
#######################################################
#                                                     #
#                        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   54 (  216),  selected   54 , name T0381AL333_3-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381AL333_3-D1.T0381_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      V      17           -
LGA    -       -      Q      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      A      21           -
LGA    R      22      R      22          1.904
LGA    G      23      G      23          1.378
LGA    L      24      L      24          1.343
LGA    A      25      A      25          1.719
LGA    V      26      V      26          1.109
LGA    I      27      I      27          0.767
LGA    R      28      R      28          1.803
LGA    C      29      C      29          1.773
LGA    F      30      F      30          2.613
LGA    D      31      D      31          4.768
LGA    H      32      H      32          4.106
LGA    -       -      R      33           -
LGA    R      33      N      34          2.574
LGA    N      34      Q      35          2.774
LGA    Q      35      R      36          3.565
LGA    R      36      -       -           -
LGA    R      37      R      37          0.445
LGA    T      38      T      38          0.812
LGA    L      39      L      39          0.652
LGA    S      40      S      40          0.292
LGA    D      41      D      41          0.982
LGA    V      42      V      42          1.179
LGA    A      43      A      43          1.005
LGA    R      44      R      44          1.570
LGA    A      45      A      45          1.932
LGA    T      46      T      46          1.708
LGA    D      47      D      47          1.993
LGA    L      48      L      48          1.688
LGA    T      49      T      49          1.511
LGA    R      50      R      50          0.441
LGA    A      51      A      51          1.151
LGA    T      52      T      52          0.966
LGA    A      53      A      53          1.238
LGA    R      54      R      54          1.251
LGA    R      55      R      55          0.739
LGA    F      56      F      56          0.339
LGA    L      57      L      57          1.178
LGA    L      58      L      58          1.730
LGA    T      59      T      59          1.601
LGA    L      60      L      60          1.758
LGA    V      61      V      61          2.717
LGA    E      62      E      62          3.124
LGA    L      63      L      63          3.025
LGA    G      64      G      64          3.244
LGA    Y      65      Y      65          0.759
LGA    V      66      V      66          1.656
LGA    A      67      A      67          2.055
LGA    T      68      T      68          2.250
LGA    D      69      D      69          2.526
LGA    G      70      G      70          4.669
LGA    S      71      S      71          4.322
LGA    A      72      A      72          1.555
LGA    F      73      F      73          0.936
LGA    W      74      W      74          1.786
LGA    L      75      L      75          1.618
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   54   61    5.0     53    2.11    94.34     74.214     2.395

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.637633 * X  +  -0.152485 * Y  +  -0.755097 * Z  +   1.438097
  Y_new =  -0.768498 * X  +  -0.193658 * Y  +  -0.609842 * Z  +  94.557281
  Z_new =  -0.053239 * X  +   0.969146 * Y  +  -0.240668 * Z  +  10.126825 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.814202   -1.327390  [ DEG:   103.9461    -76.0539 ]
  Theta =   0.053264    3.088328  [ DEG:     3.0518    176.9482 ]
  Phi   =  -0.878198    2.263395  [ DEG:   -50.3170    129.6830 ]
 
# 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: T0381AL333_3-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL333_3-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   54   61   5.0   53   2.11   94.34  74.214
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL333_3-D1
REMARK Aligment from pdb entry: 1j5y_A
ATOM     21  N   ARG    22       6.694  54.123  27.191  1.00  0.00              
ATOM     22  CA  ARG    22       6.418  54.796  25.937  1.00  0.00              
ATOM     23  C   ARG    22       7.655  54.828  25.044  1.00  0.00              
