
#######################################################
#                                                     #
#                        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   33 (  161),  selected   33 , name T0312TS239_2_2-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312TS239_2_2-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    G       9      F      12           #
LGA    K      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      L      13           #
LGA    L      13      L      14           -
LGA    L      14      R      15           -
LGA    R      15      L      16           -
LGA    L      16      D      17           -
LGA    D      17      Y      18           -
LGA    Y      18      -       -           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      G      19          5.848
LGA    -       -      K      20           -
LGA    L      22      D      21          3.331
LGA    V      23      L      22          2.643
LGA    -       -      V      23           -
LGA    R      24      R      24          1.290
LGA    Q      25      Q      25          1.442
LGA    I      26      I      26          1.408
LGA    E      27      E      27          1.009
LGA    E      28      E      28          0.765
LGA    F      29      F      29          0.773
LGA    L      30      L      30          0.803
LGA    E      31      E      31          0.567
LGA    E      32      E      32          0.810
LGA    K      33      K      33          0.900
LGA    G      34      G      34          0.489
LGA    I      35      I      35          1.944
LGA    H      36      H      36          2.869
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      H      39           -
LGA    -       -      I      40           -
LGA    -       -      S      41           -
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      I      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      G      77           -
LGA    -       -      N      78           -
LGA    -       -      V      79           -
LGA    -       -      S      80           -
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    A      37      P      86          1.747
LGA    A      38      F      87          4.362
LGA    H      39      C      88          2.659
LGA    I      40      H      89          0.613
LGA    S      41      I      90          2.968
LGA    -       -      H      91           -
LGA    -       -      V      92           -
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    -       -      E      99           -
LGA    -       -      V     100           -
LGA    -       -      Y     101           -
LGA    -       -      G     102           -
LGA    -       -      G     103           -
LGA    -       -      H     104           -
LGA    -       -      L     105           -
LGA    -       -      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    -       -      A     124           -
LGA    -       -      P     125           -
LGA    -       -      E     126           -
LGA    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33  132    5.0     21    2.32    61.90     13.642     0.867

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.556954 * X  +   0.290954 * Y  +  -0.777913 * Z  +  62.556732
  Y_new =   0.436195 * X  +  -0.694587 * Y  +  -0.572086 * Z  +  31.402380
  Z_new =  -0.706779 * X  +  -0.657947 * Y  +   0.259940 * Z  +  25.387596 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.194541    1.947052  [ DEG:   -68.4421    111.5579 ]
  Theta =   0.784935    2.356658  [ DEG:    44.9734    135.0266 ]
  Phi   =   2.477192   -0.664400  [ DEG:   141.9327    -38.0673 ]
 
