
LGA    S      36      K      45          0.787
LGA    T      37      A      46          1.803
LGA    A      38      A      47          1.100
LGA    S      39      L      48          3.362
LGA    R      40      T      49          3.087
LGA    E      51      P      50          1.623
LGA    M      52      E      51          1.530
LGA    A      53      M      52          2.276
LGA    I      54      A      53          1.850
LGA    K      55      I      54          0.389
LGA    L      56      K      55          1.023
LGA    S      57      L      56          1.309
LGA    V      58      S      57          1.024
LGA    V      59      V      58          1.080
LGA    I      60      V      59          1.465
LGA    G      61      I      60          1.011
LGA    S      62      G      61          2.142
LGA    S      63      S      62          1.658
LGA    P      64      S      63          2.091
LGA    Q      65      P      64          2.660
LGA    M      66      Q      65          3.641
LGA    N      69      M      66          3.511
LGA    L      70      W      67          3.017
LGA    Q      71      L      68          3.469
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   51   64    5.0     51    1.79     7.84     73.067     2.702

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.521410 * X  +   0.612438 * Y  +   0.594181 * Z  +  41.632812
  Y_new =  -0.383374 * X  +   0.453959 * Y  +  -0.804329 * Z  +  14.062872
  Z_new =  -0.762336 * X  +  -0.647179 * Y  +  -0.001906 * Z  +  23.429970 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.573741    1.567852  [ DEG:   -90.1687     89.8313 ]
  Theta =   0.866915    2.274678  [ DEG:    49.6706    130.3294 ]
  Phi   =  -2.507589    0.634004  [ DEG:  -143.6743     36.3257 ]
 
# 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: T0311AL509_1-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311AL509_1-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   64   5.0   51   1.79    7.84  73.067
REMARK  ---------------------------------------------------------- 
MOLECULE T0311AL509_1-D1
REMARK Aligment from pdb entry: 1utx_A
ATOM     29  N   ARG     8      28.957   4.483  14.994  1.00  0.00              
ATOM     30  CA  ARG     8      27.763   3.723  15.334  1.00  0.00              
ATOM     31  C   ARG     8      27.271   4.069  16.749  1.00  0.00              
ATOM     32  O   ARG     8      26.086   4.340  16.965  1.00  0.00              
ATOM     33  N   PRO     9      28.185   4.055  17.702  1.00  0.00              
ATOM     34  CA  PRO     9      27.843   4.336  19.096  1.00  0.00              
ATOM     35  C   PRO     9      27.363   5.759  19.276  1.00  0.00              
ATOM     36  O   PRO     9      26.397   5.984  19.987  1.00  0.00              
ATOM     37  N   GLY    10      28.014   6.697  18.609  1.00  0.00              
ATOM     38  CA  GLY    10      27.617   8.097  18.666  1.00  0.00              
ATOM     39  C   GLY    10      26.182   8.297  18.205  1.00  0.00              
ATOM     40  O   GLY    10      25.447   9.086  18.796  1.00  0.00              
ATOM     41  N   ASP    11      25.783   7.572  17.160  1.00  0.00              
ATOM     42  CA  ASP    11      24.435   7.632  16.634  1.00  0.00              
ATOM     43  C   ASP    11      23.428   6.815  17.460  1.00  0.00              
ATOM     44  O   ASP    11      22.262   6.773  17.117  1.00  0.00              
ATOM     45  N   ILE    12      23.880   6.162  18.544  1.00  0.00              
ATOM     46  CA  ILE    12      23.028   5.350  19.429  1.00  0.00              
ATOM     47  C   ILE    12      22.412   4.125  18.736  1.00  0.00              
ATOM     48  O   ILE    12      21.312   3.688  19.054  1.00  0.00              