ATOM     24  O   ARG    22       7.554  54.644  23.833  1.00  0.00              
ATOM     25  N   GLY    23       8.823  55.052  25.634  1.00  0.00              
ATOM     26  CA  GLY    23      10.054  55.109  24.844  1.00  0.00              
ATOM     27  C   GLY    23      10.325  53.752  24.182  1.00  0.00              
ATOM     28  O   GLY    23      10.744  53.696  23.021  1.00  0.00              
ATOM     29  N   LEU    24      10.083  52.667  24.921  1.00  0.00              
ATOM     30  CA  LEU    24      10.290  51.331  24.376  1.00  0.00              
ATOM     31  C   LEU    24       9.315  51.101  23.228  1.00  0.00              
ATOM     32  O   LEU    24       9.680  50.519  22.218  1.00  0.00              
ATOM     33  N   ALA    25       8.079  51.569  23.368  1.00  0.00              
ATOM     34  CA  ALA    25       7.098  51.384  22.301  1.00  0.00              
ATOM     35  C   ALA    25       7.483  52.161  21.038  1.00  0.00              
ATOM     36  O   ALA    25       7.302  51.673  19.933  1.00  0.00              
ATOM     37  N   VAL    26       8.007  53.369  21.201  1.00  0.00              
ATOM     38  CA  VAL    26       8.388  54.170  20.057  1.00  0.00              
ATOM     39  C   VAL    26       9.465  53.424  19.277  1.00  0.00              
ATOM     40  O   VAL    26       9.402  53.296  18.055  1.00  0.00              
ATOM     41  N   ILE    27      10.457  52.925  20.003  1.00  0.00              
ATOM     42  CA  ILE    27      11.537  52.226  19.358  1.00  0.00              
ATOM     43  C   ILE    27      11.008  51.021  18.604  1.00  0.00              
ATOM     44  O   ILE    27      11.377  50.805  17.457  1.00  0.00              
ATOM     45  N   ARG    28      10.139  50.242  19.237  1.00  0.00              
ATOM     46  CA  ARG    28       9.574  49.072  18.572  1.00  0.00              
ATOM     47  C   ARG    28       8.770  49.450  17.331  1.00  0.00              
ATOM     48  O   ARG    28       8.907  48.824  16.281  1.00  0.00              
ATOM     49  N   CYS    29       7.932  50.475  17.439  1.00  0.00              
ATOM     50  CA  CYS    29       7.119  50.884  16.294  1.00  0.00              
ATOM     51  C   CYS    29       7.974  51.362  15.134  1.00  0.00              
ATOM     52  O   CYS    29       7.709  51.032  13.985  1.00  0.00              
ATOM     53  N   PHE    30       8.998  52.157  15.427  1.00  0.00              
ATOM     54  CA  PHE    30       9.849  52.650  14.361  1.00  0.00              
ATOM     55  C   PHE    30      10.633  51.530  13.724  1.00  0.00              
ATOM     56  O   PHE    30      10.842  51.549  12.527  1.00  0.00              
ATOM     57  N   ASP    31      11.061  50.558  14.520  1.00  0.00              
ATOM     58  CA  ASP    31      11.848  49.450  13.987  1.00  0.00              
ATOM     59  C   ASP    31      11.044  48.481  13.151  1.00  0.00              
ATOM     60  O   ASP    31      11.515  48.019  12.121  1.00  0.00              
ATOM     61  N   HIS    32       9.830  48.180  13.585  1.00  0.00              
ATOM     62  CA  HIS    32       8.938  47.275  12.857  1.00  0.00              
ATOM     63  C   HIS    32       8.509  47.843  11.511  1.00  0.00              
ATOM     64  O   HIS    32       8.343  47.105  10.549  1.00  0.00              
ATOM     65  N   ARG    33       8.326  49.153  11.444  1.00  0.00              
ATOM     66  CA  ARG    33       7.831  49.793  10.232  1.00  0.00              
ATOM     67  C   ARG    33       8.785  49.902   9.047  1.00  0.00              
ATOM     68  O   ARG    33       9.874  50.402   9.170  1.00  0.00              
ATOM     69  N   ASN    34       8.358  49.455   7.877  1.00  0.00              
ATOM     70  CA  ASN    34       9.213  49.540   6.699  1.00  0.00              
ATOM     71  C   ASN    34       9.308  50.987   6.211  1.00  0.00              
ATOM     72  O   ASN    34      10.303  51.393   5.619  1.00  0.00              
ATOM     73  N   GLN    35       8.261  51.760   6.466  1.00  0.00              
ATOM     74  CA  GLN    35       8.217  53.152   6.039  1.00  0.00              
ATOM     75  C   GLN    35       8.364  54.155   7.183  1.00  0.00              
ATOM     76  O   GLN    35       8.314  53.806   8.358  1.00  0.00              
ATOM     77  N   ARG    36       8.560  55.431   6.837  1.00  0.00              