# 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: T0312TS239_2_2-D1                             
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS239_2_2-D1.T0312_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  132   5.0   21   2.32   61.90  13.642
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS239_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0312
PARENT 2aj6_A
ATOM     41  N   GLY     9      64.928  10.005  21.451  1.00  9.99
ATOM     42  CA  GLY     9      63.718  10.654  21.037  1.00  9.99
ATOM     43  C   GLY     9      62.523   9.740  21.344  1.00  9.99
ATOM     44  O   GLY     9      62.612   8.486  21.140  1.00  9.99
ATOM     45  N   LYS    10      61.487  10.314  21.949  1.00  9.99
ATOM     46  CA  LYS    10      60.205   9.618  22.069  1.00  9.99
ATOM     47  C   LYS    10      59.253  10.230  21.068  1.00  9.99
ATOM     48  O   LYS    10      59.242  11.443  20.857  1.00  9.99
ATOM     49  CB  LYS    10      59.587   9.649  23.486  1.00  9.99
ATOM     50  N   GLY    11      58.458   9.378  20.445  1.00  9.99
ATOM     51  CA  GLY    11      57.397   9.853  19.563  1.00  9.99
ATOM     52  C   GLY    11      56.211  10.181  20.483  1.00  9.99
ATOM     53  O   GLY    11      55.649   9.293  21.138  1.00  9.99
ATOM     54  N   PHE    12      55.891  11.463  20.582  1.00  9.99
ATOM     55  CA  PHE    12      54.776  11.961  21.394  1.00  9.99
ATOM     56  C   PHE    12      53.426  11.605  20.747  1.00  9.99
ATOM     57  O   PHE    12      52.472  11.227  21.417  1.00  9.99
ATOM     58  CB  PHE    12      54.875  13.476  21.556  1.00  9.99
ATOM     59  N   LEU    13      53.391  11.667  19.419  1.00  9.99
ATOM     60  CA  LEU    13      52.188  11.480  18.646  1.00  9.99
ATOM     61  C   LEU    13      52.552  11.277  17.174  1.00  9.99
ATOM     62  O   LEU    13      53.358  12.012  16.614  1.00  9.99
ATOM     63  CB  LEU    13      51.273  12.697  18.759  1.00  9.99
ATOM     64  N   LEU    14      51.932  10.277  16.559  1.00  9.99
ATOM     65  CA  LEU    14      51.981  10.109  15.121  1.00  9.99
ATOM     66  C   LEU    14      50.527   9.921  14.654  1.00  9.99
ATOM     67  O   LEU    14      49.837   9.019  15.150  1.00  9.99
ATOM     68  CB  LEU    14      52.782   8.896  14.749  1.00  9.99
ATOM     69  N   ARG    15      50.087  10.742  13.720  1.00  9.99
ATOM     70  CA  ARG    15      48.709  10.671  13.237  1.00  9.99
ATOM     71  C   ARG    15      48.599  10.938  11.737  1.00  9.99
ATOM     72  O   ARG    15      49.178  11.896  11.203  1.00  9.99
ATOM     73  CB  ARG    15      47.843  11.683  13.975  1.00  9.99
ATOM     74  N   LEU    16      47.812  10.104  11.076  1.00  9.99
ATOM     75  CA  LEU    16      47.457  10.335   9.684  1.00  9.99
ATOM     76  C   LEU    16      45.934  10.394   9.568  1.00  9.99
ATOM     77  O   LEU    16      45.246   9.545  10.096  1.00  9.99
ATOM     78  CB  LEU    16      47.995   9.228   8.720  1.00  9.99
ATOM     79  N   ASP    17      45.421  11.397   8.874  1.00  9.99
ATOM     80  CA  ASP    17      43.971  11.484   8.626  1.00  9.99
ATOM     81  C   ASP    17      43.503  10.180   8.023  1.00  9.99
ATOM     82  O   ASP    17      44.079   9.709   7.047  1.00  9.99
ATOM     83  CB  ASP    17      43.668  12.646   7.695  1.00  9.99
ATOM     84  N   TYR    18      42.444   9.574   8.612  1.00  9.99
ATOM     85  CA  TYR    18      41.959   8.295   8.092  1.00  9.99
ATOM     86  C   TYR    18      41.847   8.177   6.559  1.00  9.99
ATOM     87  O   TYR    18      42.255   7.173   5.976  1.00  9.99
ATOM     88  CB  TYR    18      40.599   8.153   8.774  1.00  9.99
ATOM     89  N   GLY    19      52.832   7.916   6.992  1.00  9.99
ATOM     90  CA  GLY    19      53.396   7.653   8.334  1.00  9.99
