
#######################################################
#                                                     #
#                        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   90 (   90),  selected   90 , name T0340TS393_3
# Molecule2: number of CA atoms   90 (  685),  selected   90 , name T0340.pdb
# PARAMETERS: T0340TS393_3.T0340.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           #
LGA    M       2      M       2          4.591
LGA    L       3      L       3          4.567
LGA    R       4      R       4          0.785
LGA    P       5      P       5          1.376
LGA    R       6      R       6          1.174
LGA    L       7      L       7          2.200
LGA    C       8      C       8          1.650
LGA    H       9      H       9          1.077
LGA    L      10      L      10          1.116
LGA    R      11      R      11          0.266
LGA    K      12      K      12          0.341
LGA    G      13      G      13          2.849
LGA    P      14      P      14          1.754
LGA    Q      15      Q      15          2.001
LGA    G      16      G      16          1.133
LGA    Y      17      Y      17          0.969
LGA    G      18      G      18          1.258
LGA    F      19      F      19          1.387
LGA    N      20      N      20          1.889
LGA    L      21      L      21          0.794
LGA    H      22      H      22          1.065
LGA    S      23      S      23          1.414
LGA    D      24      D      24          2.497
LGA    K      25      K      25          4.464
LGA    S      26      S      26          6.051
LGA    R      27      R      27          1.995
LGA    P      28      P      28          1.653
LGA    G      29      G      29          1.212
LGA    Q      30      Q      30          0.430
LGA    Y      31      Y      31          0.829
LGA    I      32      I      32          0.655
LGA    R      33      R      33          0.944
LGA    S      34      S      34          2.897
LGA    V      35      V      35          1.482
LGA    D      36      D      36          2.031
LGA    P      37      P      37          2.363
LGA    G      38      G      38          1.235
LGA    S      39      S      39          1.842
LGA    P      40      P      40          1.493
LGA    -       -      A      41           -
LGA    A      41      A      42           #
LGA    A      42      R      43          1.043
LGA    R      43      S      44           #
LGA    S      44      -       -           -
LGA    G      45      G      45          1.966
LGA    L      46      L      46          1.255
LGA    R      47      R      47          1.687
LGA    A      48      A      48          0.662
LGA    Q      49      Q      49          0.634
LGA    D      50      D      50          0.981
LGA    R      51      R      51          0.883
LGA    L      52      L      52          1.734
LGA    I      53      I      53          1.760
LGA    E      54      E      54          0.881
LGA    V      55      V      55          1.358
LGA    N      56      N      56          1.767
LGA    G      57      G      57          1.924
LGA    Q      58      Q      58          2.208
LGA    N      59      N      59          3.284
LGA    V      60      V      60          1.716
LGA    E      61      E      61          0.418
LGA    G      62      G      62          0.563
LGA    L      63      L      63          2.542
LGA    R      64      R      64          2.603
LGA    H      65      H      65          1.188
LGA    A      66      A      66          1.229
LGA    E      67      E      67          0.932
LGA    V      68      V      68          0.948
LGA    V      69      V      69          1.265
LGA    A      70      A      70          1.560
LGA    S      71      S      71          1.520
LGA    I      72      I      72          1.595
LGA    K      73      K      73          2.129
LGA    A      74      A      74          2.344
LGA    R      75      R      75          1.976
LGA    E      76      E      76          1.348
LGA    D      77      D      77          2.221
LGA    E      78      E      78          1.918
LGA    A      79      A      79          0.771
LGA    R      80      R      80          0.638
LGA    L      81      L      81          1.092
LGA    L      82      L      82          1.189
