
#######################################################
#                                                     #
#                        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   93 (   93),  selected   93 , name T0288TS393_2
# Molecule2: number of CA atoms   91 (  667),  selected   91 , name T0288
# PARAMETERS: T0288TS393_2.T0288  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      V       3          5.425
LGA    P       4      P       4          2.388
LGA    G       5      G       5          2.446
LGA    K       6      K       6          1.087
LGA    V       7      V       7          2.388
LGA    T       8      T       8          2.947
LGA    L       9      L       9          1.339
LGA    Q      10      Q      10          1.632
LGA    K      11      K      11          1.515
LGA    D      12      D      12          2.587
LGA    A      13      A      13          1.132
LGA    Q      14      Q      14          3.670
LGA    N      15      N      15          2.918
LGA    L      16      L      16          1.437
LGA    I      17      I      17          0.799
LGA    G      18      G      18          1.771
LGA    I      19      I      19          1.679
LGA    S      20      S      20          1.784
LGA    I      21      I      21          1.484
LGA    G      22      G      22          1.451
LGA    G      23      G      23          1.190
LGA    G      24      G      24          3.213
LGA    A      25      A      25          3.648
LGA    Q      26      Q      26          1.538
LGA    Y      27      -       -           -
LGA    C      28      -       -           -
LGA    P      29      P      29          2.394
LGA    C      30      C      30          1.741
LGA    L      31      L      31          0.555
LGA    Y      32      Y      32          1.533
LGA    I      33      I      33          1.028
LGA    V      34      V      34          1.095
LGA    Q      35      Q      35          0.624
LGA    V      36      V      36          2.658
LGA    F      37      F      37          1.513
LGA    D      38      D      38          1.574
LGA    N      39      N      39          0.900
LGA    T      40      T      40          1.220
LGA    P      41      P      41          0.587
LGA    A      42      A      42          0.482
LGA    A      43      A      43          1.007
LGA    L      44      L      44          1.266
LGA    D      45      D      45          0.849
LGA    G      46      G      46          0.731
LGA    T      47      T      47          1.596
LGA    V      48      V      48          2.031
LGA    A      49      A      49          0.722
LGA    A      50      A      50          1.269
LGA    G      51      G      51          1.233
LGA    D      52      D      52          1.103
LGA    E      53      E      53          0.917
LGA    I      54      I      54          0.655
LGA    T      55      T      55          0.724
LGA    G      56      G      56          0.583
LGA    V      57      V      57          1.729
LGA    N      58      N      58          0.892
LGA    G      59      G      59          1.270
LGA    R      60      R      60          1.281
LGA    S      61      S      61          1.445
LGA    I      62      I      62          1.244
LGA    K      63      K      63          2.035
LGA    G      64      G      64          1.986
LGA    K      65      K      65          1.304
LGA    T      66      T      66          2.453
LGA    K      67      K      67          0.651
LGA    V      68      V      68          0.624
LGA    E      69      E      69          0.669
LGA    V      70      V      70          0.846
LGA    A      71      A      71          0.581
LGA    K      72      K      72          0.532
LGA    M      73      M      73          0.895
LGA    I      74      I      74          1.174
LGA    Q      75      Q      75          0.536
LGA    E      76      E      76          0.860
LGA    V      77      V      77          0.897
LGA    K      78      K      78          1.936
LGA    G      79      G      79          3.032
LGA    E      80      E      80          2.508
LGA    V      81      V      81          1.323
LGA    T      82      T      82          0.867
LGA    I      83      I      83          1.136
LGA    H      84      H      84          2.089