ATOM     91  C   GLY    19      54.857   7.189   8.198  1.00  9.99
ATOM     92  O   GLY    19      55.733   7.656   8.937  1.00  9.99
ATOM     93  N   LYS    20      55.127   6.314   7.235  1.00  9.99
ATOM     94  CA  LYS    20      56.483   5.825   7.014  1.00  9.99
ATOM     95  C   LYS    20      57.449   6.963   6.704  1.00  9.99
ATOM     96  O   LYS    20      58.563   7.058   7.277  1.00  9.99
ATOM     97  CB  LYS    20      56.480   4.807   5.868  1.00  9.99
ATOM     98  N   ASP    21      57.026   7.834   5.797  1.00  9.99
ATOM     99  CA  ASP    21      57.794   9.033   5.443  1.00  9.99
ATOM    100  C   ASP    21      58.051   9.944   6.659  1.00  9.99
ATOM    101  O   ASP    21      59.169  10.460   6.855  1.00  9.99
ATOM    102  CB  ASP    21      57.034   9.762   4.321  1.00  9.99
ATOM    103  N   LEU    22      57.031  10.131   7.484  1.00  9.99
ATOM    104  CA  LEU    22      57.140  10.967   8.669  1.00  9.99
ATOM    105  C   LEU    22      58.134  10.356   9.664  1.00  9.99
ATOM    106  O   LEU    22      58.964  11.083  10.248  1.00  9.99
ATOM    107  CB  LEU    22      55.777  11.184   9.337  1.00  9.99
ATOM    108  N   VAL    23      58.051   9.045   9.863  1.00  9.99
ATOM    109  CA  VAL    23      58.995   8.346  10.781  1.00  9.99
ATOM    110  C   VAL    23      60.443   8.475  10.297  1.00  9.99
ATOM    111  O   VAL    23      61.369   8.711  11.087  1.00  9.99
ATOM    112  CB  VAL    23      58.578   6.895  10.997  1.00  9.99
ATOM    113  N   ARG    24      60.640   8.340   8.992  1.00  9.99
ATOM    114  CA  ARG    24      61.970   8.429   8.423  1.00  9.99
ATOM    115  C   ARG    24      62.516   9.837   8.693  1.00  9.99
ATOM    116  O   ARG    24      63.671  10.013   9.076  1.00  9.99
ATOM    117  CB  ARG    24      61.917   8.128   6.914  1.00  9.99
ATOM    118  N   GLN    25      61.686  10.844   8.437  1.00  9.99
ATOM    119  CA  GLN    25      62.099  12.215   8.679  1.00  9.99
ATOM    120  C   GLN    25      62.455  12.433  10.156  1.00  9.99
ATOM    121  O   GLN    25      63.513  13.030  10.487  1.00  9.99
ATOM    122  CB  GLN    25      61.036  13.155   8.253  1.00  9.99
ATOM    123  N   ILE    26      61.620  11.921  11.062  1.00  9.99
ATOM    124  CA  ILE    26      61.875  12.129  12.489  1.00  9.99
ATOM    125  C   ILE    26      63.157  11.425  12.913  1.00  9.99
ATOM    126  O   ILE    26      63.951  12.003  13.678  1.00  9.99
ATOM    127  CB  ILE    26      60.668  11.689  13.349  1.00  9.99
ATOM    128  N   GLU    27      63.435  10.245  12.363  1.00  9.99
ATOM    129  CA  GLU    27      64.640   9.515  12.696  1.00  9.99
ATOM    130  C   GLU    27      65.876  10.292  12.222  1.00  9.99
ATOM    131  O   GLU    27      66.895  10.343  12.917  1.00  9.99
ATOM    132  CB  GLU    27      64.633   8.112  12.098  1.00  9.99
ATOM    133  N   GLU    28      65.798  10.887  11.034  1.00  9.99
ATOM    134  CA  GLU    28      66.920  11.734  10.592  1.00  9.99
ATOM    135  C   GLU    28      67.155  12.896  11.554  1.00  9.99
ATOM    136  O   GLU    28      68.289  13.262  11.837  1.00  9.99
ATOM    137  CB  GLU    28      66.717  12.246   9.169  1.00  9.99
ATOM    138  N   PHE    29      66.080  13.500  12.037  1.00  9.99
ATOM    139  CA  PHE    29      66.176  14.577  13.033  1.00  9.99
ATOM    140  C   PHE    29      66.812  14.044  14.323  1.00  9.99
ATOM    141  O   PHE    29      67.738  14.654  14.876  1.00  9.99
ATOM    142  CB  PHE    29      64.819  15.175  13.354  1.00  9.99
ATOM    143  N   LEU    30      66.348  12.861  14.756  1.00  9.99
ATOM    144  CA  LEU    30      66.912  12.250  15.965  1.00  9.99
ATOM    145  C   LEU    30      68.427  12.103  15.847  1.00  9.99
ATOM    146  O   LEU    30      69.153  12.341  16.783  1.00  9.99