LGA    V      83      V      83          1.414
LGA    V      84      V      84          1.649
LGA    G      85      G      85          1.355
LGA    P      86      P      86          1.627
LGA    S      87      S      87          2.777
LGA    T      88      T      88          3.307
LGA    R      89      R      89          4.247
LGA    L      90      L      90           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     85    1.98    98.82     82.753     4.093

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.489563 * X  +  -0.260186 * Y  +   0.832245 * Z  +   9.934916
  Y_new =   0.793572 * X  +  -0.528473 * Y  +   0.301597 * Z  +  25.860437
  Z_new =   0.361347 * X  +   0.808097 * Y  +   0.465197 * Z  +   9.044456 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.048459   -2.093133  [ DEG:    60.0723   -119.9277 ]
  Theta =  -0.369713   -2.771880  [ DEG:   -21.1830   -158.8170 ]
  Phi   =   2.123558   -1.018035  [ DEG:   121.6709    -58.3291 ]
 
# 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: T0340TS393_3                                  
REMARK     2: T0340.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS393_3.T0340.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   90   90   5.0   85   1.98   98.82  82.753
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS393_3
PFRMAT TS
TARGET T0340
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1      15.718  44.972   3.768  1.00 25.00           C
ATOM      2  CA  MET     2      16.861  44.315   7.380  1.00 25.00           C
ATOM      3  CA  LEU     3      18.031  40.693   6.827  1.00 25.00           C
ATOM      4  CA  ARG     4      14.393  39.962   7.661  1.00 25.00           C
ATOM      5  CA  PRO     5      13.876  37.233  10.261  1.00 25.00           C
ATOM      6  CA  ARG     6      10.185  36.639  10.023  1.00 25.00           C
ATOM      7  CA  LEU     7       8.540  34.599  12.755  1.00 25.00           C
ATOM      8  CA  CYS     8       5.804  31.920  12.867  1.00 25.00           C
ATOM      9  CA  HIS     9       5.697  31.208  16.620  1.00 25.00           C
ATOM     10  CA  LEU    10       3.363  28.138  16.816  1.00 25.00           C
ATOM     11  CA  ARG    11       1.527  25.637  19.031  1.00 25.00           C
ATOM     12  CA  LYS    12       1.504  21.863  18.541  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.777  21.875  20.422  1.00 25.00           C
ATOM     14  CA  PRO    14      -3.278  18.706  18.909  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.381  15.993  16.420  1.00 25.00           C
ATOM     16  CA  GLY    16       1.018  17.617  15.788  1.00 25.00           C
ATOM     17  CA  TYR    17       1.910  20.551  13.456  1.00 25.00           C
ATOM     18  CA  GLY    18       0.754  22.084  10.133  1.00 25.00           C
ATOM     19  CA  PHE    19       4.038  21.797   8.216  1.00 25.00           C
ATOM     20  CA  ASN    20       5.987  18.961   6.506  1.00 25.00           C
ATOM     21  CA  LEU    21       9.464  19.607   5.104  1.00 25.00           C
ATOM     22  CA  HIS    22      10.118  19.106   1.383  1.00 25.00           C
ATOM     23  CA  SER    23      13.539  19.712  -0.095  1.00 25.00           C
ATOM     24  CA  ASP    24      16.849  19.039  -1.754  1.00 25.00           C
ATOM     25  CA  LYS    25      20.141  17.463  -2.774  1.00 25.00           C
ATOM     26  CA  SER    26      22.864  20.063  -2.559  1.00 25.00           C
ATOM     27  CA  ARG    27      20.491  23.074  -2.275  1.00 25.00           C
ATOM     28  CA  PRO    28      21.202  23.235   1.493  1.00 25.00           C
ATOM     29  CA  GLY    29      18.132  24.912   2.991  1.00 25.00           C
ATOM     30  CA  GLN    30      14.944  23.011   3.944  1.00 25.00           C
ATOM     31  CA  TYR    31      11.336  23.731   2.958  1.00 25.00           C
ATOM     32  CA  ILE    32       7.674  24.609   3.241  1.00 25.00           C
ATOM     33  CA  ARG    33       5.654  22.345   0.865  1.00 25.00           C
ATOM     34  CA  SER    34       2.878  20.878   3.001  1.00 25.00           C
ATOM     35  CA  VAL    35       0.613  23.507   4.569  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.339  21.361   5.813  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.297  23.632   6.594  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.074  25.651   9.702  1.00 25.00           C