ATOM     78  CA  ARG    36       8.681  56.386   7.939  1.00  0.00              
ATOM     79  C   ARG    36       7.332  56.520   8.665  1.00  0.00              
ATOM     80  O   ARG    36       6.256  56.389   8.056  1.00  0.00              
ATOM     81  N   ARG    37       7.396  56.760   9.974  1.00  0.00              
ATOM     82  CA  ARG    37       6.199  56.897  10.787  1.00  0.00              
ATOM     83  C   ARG    37       6.083  58.340  11.249  1.00  0.00              
ATOM     84  O   ARG    37       6.940  58.824  11.985  1.00  0.00              
ATOM     85  N   THR    38       5.025  59.033  10.851  1.00  0.00              
ATOM     86  CA  THR    38       4.919  60.422  11.247  1.00  0.00              
ATOM     87  C   THR    38       4.758  60.627  12.749  1.00  0.00              
ATOM     88  O   THR    38       4.273  59.752  13.478  1.00  0.00              
ATOM     89  N   LEU    39       5.207  61.784  13.210  1.00  0.00              
ATOM     90  CA  LEU    39       5.070  62.117  14.610  1.00  0.00              
ATOM     91  C   LEU    39       3.597  62.203  14.996  1.00  0.00              
ATOM     92  O   LEU    39       3.246  61.927  16.142  1.00  0.00              
ATOM     93  N   SER    40       2.739  62.595  14.056  1.00  0.00              
ATOM     94  CA  SER    40       1.310  62.672  14.340  1.00  0.00              
ATOM     95  C   SER    40       0.777  61.267  14.596  1.00  0.00              
ATOM     96  O   SER    40      -0.084  61.078  15.449  1.00  0.00              
ATOM     97  N   ASP    41       1.292  60.280  13.862  1.00  0.00              
ATOM     98  CA  ASP    41       0.843  58.907  14.066  1.00  0.00              
ATOM     99  C   ASP    41       1.362  58.350  15.386  1.00  0.00              
ATOM    100  O   ASP    41       0.632  57.641  16.082  1.00  0.00              
ATOM    101  N   VAL    42       2.611  58.642  15.735  1.00  0.00              
ATOM    102  CA  VAL    42       3.139  58.152  17.003  1.00  0.00              
ATOM    103  C   VAL    42       2.306  58.755  18.133  1.00  0.00              
ATOM    104  O   VAL    42       1.988  58.065  19.094  1.00  0.00              
ATOM    105  N   ALA    43       1.964  60.043  18.008  1.00  0.00              
ATOM    106  CA  ALA    43       1.159  60.748  19.015  1.00  0.00              
ATOM    107  C   ALA    43      -0.221  60.102  19.143  1.00  0.00              
ATOM    108  O   ALA    43      -0.713  59.894  20.236  1.00  0.00              
ATOM    109  N   ARG    44      -0.841  59.789  18.010  1.00  0.00              
ATOM    110  CA  ARG    44      -2.156  59.148  18.005  1.00  0.00              
ATOM    111  C   ARG    44      -2.038  57.755  18.615  1.00  0.00              
ATOM    112  O   ARG    44      -2.796  57.380  19.497  1.00  0.00              
ATOM    113  N   ALA    45      -1.066  56.991  18.149  1.00  0.00              
ATOM    114  CA  ALA    45      -0.866  55.637  18.639  1.00  0.00              
ATOM    115  C   ALA    45      -0.511  55.550  20.136  1.00  0.00              
ATOM    116  O   ALA    45      -0.916  54.622  20.832  1.00  0.00              
ATOM    117  N   THR    46       0.240  56.515  20.641  1.00  0.00              
ATOM    118  CA  THR    46       0.638  56.489  22.052  1.00  0.00              
ATOM    119  C   THR    46      -0.194  57.386  22.959  1.00  0.00              
ATOM    120  O   THR    46       0.068  57.467  24.141  1.00  0.00              
ATOM    121  N   ASP    47      -1.202  58.060  22.405  1.00  0.00              
ATOM    122  CA  ASP    47      -2.049  58.941  23.196  1.00  0.00              
ATOM    123  C   ASP    47      -1.306  60.048  23.941  1.00  0.00              
ATOM    124  O   ASP    47      -1.561  60.289  25.126  1.00  0.00              
ATOM    125  N   LEU    48      -0.377  60.714  23.263  1.00  0.00              
ATOM    126  CA  LEU    48       0.337  61.837  23.875  1.00  0.00              
ATOM    127  C   LEU    48       0.371  62.892  22.789  1.00  0.00              
ATOM    128  O   LEU    48       0.053  62.598  21.637  1.00  0.00              
ATOM    129  N   THR    49       0.736  64.116  23.149  1.00  0.00              
ATOM    130  CA  THR    49       0.778  65.210  22.180  1.00  0.00              
