
#######################################################
#                                                     #
#                        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 T0363AL333_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_3-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11           -
LGA    Q      12      -       -           -
LGA    I      13      -       -           -
LGA    N      14      -       -           -
LGA    I      15      -       -           -
LGA    E      16      -       -           -
LGA    I      17      -       -           -
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      Q      12          4.128
LGA    E      23      I      13          3.754
LGA    R      24      N      14          4.745
LGA    Y      25      I      15          1.993
LGA    Y      26      E      16          2.201
LGA    L      27      I      17          1.423
LGA    K      28      A      18          2.678
LGA    S      29      Y      19           -
LGA    F      30      A      20           -
LGA    Q      31      F      21           -
LGA    G      35      P      22           -
LGA    I      36      E      23           -
LGA    T      37      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    V      38      I      36           #
LGA    Q      39      -       -           -
LGA    T      40      T      37           #
LGA    A      41      V      38          4.990
LGA    I      42      Q      39           #
LGA    -       -      T      40           -
LGA    T      43      A      41          2.052
LGA    Q      44      I      42          4.013
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    S      45      G      46          4.779
LGA    G      46      I      47          1.710
LGA    -       -      L      48           -
LGA    -       -      S      49           -
LGA    I      47      Q      50          2.696
LGA    L      48      F      51          3.755
LGA    S      49      P      52          2.035
LGA    Q      50      E      53          1.216
LGA    -       -      I      54           -
LGA    F      51      D      55          4.647
LGA    P      52      L      56           #
LGA    E      53      -       -           -
LGA    I      54      -       -           -
LGA    D      55      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     17    3.35     0.00     23.912     0.492

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.773745 * X  +   0.541458 * Y  +  -0.328848 * Z  + -10.991633
  Y_new =  -0.604047 * X  +   0.787020 * Y  +  -0.125405 * Z  + -37.748024
  Z_new =   0.190908 * X  +   0.295671 * Y  +   0.936019 * Z  + -38.150940 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.305963   -2.835630  [ DEG:    17.5304   -162.4696 ]
  Theta =  -0.192087   -2.949505  [ DEG:   -11.0058   -168.9942 ]
  Phi   =  -0.662848    2.478745  [ DEG:   -37.9784    142.0216 ]
 
# 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: T0363AL333_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   17   3.35    0.00  23.912
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_3-D1
REMARK Aligment from pdb entry: 1ltl_A
ATOM     41  N   ASN    11      40.542  -2.739  34.648  1.00  0.00              
ATOM     42  CA  ASN    11      41.608  -1.844  34.220  1.00  0.00              
ATOM     43  C   ASN    11      41.121  -0.476  33.732  1.00  0.00              
ATOM     44  O   ASN    11      41.856   0.231  33.040  1.00  0.00              
ATOM     45  N   GLN    12      39.897  -0.101  34.102  1.00  0.00              
ATOM     46  CA  GLN    12      39.317   1.177  33.683  1.00  0.00              
ATOM     47  C   GLN    12      39.078   1.153  32.164  1.00  0.00              
ATOM     48  O   GLN    12      38.007   0.759  31.701  1.00  0.00              
ATOM     49  N   ILE    13      40.087   1.575  31.402  1.00  0.00              
ATOM     50  CA  ILE    13      40.040   1.612  29.938  1.00  0.00              
ATOM     51  C   ILE    13      38.859   2.367  29.330  1.00  0.00              
ATOM     52  O   ILE    13      37.712   1.906  29.339  1.00  0.00              
ATOM     53  N   ASN    14      39.156   3.544  28.802  1.00  0.00              
ATOM     54  CA  ASN    14      38.149   4.368  28.163  1.00  0.00              