ATOM     49  N   ILE    13      23.157   3.561  17.800  1.00  0.00              
ATOM     50  CA  ILE    13      22.719   2.389  17.044  1.00  0.00              
ATOM     51  C   ILE    13      23.416   1.185  17.634  1.00  0.00              
ATOM     52  O   ILE    13      24.633   1.191  17.718  1.00  0.00              
ATOM     53  N   GLN    14      22.674   0.153  18.032  1.00  0.00              
ATOM     54  CA  GLN    14      23.332  -1.061  18.552  1.00  0.00              
ATOM     55  C   GLN    14      23.856  -1.901  17.404  1.00  0.00              
ATOM     56  O   GLN    14      23.470  -1.703  16.259  1.00  0.00              
ATOM     57  N   GLU    15      24.715  -2.866  17.712  1.00  0.00              
ATOM     58  CA  GLU    15      25.221  -3.771  16.685  1.00  0.00              
ATOM     59  C   GLU    15      24.091  -4.530  15.998  1.00  0.00              
ATOM     60  O   GLU    15      24.099  -4.638  14.776  1.00  0.00              
ATOM     61  N   SER    16      23.119  -5.058  16.754  1.00  0.00              
ATOM     62  CA  SER    16      22.014  -5.801  16.147  1.00  0.00              
ATOM     63  C   SER    16      21.161  -4.884  15.295  1.00  0.00              
ATOM     64  O   SER    16      20.635  -5.299  14.279  1.00  0.00              
ATOM     65  N   LEU    17      21.004  -3.643  15.718  1.00  0.00              
ATOM     66  CA  LEU    17      20.228  -2.671  14.929  1.00  0.00              
ATOM     67  C   LEU    17      20.866  -2.422  13.553  1.00  0.00              
ATOM     68  O   LEU    17      20.185  -2.450  12.513  1.00  0.00              
ATOM     69  N   ASP    18      22.175  -2.186  13.553  1.00  0.00              
ATOM     70  CA  ASP    18      22.902  -1.961  12.304  1.00  0.00              
ATOM     71  C   ASP    18      22.882  -3.190  11.409  1.00  0.00              
ATOM     72  O   ASP    18      22.672  -3.074  10.214  1.00  0.00              
ATOM     73  N   GLU    19      23.100  -4.364  11.994  1.00  0.00              
ATOM     74  CA  GLU    19      23.099  -5.637  11.268  1.00  0.00              
ATOM     75  C   GLU    19      21.752  -5.854  10.543  1.00  0.00              
ATOM     76  O   GLU    19      21.707  -6.247   9.372  1.00  0.00              
ATOM     77  N   LEU    20      20.664  -5.596  11.261  1.00  0.00              
ATOM     78  CA  LEU    20      19.325  -5.718  10.710  1.00  0.00              
ATOM     79  C   LEU    20      19.118  -4.756   9.527  1.00  0.00              
ATOM     80  O   LEU    20      18.621  -5.157   8.486  1.00  0.00              
ATOM     81  N   ASN    21      21.388  -3.445   7.560  1.00  0.00              
ATOM     82  CA  ASN    21      22.294  -3.780   6.469  1.00  0.00              
ATOM     83  C   ASN    21      22.090  -5.195   5.949  1.00  0.00              
ATOM     84  O   ASN    21      22.747  -5.600   4.990  1.00  0.00              
ATOM     85  N   VAL    22      21.196  -5.938   6.586  1.00  0.00              
ATOM     86  CA  VAL    22      20.973  -7.343   6.264  1.00  0.00              
ATOM     87  C   VAL    22      22.253  -8.182   6.301  1.00  0.00              
ATOM     88  O   VAL    22      22.545  -8.936   5.369  1.00  0.00              
ATOM     89  N   SER    23      23.040  -8.009   7.370  1.00  0.00              
ATOM     90  CA  SER    23      24.166  -8.876   7.665  1.00  0.00              
ATOM     91  C   SER    23      24.057  -9.354   9.115  1.00  0.00              
ATOM     92  O   SER    23      23.174  -8.923   9.862  1.00  0.00              
ATOM     93  N   LEU    24      24.967 -10.226   9.521  1.00  0.00              
ATOM     94  CA  LEU    24      24.976 -10.733  10.879  1.00  0.00              