ATOM    147  CB  LEU    30      66.242  10.917  16.271  1.00  9.99
ATOM    148  N   GLU    31      68.944  11.749  14.674  1.00  9.99
ATOM    149  CA  GLU    31      70.377  11.605  14.499  1.00  9.99
ATOM    150  C   GLU    31      71.156  12.930  14.646  1.00  9.99
ATOM    151  O   GLU    31      72.318  12.941  15.066  1.00  9.99
ATOM    152  CB  GLU    31      70.684  10.918  13.180  1.00  9.99
ATOM    153  N   GLU    32      70.507  14.037  14.279  1.00  9.99
ATOM    154  CA  GLU    32      71.175  15.337  14.378  1.00  9.99
ATOM    155  C   GLU    32      71.318  15.763  15.845  1.00  9.99
ATOM    156  O   GLU    32      72.102  16.640  16.169  1.00  9.99
ATOM    157  CB  GLU    32      70.447  16.466  13.562  1.00  9.99
ATOM    158  N   LYS    33      70.518  15.128  16.705  1.00  9.99
ATOM    159  CA  LYS    33      70.503  15.440  18.135  1.00  9.99
ATOM    160  C   LYS    33      71.376  14.456  18.886  1.00  9.99
ATOM    161  O   LYS    33      71.532  14.563  20.110  1.00  9.99
ATOM    162  CB  LYS    33      69.070  15.391  18.689  1.00  9.99
ATOM    163  N   GLY    34      71.964  13.510  18.155  1.00  9.99
ATOM    164  CA  GLY    34      72.838  12.509  18.732  1.00  9.99
ATOM    165  C   GLY    34      71.985  11.625  19.667  1.00  9.99
ATOM    166  O   GLY    34      72.382  11.256  20.777  1.00  9.99
ATOM    167  N   ILE    35      70.785  11.312  19.201  1.00  9.99
ATOM    168  CA  ILE    35      69.858  10.454  19.935  1.00  9.99
ATOM    169  C   ILE    35      70.106   9.039  19.477  1.00  9.99
ATOM    170  O   ILE    35      70.360   8.812  18.266  1.00  9.99
ATOM    171  CB  ILE    35      68.425  10.834  19.621  1.00  9.99
ATOM    172  N   HIS    36      69.999   8.092  20.421  1.00  9.99
ATOM    173  CA  HIS    36      70.197   6.655  20.140  1.00  9.99
ATOM    174  C   HIS    36      69.179   6.115  19.126  1.00  9.99
ATOM    175  O   HIS    36      69.505   5.292  18.272  1.00  9.99
ATOM    176  CB  HIS    36      70.110   5.837  21.442  1.00  9.99
ATOM    177  N   ALA    37      67.946   6.591  19.229  1.00  9.99
ATOM    178  CA  ALA    37      66.850   6.079  18.414  1.00  9.99
ATOM    179  C   ALA    37      65.632   6.957  18.641  1.00  9.99
ATOM    180  O   ALA    37      65.690   7.876  19.475  1.00  9.99
ATOM    181  CB  ALA    37      66.507   4.637  18.830  1.00  9.99
ATOM    182  N   ALA    38      64.561   6.650  17.890  1.00  9.99
ATOM    183  CA  ALA    38      63.187   7.103  18.160  1.00  9.99
ATOM    184  C   ALA    38      62.402   5.984  18.879  1.00  9.99
ATOM    185  O   ALA    38      62.876   4.828  19.010  1.00  9.99
ATOM    186  CB  ALA    38      62.418   7.429  16.851  1.00  9.99
ATOM    187  N   HIS    39      61.189   6.330  19.315  1.00  9.99
ATOM    188  CA  HIS    39      60.282   5.378  19.995  1.00  9.99
ATOM    189  C   HIS    39      60.036   4.033  19.304  1.00  9.99
ATOM    190  O   HIS    39      59.906   3.974  18.069  1.00  9.99
ATOM    191  CB  HIS    39      58.887   5.994  20.133  1.00  9.99
ATOM    192  N   ILE    40      59.909   2.978  20.126  1.00  9.99
ATOM    193  CA  ILE    40      59.251   1.744  19.703  1.00  9.99
ATOM    194  C   ILE    40      57.731   1.956  19.695  1.00  9.99
ATOM    195  O   ILE    40      57.219   2.961  20.203  1.00  9.99
ATOM    196  CB  ILE    40      59.564   0.566  20.647  1.00  9.99
ATOM    197  N   SER    41      57.026   0.973  19.131  1.00  9.99
ATOM    198  CA  SER    41      55.559   0.968  19.079  1.00  9.99
ATOM    199  C   SER    41      55.060  -0.474  19.004  1.00  9.99
ATOM    200  O   SER    41      55.844  -1.372  18.684  1.00  9.99
ATOM    201  CB  SER    41      55.022   1.804  17.869  1.00  9.99
TER
END