ATOM     55  C   ASN    14      38.184   3.960  26.680  1.00  0.00              
ATOM     56  O   ASN    14      38.962   4.499  25.895  1.00  0.00              
ATOM     57  N   ILE    15      37.369   2.984  26.301  1.00  0.00              
ATOM     58  CA  ILE    15      37.357   2.542  24.918  1.00  0.00              
ATOM     59  C   ILE    15      36.386   3.339  24.074  1.00  0.00              
ATOM     60  O   ILE    15      35.398   3.867  24.572  1.00  0.00              
ATOM     61  N   GLU    16      36.670   3.428  22.786  1.00  0.00              
ATOM     62  CA  GLU    16      35.802   4.158  21.897  1.00  0.00              
ATOM     63  C   GLU    16      34.929   3.198  21.144  1.00  0.00              
ATOM     64  O   GLU    16      35.430   2.392  20.372  1.00  0.00              
ATOM     65  N   ILE    17      33.624   3.267  21.359  1.00  0.00              
ATOM     66  CA  ILE    17      32.735   2.393  20.620  1.00  0.00              
ATOM     67  C   ILE    17      32.431   3.075  19.287  1.00  0.00              
ATOM     68  O   ILE    17      31.930   4.186  19.263  1.00  0.00              
ATOM     69  N   ALA    18      30.342   2.704  15.713  1.00  0.00              
ATOM     70  CA  ALA    18      29.383   1.933  14.932  1.00  0.00              
ATOM     71  C   ALA    18      29.591   1.985  13.445  1.00  0.00              
ATOM     72  O   ALA    18      29.860   3.039  12.886  1.00  0.00              
ATOM     73  N   TYR    19      29.462   0.834  12.798  1.00  0.00              
ATOM     74  CA  TYR    19      29.625   0.776  11.353  1.00  0.00              
ATOM     75  C   TYR    19      28.316   0.426  10.638  1.00  0.00              
ATOM     76  O   TYR    19      27.476  -0.289  11.176  1.00  0.00              
ATOM     77  N   ALA    20      28.162   0.939   9.420  1.00  0.00              
ATOM     78  CA  ALA    20      26.957   0.684   8.659  1.00  0.00              
ATOM     79  C   ALA    20      25.727   1.291   9.313  1.00  0.00              
ATOM     80  O   ALA    20      24.914   0.596   9.939  1.00  0.00              
ATOM     81  N   PHE    21      25.591   2.603   9.182  1.00  0.00              
ATOM     82  CA  PHE    21      24.451   3.289   9.758  1.00  0.00              
ATOM     83  C   PHE    21      23.483   3.620   8.644  1.00  0.00              
ATOM     84  O   PHE    21      23.852   4.230   7.638  1.00  0.00              
ATOM     85  N   PRO    22      22.242   3.186   8.826  1.00  0.00              
ATOM     86  CA  PRO    22      21.183   3.400   7.845  1.00  0.00              
ATOM     87  C   PRO    22      20.763   4.864   7.738  1.00  0.00              
ATOM     88  O   PRO    22      20.366   5.335   6.663  1.00  0.00              
ATOM     89  N   GLU    23      20.861   5.578   8.860  1.00  0.00              
ATOM     90  CA  GLU    23      20.481   6.989   8.927  1.00  0.00              
ATOM     91  C   GLU    23      21.420   7.884   8.130  1.00  0.00              
ATOM     92  O   GLU    23      22.089   8.740   8.688  1.00  0.00              
ATOM     93  N   ARG    24      21.460   7.691   6.820  1.00  0.00              
ATOM     94  CA  ARG    24      22.333   8.490   5.975  1.00  0.00              
ATOM     95  C   ARG    24      21.628   9.749   5.473  1.00  0.00              
ATOM     96  O   ARG    24      20.633   9.686   4.746  1.00  0.00              
ATOM     97  N   TYR    25      22.155  10.901   5.865  1.00  0.00              
ATOM     98  CA  TYR    25      21.562  12.153   5.459  1.00  0.00              
ATOM     99  C   TYR    25      22.418  12.945   4.500  1.00  0.00              
ATOM    100  O   TYR    25      23.613  13.054   4.663  1.00  0.00              
ATOM    101  N   TYR    26      21.810  13.509   3.459  1.00  0.00              
ATOM    102  CA  TYR    26      22.665  14.281   2.554  1.00  0.00              
ATOM    103  C   TYR    26      23.182  15.538   3.245  1.00  0.00              
ATOM    104  O   TYR    26      22.505  16.128   4.072  1.00  0.00              
ATOM    105  N   LEU    27      24.387  15.943   2.891  1.00  0.00              
ATOM    106  CA  LEU    27      25.002  17.109   3.494  1.00  0.00              
ATOM    107  C   LEU    27      24.149  18.366   3.599  1.00  0.00              