ATOM     95  C   LEU    24      25.604  -9.742  11.842  1.00  0.00              
ATOM     96  O   LEU    24      26.440  -8.932  11.464  1.00  0.00              
ATOM     97  N   ARG    25      25.199  -9.819  13.102  1.00  0.00              
ATOM     98  CA  ARG    25      25.847  -9.052  14.141  1.00  0.00              
ATOM     99  C   ARG    25      27.331  -9.388  14.222  1.00  0.00              
ATOM    100  O   ARG    25      28.139  -8.501  14.425  1.00  0.00              
ATOM    101  N   GLU    26      27.678 -10.665  14.046  1.00  0.00              
ATOM    102  CA  GLU    26      29.079 -11.118  14.046  1.00  0.00              
ATOM    103  C   GLU    26      29.893 -10.365  13.003  1.00  0.00              
ATOM    104  O   GLU    26      31.029 -10.002  13.246  1.00  0.00              
ATOM    105  N   PHE    27      29.314 -10.132  11.834  1.00  0.00              
ATOM    106  CA  PHE    27      29.997  -9.344  10.806  1.00  0.00              
ATOM    107  C   PHE    27      30.319  -7.925  11.258  1.00  0.00              
ATOM    108  O   PHE    27      31.428  -7.456  11.052  1.00  0.00              
ATOM    109  N   ALA    28      29.339  -7.244  11.848  1.00  0.00              
ATOM    110  CA  ALA    28      29.541  -5.885  12.330  1.00  0.00              
ATOM    111  C   ALA    28      30.618  -5.895  13.421  1.00  0.00              
ATOM    112  O   ALA    28      31.549  -5.085  13.391  1.00  0.00              
ATOM    113  N   ALA    30      30.510  -6.832  14.362  1.00  0.00              
ATOM    114  CA  ALA    30      31.449  -6.903  15.470  1.00  0.00              
ATOM    115  C   ALA    30      32.878  -7.191  14.973  1.00  0.00              
ATOM    116  O   ALA    30      33.829  -6.579  15.441  1.00  0.00              
ATOM    117  N   MET    31      32.994  -8.081  13.985  1.00  0.00              
ATOM    118  CA  MET    31      34.257  -8.421  13.364  1.00  0.00              
ATOM    119  C   MET    31      34.957  -7.234  12.738  1.00  0.00              
ATOM    120  O   MET    31      36.159  -7.085  12.891  1.00  0.00              
ATOM    121  N   GLU    32      34.209  -6.385  12.045  1.00  0.00              
ATOM    122  CA  GLU    32      34.768  -5.183  11.469  1.00  0.00              
ATOM    123  C   GLU    32      35.297  -4.285  12.577  1.00  0.00              
ATOM    124  O   GLU    32      36.416  -3.775  12.496  1.00  0.00              
ATOM    125  N   ILE    33      34.491  -4.107  13.618  1.00  0.00              
ATOM    126  CA  ILE    33      34.861  -3.227  14.727  1.00  0.00              
ATOM    127  C   ILE    33      36.041  -3.751  15.544  1.00  0.00              
ATOM    128  O   ILE    33      36.801  -2.966  16.096  1.00  0.00              
ATOM    129  N   ALA    34      36.202  -5.060  15.619  1.00  0.00              
ATOM    130  CA  ALA    34      37.344  -5.657  16.324  1.00  0.00              
ATOM    131  C   ALA    34      38.552  -5.843  15.379  1.00  0.00              
ATOM    132  O   ALA    34      39.543  -6.462  15.753  1.00  0.00              
ATOM    133  N   PRO    35      38.464  -5.297  14.163  1.00  0.00              
ATOM    134  CA  PRO    35      39.564  -5.317  13.197  1.00  0.00              
ATOM    135  C   PRO    35      40.018  -6.729  12.837  1.00  0.00              
ATOM    136  O   PRO    35      41.203  -6.974  12.609  1.00  0.00              
ATOM    137  N   SER    36      39.089  -7.664  12.805  1.00  0.00              
ATOM    138  CA  SER    36      39.414  -9.007  12.387  1.00  0.00              
ATOM    139  C   SER    36      39.547  -9.052  10.861  1.00  0.00              
ATOM    140  O   SER    36      40.207  -9.939  10.326  1.00  0.00              