ATOM    131  C   THR    49       1.967  65.099  21.230  1.00  0.00              
ATOM    132  O   THR    49       2.952  64.412  21.512  1.00  0.00              
ATOM    133  N   ARG    50       1.873  65.792  20.105  1.00  0.00              
ATOM    134  CA  ARG    50       2.945  65.801  19.123  1.00  0.00              
ATOM    135  C   ARG    50       4.243  66.284  19.773  1.00  0.00              
ATOM    136  O   ARG    50       5.324  65.784  19.472  1.00  0.00              
ATOM    137  N   ALA    51       4.123  67.269  20.657  1.00  0.00              
ATOM    138  CA  ALA    51       5.273  67.840  21.336  1.00  0.00              
ATOM    139  C   ALA    51       5.963  66.825  22.253  1.00  0.00              
ATOM    140  O   ALA    51       7.198  66.817  22.363  1.00  0.00              
ATOM    141  N   THR    52       5.183  65.980  22.924  1.00  0.00              
ATOM    142  CA  THR    52       5.774  64.946  23.773  1.00  0.00              
ATOM    143  C   THR    52       6.624  64.021  22.900  1.00  0.00              
ATOM    144  O   THR    52       7.703  63.597  23.304  1.00  0.00              
ATOM    145  N   ALA    53       6.148  63.712  21.696  1.00  0.00              
ATOM    146  CA  ALA    53       6.919  62.850  20.821  1.00  0.00              
ATOM    147  C   ALA    53       8.239  63.523  20.408  1.00  0.00              
ATOM    148  O   ALA    53       9.286  62.887  20.415  1.00  0.00              
ATOM    149  N   ARG    54       8.186  64.805  20.051  1.00  0.00              
ATOM    150  CA  ARG    54       9.394  65.540  19.659  1.00  0.00              
ATOM    151  C   ARG    54      10.446  65.454  20.761  1.00  0.00              
ATOM    152  O   ARG    54      11.626  65.237  20.488  1.00  0.00              
ATOM    153  N   ARG    55      10.015  65.589  22.009  1.00  0.00              
ATOM    154  CA  ARG    55      10.933  65.526  23.136  1.00  0.00              
ATOM    155  C   ARG    55      11.429  64.105  23.363  1.00  0.00              
ATOM    156  O   ARG    55      12.604  63.911  23.638  1.00  0.00              
ATOM    157  N   PHE    56      10.549  63.113  23.239  1.00  0.00              
ATOM    158  CA  PHE    56      10.955  61.723  23.430  1.00  0.00              
ATOM    159  C   PHE    56      12.011  61.331  22.401  1.00  0.00              
ATOM    160  O   PHE    56      13.011  60.677  22.726  1.00  0.00              
ATOM    161  N   LEU    57      11.773  61.707  21.149  1.00  0.00              
ATOM    162  CA  LEU    57      12.711  61.374  20.084  1.00  0.00              
ATOM    163  C   LEU    57      14.085  62.028  20.302  1.00  0.00              
ATOM    164  O   LEU    57      15.116  61.399  20.046  1.00  0.00              
ATOM    165  N   LEU    58      14.106  63.281  20.760  1.00  0.00              
ATOM    166  CA  LEU    58      15.374  63.962  20.994  1.00  0.00              
ATOM    167  C   LEU    58      16.115  63.222  22.104  1.00  0.00              
ATOM    168  O   LEU    58      17.335  63.027  22.034  1.00  0.00              
ATOM    169  N   THR    59      15.362  62.794  23.114  1.00  0.00              
ATOM    170  CA  THR    59      15.933  62.055  24.230  1.00  0.00              
ATOM    171  C   THR    59      16.494  60.721  23.729  1.00  0.00              
ATOM    172  O   THR    59      17.638  60.391  24.013  1.00  0.00              
ATOM    173  N   LEU    60      15.690  59.958  22.987  1.00  0.00              
ATOM    174  CA  LEU    60      16.147  58.686  22.440  1.00  0.00              
ATOM    175  C   LEU    60      17.432  58.866  21.604  1.00  0.00              
ATOM    176  O   LEU    60      18.340  58.050  21.671  1.00  0.00              
ATOM    177  N   VAL    61      17.527  59.944  20.839  1.00  0.00              
ATOM    178  CA  VAL    61      18.724  60.137  20.030  1.00  0.00              
ATOM    179  C   VAL    61      19.961  60.421  20.881  1.00  0.00              
ATOM    180  O   VAL    61      21.049  59.934  20.584  1.00  0.00              
ATOM    181  N   GLU    62      19.786  61.190  21.949  1.00  0.00              
ATOM    182  CA  GLU    62      20.908  61.517  22.794  1.00  0.00              
ATOM    183  C   GLU    62      21.392  60.262  23.517  1.00  0.00              