ATOM    108  O   LEU    27      23.972  18.893   4.691  1.00  0.00              
ATOM    109  N   LYS    28      23.631  18.855   2.477  1.00  0.00              
ATOM    110  CA  LYS    28      22.826  20.075   2.487  1.00  0.00              
ATOM    111  C   LYS    28      21.633  20.020   3.436  1.00  0.00              
ATOM    112  O   LYS    28      21.065  21.044   3.745  1.00  0.00              
ATOM    113  N   SER    29      21.248  18.843   3.900  1.00  0.00              
ATOM    114  CA  SER    29      20.083  18.738   4.776  1.00  0.00              
ATOM    115  C   SER    29      20.372  18.627   6.265  1.00  0.00              
ATOM    116  O   SER    29      19.477  18.292   7.048  1.00  0.00              
ATOM    117  N   PHE    30      21.617  18.870   6.655  1.00  0.00              
ATOM    118  CA  PHE    30      22.032  18.785   8.063  1.00  0.00              
ATOM    119  C   PHE    30      21.626  20.048   8.845  1.00  0.00              
ATOM    120  O   PHE    30      22.470  20.853   9.252  1.00  0.00              
ATOM    121  N   GLN    31      20.317  20.194   9.034  1.00  0.00              
ATOM    122  CA  GLN    31      19.731  21.321   9.732  1.00  0.00              
ATOM    123  C   GLN    31      19.471  20.973  11.195  1.00  0.00              
ATOM    124  O   GLN    31      19.884  19.926  11.693  1.00  0.00              
ATOM    125  N   GLY    35      18.728  21.840  11.866  1.00  0.00              
ATOM    126  CA  GLY    35      18.455  21.673  13.275  1.00  0.00              
ATOM    127  C   GLY    35      17.842  20.396  13.728  1.00  0.00              
ATOM    128  O   GLY    35      18.201  19.894  14.784  1.00  0.00              
ATOM    129  N   ILE    36      16.909  19.855  12.963  1.00  0.00              
ATOM    130  CA  ILE    36      16.269  18.620  13.419  1.00  0.00              
ATOM    131  C   ILE    36      17.294  17.536  13.731  1.00  0.00              
ATOM    132  O   ILE    36      17.032  16.664  14.563  1.00  0.00              
ATOM    133  N   THR    37      18.466  17.617  13.097  1.00  0.00              
ATOM    134  CA  THR    37      19.535  16.628  13.288  1.00  0.00              
ATOM    135  C   THR    37      20.598  16.969  14.344  1.00  0.00              
ATOM    136  O   THR    37      21.575  16.246  14.499  1.00  0.00              
ATOM    137  N   VAL    38      20.416  18.066  15.067  1.00  0.00              
ATOM    138  CA  VAL    38      21.383  18.433  16.086  1.00  0.00              
ATOM    139  C   VAL    38      21.245  17.469  17.241  1.00  0.00              
ATOM    140  O   VAL    38      20.157  17.283  17.785  1.00  0.00              
ATOM    141  N   GLN    39      22.362  16.850  17.607  1.00  0.00              
ATOM    142  CA  GLN    39      22.359  15.895  18.697  1.00  0.00              
ATOM    143  C   GLN    39      22.053  14.483  18.222  1.00  0.00              
ATOM    144  O   GLN    39      22.061  13.553  19.016  1.00  0.00              
ATOM    145  N   THR    40      21.817  14.316  16.924  1.00  0.00              
ATOM    146  CA  THR    40      21.481  13.012  16.357  1.00  0.00              
ATOM    147  C   THR    40      22.659  12.310  15.704  1.00  0.00              
ATOM    148  O   THR    40      23.623  12.947  15.274  1.00  0.00              
ATOM    149  N   ALA    41      22.558  10.993  15.584  1.00  0.00              
ATOM    150  CA  ALA    41      23.630  10.223  14.974  1.00  0.00              
ATOM    151  C   ALA    41      23.424  10.203  13.465  1.00  0.00              
ATOM    152  O   ALA    41      22.464   9.621  12.988  1.00  0.00              
ATOM    153  N   ILE    42      24.299  10.845  12.703  1.00  0.00              
ATOM    154  CA  ILE    42      24.106  10.844  11.260  1.00  0.00              
ATOM    155  C   ILE    42      25.241  10.199  10.505  1.00  0.00              
ATOM    156  O   ILE    42      26.244   9.786  11.082  1.00  0.00              
ATOM    157  N   THR    43      25.073  10.113   9.197  1.00  0.00              
ATOM    158  CA  THR    43      26.077   9.512   8.348  1.00  0.00              
ATOM    159  C   THR    43      25.944  10.284   7.065  1.00  0.00              