ATOM    141  N   THR    37      38.918  -8.101  10.169  1.00  0.00              
ATOM    142  CA  THR    37      38.940  -8.039   8.703  1.00  0.00              
ATOM    143  C   THR    37      38.207  -6.818   8.162  1.00  0.00              
ATOM    144  O   THR    37      37.380  -6.200   8.842  1.00  0.00              
ATOM    145  N   ALA    38      38.479  -6.515   6.898  1.00  0.00              
ATOM    146  CA  ALA    38      37.756  -5.461   6.218  1.00  0.00              
ATOM    147  C   ALA    38      36.505  -5.998   5.515  1.00  0.00              
ATOM    148  O   ALA    38      36.469  -7.125   5.017  1.00  0.00              
ATOM    149  N   SER    39      35.485  -5.168   5.462  1.00  0.00              
ATOM    150  CA  SER    39      34.291  -5.484   4.681  1.00  0.00              
ATOM    151  C   SER    39      34.564  -5.460   3.174  1.00  0.00              
ATOM    152  O   SER    39      35.522  -4.841   2.725  1.00  0.00              
ATOM    153  N   ARG    40      33.688  -6.105   2.417  1.00  0.00              
ATOM    154  CA  ARG    40      33.641  -5.966   0.972  1.00  0.00              
ATOM    155  C   ARG    40      33.380  -4.505   0.607  1.00  0.00              
ATOM    156  O   ARG    40      32.882  -3.712   1.422  1.00  0.00              
ATOM    157  N   GLU    51      33.712  -4.147  -0.625  1.00  0.00              
ATOM    158  CA  GLU    51      33.383  -2.831  -1.128  1.00  0.00              
ATOM    159  C   GLU    51      31.895  -2.561  -0.998  1.00  0.00              
ATOM    160  O   GLU    51      31.493  -1.492  -0.531  1.00  0.00              
ATOM    161  N   MET    52      31.069  -3.527  -1.393  1.00  0.00              
ATOM    162  CA  MET    52      29.618  -3.299  -1.341  1.00  0.00              
ATOM    163  C   MET    52      29.116  -3.026   0.083  1.00  0.00              
ATOM    164  O   MET    52      28.293  -2.147   0.298  1.00  0.00              
ATOM    165  N   ALA    53      29.609  -3.772   1.059  1.00  0.00              
ATOM    166  CA  ALA    53      29.169  -3.581   2.441  1.00  0.00              
ATOM    167  C   ALA    53      29.655  -2.240   2.992  1.00  0.00              
ATOM    168  O   ALA    53      28.892  -1.531   3.678  1.00  0.00              
ATOM    169  N   ILE    54      30.904  -1.884   2.692  1.00  0.00              
ATOM    170  CA  ILE    54      31.433  -0.564   3.041  1.00  0.00              
ATOM    171  C   ILE    54      30.531   0.541   2.501  1.00  0.00              
ATOM    172  O   ILE    54      30.209   1.498   3.220  1.00  0.00              
ATOM    173  N   LYS    55      30.107   0.403   1.245  1.00  0.00              
ATOM    174  CA  LYS    55      29.256   1.422   0.618  1.00  0.00              
ATOM    175  C   LYS    55      27.874   1.506   1.278  1.00  0.00              
ATOM    176  O   LYS    55      27.341   2.592   1.447  1.00  0.00              
ATOM    177  N   LEU    56      27.321   0.364   1.672  1.00  0.00              
ATOM    178  CA  LEU    56      26.027   0.334   2.358  1.00  0.00              
ATOM    179  C   LEU    56      26.138   0.985   3.721  1.00  0.00              
ATOM    180  O   LEU    56      25.265   1.732   4.122  1.00  0.00              
ATOM    181  N   SER    57      27.231   0.695   4.420  1.00  0.00              
ATOM    182  CA  SER    57      27.496   1.307   5.730  1.00  0.00              
ATOM    183  C   SER    57      27.527   2.823   5.584  1.00  0.00              
ATOM    184  O   SER    57      26.886   3.514   6.365  1.00  0.00              
ATOM    185  N   VAL    58      28.273   3.344   4.613  1.00  0.00              
ATOM    186  CA  VAL    58      28.419   4.790   4.433  1.00  0.00              