ATOM     39  CA  SER    39      -3.892  23.228  11.632  1.00 25.00           C
ATOM     40  CA  PRO    40      -1.470  25.999  12.545  1.00 25.00           C
ATOM     41  CA  ALA    41      -1.514  28.276  15.624  1.00 25.00           C
ATOM     42  CA  ALA    42      -0.914  31.336  13.400  1.00 25.00           C
ATOM     43  CA  ARG    43      -3.778  30.256  11.100  1.00 25.00           C
ATOM     44  CA  SER    44      -1.282  30.680   8.291  1.00 25.00           C
ATOM     45  CA  GLY    45       1.498  33.219   8.901  1.00 25.00           C
ATOM     46  CA  LEU    46       3.917  30.789   7.316  1.00 25.00           C
ATOM     47  CA  ARG    47       4.170  31.695   3.580  1.00 25.00           C
ATOM     48  CA  ALA    48       4.485  28.411   1.713  1.00 25.00           C
ATOM     49  CA  GLN    49       7.772  28.289  -0.273  1.00 25.00           C
ATOM     50  CA  ASP    50      10.072  28.972   2.731  1.00 25.00           C
ATOM     51  CA  ARG    51      13.708  28.181   3.341  1.00 25.00           C
ATOM     52  CA  LEU    52      12.584  27.140   6.853  1.00 25.00           C
ATOM     53  CA  ILE    53      15.579  28.069   8.946  1.00 25.00           C
ATOM     54  CA  GLU    54      16.063  27.497  12.658  1.00 25.00           C
ATOM     55  CA  VAL    55      15.780  25.376  15.823  1.00 25.00           C
ATOM     56  CA  ASN    56      15.484  27.744  18.827  1.00 25.00           C
ATOM     57  CA  GLY    57      18.799  29.214  17.595  1.00 25.00           C
ATOM     58  CA  GLN    58      20.873  27.111  15.192  1.00 25.00           C
ATOM     59  CA  ASN    59      20.122  23.741  13.557  1.00 25.00           C
ATOM     60  CA  VAL    60      18.518  23.813  10.046  1.00 25.00           C
ATOM     61  CA  GLU    61      21.266  24.708   7.547  1.00 25.00           C
ATOM     62  CA  GLY    62      23.866  21.914   7.750  1.00 25.00           C
ATOM     63  CA  LEU    63      20.990  19.708   6.599  1.00 25.00           C
ATOM     64  CA  ARG    64      19.573  16.827   4.561  1.00 25.00           C
ATOM     65  CA  HIS    65      16.210  17.406   6.172  1.00 25.00           C
ATOM     66  CA  ALA    66      15.462  14.352   8.358  1.00 25.00           C
ATOM     67  CA  GLU    67      17.097  16.071  11.364  1.00 25.00           C
ATOM     68  CA  VAL    68      15.004  19.216  10.734  1.00 25.00           C
ATOM     69  CA  VAL    69      11.823  17.092  10.546  1.00 25.00           C
ATOM     70  CA  ALA    70      12.748  15.372  13.841  1.00 25.00           C
ATOM     71  CA  SER    71      13.335  18.780  15.484  1.00 25.00           C
ATOM     72  CA  ILE    72       9.934  20.005  14.218  1.00 25.00           C
ATOM     73  CA  LYS    73       8.255  16.858  15.614  1.00 25.00           C
ATOM     74  CA  ALA    74       9.966  17.415  18.995  1.00 25.00           C
ATOM     75  CA  ARG    75       9.428  20.745  20.655  1.00 25.00           C
ATOM     76  CA  GLU    76       6.157  19.433  22.210  1.00 25.00           C
ATOM     77  CA  ASP    77       5.858  22.775  23.911  1.00 25.00           C
ATOM     78  CA  GLU    78       6.457  25.523  21.357  1.00 25.00           C
ATOM     79  CA  ALA    79       7.813  25.321  17.792  1.00 25.00           C
ATOM     80  CA  ARG    80      10.081  28.291  17.760  1.00 25.00           C
ATOM     81  CA  LEU    81      10.006  28.293  13.982  1.00 25.00           C
ATOM     82  CA  LEU    82      12.216  31.186  12.956  1.00 25.00           C
ATOM     83  CA  VAL    83      12.868  32.397   9.376  1.00 25.00           C
ATOM     84  CA  VAL    84      14.227  32.654   5.844  1.00 25.00           C
ATOM     85  CA  GLY    85      11.688  34.031   3.369  1.00 25.00           C
ATOM     86  CA  PRO    86      12.104  34.191  -0.354  1.00 25.00           C
ATOM     87  CA  SER    87      12.858  35.217  -3.888  1.00 25.00           C
ATOM     88  CA  THR    88      15.536  36.707  -6.137  1.00 25.00           C
ATOM     89  CA  ARG    89      18.832  38.578  -5.846  1.00 25.00           C
ATOM     90  CA  LEU    90      22.249  37.197  -4.790  1.00 25.00           C
TER
END