ATOM    184  O   GLU    62      22.520  60.225  23.995  1.00  0.00              
ATOM    185  N   LEU    63      20.544  59.239  23.597  1.00  0.00              
ATOM    186  CA  LEU    63      20.939  57.986  24.232  1.00  0.00              
ATOM    187  C   LEU    63      21.683  57.091  23.231  1.00  0.00              
ATOM    188  O   LEU    63      22.360  56.161  23.631  1.00  0.00              
ATOM    189  N   GLY    64      21.549  57.352  21.936  1.00  0.00              
ATOM    190  CA  GLY    64      22.236  56.524  20.955  1.00  0.00              
ATOM    191  C   GLY    64      21.370  55.964  19.841  1.00  0.00              
ATOM    192  O   GLY    64      21.878  55.390  18.883  1.00  0.00              
ATOM    193  N   TYR    65      20.053  56.116  19.944  1.00  0.00              
ATOM    194  CA  TYR    65      19.178  55.593  18.897  1.00  0.00              
ATOM    195  C   TYR    65      19.350  56.331  17.584  1.00  0.00              
ATOM    196  O   TYR    65      19.240  57.560  17.528  1.00  0.00              
ATOM    197  N   VAL    66      17.807  57.490  15.118  1.00  0.00              
ATOM    198  CA  VAL    66      16.556  57.949  14.541  1.00  0.00              
ATOM    199  C   VAL    66      16.729  59.218  13.726  1.00  0.00              
ATOM    200  O   VAL    66      17.471  60.113  14.113  1.00  0.00              
ATOM    201  N   ALA    67      16.036  59.301  12.599  1.00  0.00              
ATOM    202  CA  ALA    67      16.101  60.499  11.780  1.00  0.00              
ATOM    203  C   ALA    67      14.679  60.975  11.484  1.00  0.00              
ATOM    204  O   ALA    67      13.778  60.184  11.198  1.00  0.00              
ATOM    205  N   THR    68      14.473  62.278  11.606  1.00  0.00              
ATOM    206  CA  THR    68      13.170  62.883  11.342  1.00  0.00              
ATOM    207  C   THR    68      13.153  63.347   9.879  1.00  0.00              
ATOM    208  O   THR    68      13.835  64.293   9.538  1.00  0.00              
ATOM    209  N   ASP    69      12.396  62.679   9.015  1.00  0.00              
ATOM    210  CA  ASP    69      12.327  63.067   7.609  1.00  0.00              
ATOM    211  C   ASP    69      10.965  63.719   7.384  1.00  0.00              
ATOM    212  O   ASP    69      10.089  63.606   8.224  1.00  0.00              
ATOM    213  N   GLY    70      10.766  64.407   6.246  1.00  0.00              
ATOM    214  CA  GLY    70       9.464  65.049   6.024  1.00  0.00              
ATOM    215  C   GLY    70       8.266  64.116   6.106  1.00  0.00              
ATOM    216  O   GLY    70       7.171  64.533   6.483  1.00  0.00              
ATOM    217  N   SER    71       8.457  62.857   5.747  1.00  0.00              
ATOM    218  CA  SER    71       7.350  61.909   5.795  1.00  0.00              
ATOM    219  C   SER    71       7.267  61.132   7.114  1.00  0.00              
ATOM    220  O   SER    71       6.392  60.276   7.287  1.00  0.00              
ATOM    221  N   ALA    72       8.162  61.432   8.049  1.00  0.00              
ATOM    222  CA  ALA    72       8.117  60.746   9.333  1.00  0.00              
ATOM    223  C   ALA    72       9.459  60.319   9.879  1.00  0.00              
ATOM    224  O   ALA    72      10.486  60.519   9.238  1.00  0.00              
ATOM    225  N   PHE    73       9.446  59.737  11.073  1.00  0.00              
ATOM    226  CA  PHE    73      10.659  59.276  11.719  1.00  0.00              
ATOM    227  C   PHE    73      11.121  57.966  11.150  1.00  0.00              
ATOM    228  O   PHE    73      10.319  57.099  10.852  1.00  0.00              
ATOM    229  N   TRP    74      12.433  57.816  11.028  1.00  0.00              
ATOM    230  CA  TRP    74      13.020  56.603  10.486  1.00  0.00              
ATOM    231  C   TRP    74      14.055  56.039  11.453  1.00  0.00              
ATOM    232  O   TRP    74      14.892  56.773  11.970  1.00  0.00              
ATOM    233  N   LEU    75      13.978  54.736  11.694  1.00  0.00              
ATOM    234  CA  LEU    75      14.903  54.027  12.576  1.00  0.00              
ATOM    235  C   LEU    75      15.021  52.649  11.980  1.00  0.00              
ATOM    236  O   LEU    75      14.063  51.898  12.039  1.00  0.00              
END