ATOM    187  C   VAL    58      27.095   5.439   4.057  1.00  0.00              
ATOM    188  O   VAL    58      26.772   6.575   4.470  1.00  0.00              
ATOM    189  N   VAL    59      26.341   4.719   3.252  1.00  0.00              
ATOM    190  CA  VAL    59      25.058   5.200   2.781  1.00  0.00              
ATOM    191  C   VAL    59      24.125   5.414   3.981  1.00  0.00              
ATOM    192  O   VAL    59      23.594   6.515   4.191  1.00  0.00              
ATOM    193  N   ILE    60      23.947   4.379   4.779  1.00  0.00              
ATOM    194  CA  ILE    60      22.969   4.440   5.863  1.00  0.00              
ATOM    195  C   ILE    60      23.457   5.296   7.021  1.00  0.00              
ATOM    196  O   ILE    60      22.667   6.008   7.642  1.00  0.00              
ATOM    197  N   GLY    61      24.766   5.271   7.278  1.00  0.00              
ATOM    198  CA  GLY    61      25.319   6.135   8.311  1.00  0.00              
ATOM    199  C   GLY    61      25.487   7.597   7.874  1.00  0.00              
ATOM    200  O   GLY    61      25.938   8.423   8.665  1.00  0.00              
ATOM    201  N   SER    62      25.104   7.918   6.642  1.00  0.00              
ATOM    202  CA  SER    62      25.146   9.282   6.127  1.00  0.00              
ATOM    203  C   SER    62      26.456   9.982   6.469  1.00  0.00              
ATOM    204  O   SER    62      26.489  11.106   6.988  1.00  0.00              
ATOM    205  N   SER    63      27.543   9.264   6.190  1.00  0.00              
ATOM    206  CA  SER    63      28.893   9.706   6.506  1.00  0.00              
ATOM    207  C   SER    63      29.778   9.369   5.302  1.00  0.00              
ATOM    208  O   SER    63      29.675   8.250   4.777  1.00  0.00              
ATOM    209  N   PRO    64      30.641  10.296   4.858  1.00  0.00              
ATOM    210  CA  PRO    64      31.570   9.972   3.769  1.00  0.00              
ATOM    211  C   PRO    64      32.309   8.708   4.126  1.00  0.00              
ATOM    212  O   PRO    64      32.757   8.551   5.270  1.00  0.00              
ATOM    213  N   GLN    65      32.391   7.803   3.167  1.00  0.00              
ATOM    214  CA  GLN    65      33.004   6.507   3.366  1.00  0.00              
ATOM    215  C   GLN    65      34.405   6.635   3.949  1.00  0.00              
ATOM    216  O   GLN    65      34.788   5.861   4.810  1.00  0.00              
ATOM    217  N   MET    66      35.161   7.631   3.506  1.00  0.00              
ATOM    218  CA  MET    66      36.533   7.774   3.971  1.00  0.00              
ATOM    219  C   MET    66      36.669   8.296   5.388  1.00  0.00              
ATOM    220  O   MET    66      37.719   8.141   5.982  1.00  0.00              
ATOM    221  N   ASN    69      35.599   8.840   5.954  1.00  0.00              
ATOM    222  CA  ASN    69      35.549   9.119   7.386  1.00  0.00              
ATOM    223  C   ASN    69      35.380   7.843   8.204  1.00  0.00              
ATOM    224  O   ASN    69      35.721   7.822   9.385  1.00  0.00              
ATOM    225  N   LEU    70      34.873   6.781   7.586  1.00  0.00              
ATOM    226  CA  LEU    70      34.680   5.520   8.276  1.00  0.00              
ATOM    227  C   LEU    70      35.825   4.540   8.044  1.00  0.00              
ATOM    228  O   LEU    70      36.211   3.825   8.953  1.00  0.00              
ATOM    229  N   GLN    71      36.302   4.442   6.811  1.00  0.00              
ATOM    230  CA  GLN    71      37.363   3.493   6.458  1.00  0.00              
ATOM    231  C   GLN    71      38.465   4.323   5.827  1.00  0.00              
ATOM    232  O   GLN    71      38.279   4.923   4.774  1.00  0.00              
END