ATOM    160  O   THR    43      24.893  10.270   6.442  1.00  0.00              
ATOM    161  N   GLN    44      27.028  10.938   6.683  1.00  0.00              
ATOM    162  CA  GLN    44      27.062  11.801   5.535  1.00  0.00              
ATOM    163  C   GLN    44      28.174  11.450   4.606  1.00  0.00              
ATOM    164  O   GLN    44      29.282  11.214   5.066  1.00  0.00              
ATOM    165  N   SER    45      27.905  11.456   3.298  1.00  0.00              
ATOM    166  CA  SER    45      28.941  11.154   2.291  1.00  0.00              
ATOM    167  C   SER    45      29.469  12.446   1.678  1.00  0.00              
ATOM    168  O   SER    45      28.769  13.451   1.646  1.00  0.00              
ATOM    169  N   GLY    46      30.697  12.409   1.181  1.00  0.00              
ATOM    170  CA  GLY    46      31.285  13.587   0.577  1.00  0.00              
ATOM    171  C   GLY    46      32.750  13.355   0.279  1.00  0.00              
ATOM    172  O   GLY    46      33.194  12.213   0.266  1.00  0.00              
ATOM    173  N   ILE    47      33.509  14.422   0.055  1.00  0.00              
ATOM    174  CA  ILE    47      34.925  14.280  -0.240  1.00  0.00              
ATOM    175  C   ILE    47      35.802  15.194   0.611  1.00  0.00              
ATOM    176  O   ILE    47      35.641  16.415   0.595  1.00  0.00              
ATOM    177  N   LEU    48      36.740  14.602   1.344  1.00  0.00              
ATOM    178  CA  LEU    48      37.633  15.384   2.191  1.00  0.00              
ATOM    179  C   LEU    48      38.379  16.449   1.414  1.00  0.00              
ATOM    180  O   LEU    48      39.211  16.134   0.589  1.00  0.00              
ATOM    181  N   SER    49      38.102  17.709   1.708  1.00  0.00              
ATOM    182  CA  SER    49      38.758  18.788   1.007  1.00  0.00              
ATOM    183  C   SER    49      40.013  19.250   1.732  1.00  0.00              
ATOM    184  O   SER    49      41.112  18.843   1.383  1.00  0.00              
ATOM    185  N   GLN    50      39.862  20.089   2.750  1.00  0.00              
ATOM    186  CA  GLN    50      41.018  20.602   3.487  1.00  0.00              
ATOM    187  C   GLN    50      41.217  19.949   4.841  1.00  0.00              
ATOM    188  O   GLN    50      40.257  19.747   5.583  1.00  0.00              
ATOM    189  N   PHE    51      42.470  19.640   5.165  1.00  0.00              
ATOM    190  CA  PHE    51      42.802  19.009   6.443  1.00  0.00              
ATOM    191  C   PHE    51      43.674  19.885   7.346  1.00  0.00              
ATOM    192  O   PHE    51      44.700  20.404   6.917  1.00  0.00              
ATOM    193  N   PRO    52      43.268  20.043   8.602  1.00  0.00              
ATOM    194  CA  PRO    52      44.022  20.872   9.539  1.00  0.00              
ATOM    195  C   PRO    52      45.016  20.104  10.402  1.00  0.00              
ATOM    196  O   PRO    52      44.965  18.882  10.505  1.00  0.00              
ATOM    197  N   GLU    53      45.914  20.856  11.030  1.00  0.00              
ATOM    198  CA  GLU    53      46.954  20.323  11.902  1.00  0.00              
ATOM    199  C   GLU    53      46.344  19.620  13.109  1.00  0.00              
ATOM    200  O   GLU    53      45.286  20.007  13.598  1.00  0.00              
ATOM    201  N   ILE    54      47.012  18.581  13.581  1.00  0.00              
ATOM    202  CA  ILE    54      46.520  17.868  14.741  1.00  0.00              
ATOM    203  C   ILE    54      46.981  18.624  15.993  1.00  0.00              
ATOM    204  O   ILE    54      48.156  18.949  16.110  1.00  0.00              
ATOM    205  N   ASP    55      29.053  15.433  -2.356  1.00  0.00              
ATOM    206  CA  ASP    55      29.332  14.756  -3.614  1.00  0.00              
ATOM    207  C   ASP    55      28.905  15.672  -4.756  1.00  0.00              
ATOM    208  O   ASP    55      27.815  16.256  -4.729  1.00  0.00              
ATOM    209  N   LEU    56      29.778  15.808  -5.750  1.00  0.00              
ATOM    210  CA  LEU    56      29.516  16.652  -6.910  1.00  0.00              
ATOM    211  C   LEU    56      28.415  16.099  -7.802  1.00  0.00              
ATOM    212  O   LEU    56      27.645  16.864  -8.380  1.00  0.00              
END