LGA    Y      85      Y      85          1.678
LGA    N      86      N      86          0.672
LGA    K      87      K      87          1.226
LGA    L      88      L      88          1.181
LGA    Q      89      Q      89          2.123
LGA    -       -      Y      90           -
LGA    Y      90      Y      91          6.565
LGA    Y      91      K      92           -
LGA    K      92      V      93           -
LGA    V      93      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   93   91    5.0     86    1.86   100.00     85.242     4.388

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.546901 * X  +   0.339602 * Y  +  -0.765225 * Z  +  27.640612
  Y_new =  -0.563583 * X  +  -0.825251 * Y  +   0.036548 * Z  +  17.317062
  Z_new =  -0.619091 * X  +   0.451256 * Y  +   0.642724 * Z  +  13.250844 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.612133   -2.529460  [ DEG:    35.0726   -144.9274 ]
  Theta =   0.667584    2.474008  [ DEG:    38.2498    141.7502 ]
  Phi   =  -2.341174    0.800419  [ DEG:  -134.1394     45.8606 ]
 
# 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: T0288TS393_2                                  
REMARK     2: T0288                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_2.T0288 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   93   91   5.0   86   1.86  100.00  85.242
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_2
PFRMAT TS
TARGET T0288
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1      24.348   8.398  32.975  1.00 25.00           C
ATOM      2  CA  MET     2      24.950  10.567  29.885  1.00 25.00           C
ATOM      3  CA  VAL     3      23.309  13.246  27.750  1.00 25.00           C
ATOM      4  CA  PRO     4      24.217  14.108  24.120  1.00 25.00           C
ATOM      5  CA  GLY     5      23.154  17.776  24.131  1.00 25.00           C
ATOM      6  CA  LYS     6      21.295  16.929  20.927  1.00 25.00           C
ATOM      7  CA  VAL     7      22.470  19.974  19.067  1.00 25.00           C
ATOM      8  CA  THR     8      19.286  21.612  17.900  1.00 25.00           C
ATOM      9  CA  LEU     9      19.546  23.310  14.503  1.00 25.00           C
ATOM     10  CA  GLN    10      18.003  25.788  12.062  1.00 25.00           C
ATOM     11  CA  LYS    11      18.180  26.060   8.320  1.00 25.00           C
ATOM     12  CA  ASP    12      17.406  29.259   6.330  1.00 25.00           C
ATOM     13  CA  ALA    13      19.204  29.379   2.949  1.00 25.00           C
ATOM     14  CA  GLN    14      20.001  25.895   1.528  1.00 25.00           C
ATOM     15  CA  ASN    15      23.497  26.825   2.613  1.00 25.00           C
ATOM     16  CA  LEU    16      23.336  23.822   5.032  1.00 25.00           C
ATOM     17  CA  ILE    17      24.470  24.902   8.534  1.00 25.00           C
ATOM     18  CA  GLY    18      27.959  25.631   7.377  1.00 25.00           C
ATOM     19  CA  ILE    19      29.096  22.153   8.561  1.00 25.00           C
ATOM     20  CA  SER    20      31.888  20.721   6.413  1.00 25.00           C
ATOM     21  CA  ILE    21      32.183  17.046   7.354  1.00 25.00           C
ATOM     22  CA  GLY    22      35.080  14.720   7.837  1.00 25.00           C
ATOM     23  CA  GLY    23      38.056  13.144   9.566  1.00 25.00           C
ATOM     24  CA  GLY    24      39.008  10.752   6.730  1.00 25.00           C
ATOM     25  CA  ALA    25      38.049   7.053   6.704  1.00 25.00           C
ATOM     26  CA  GLN    26      41.036   5.880   8.850  1.00 25.00           C
ATOM     27  CA  TYR    27      39.304   7.338  11.917  1.00 25.00           C
ATOM     28  CA  CYS    28      37.562   4.480  13.727  1.00 25.00           C
ATOM     29  CA  PRO    29      33.860   5.191  13.414  1.00 25.00           C
ATOM     30  CA  CYS    30      32.464   8.728  13.758  1.00 25.00           C
ATOM     31  CA  LEU    31      32.773  12.076  12.010  1.00 25.00           C
ATOM     32  CA  TYR    32      33.274  15.835  12.481  1.00 25.00           C
ATOM     33  CA  ILE    33      32.519  19.581  12.964  1.00 25.00           C
ATOM     34  CA  VAL    34      35.563  20.794  10.964  1.00 25.00           C
ATOM     35  CA  GLN    35      34.955  24.351  12.198  1.00 25.00           C
ATOM     36  CA  VAL    36      32.189  26.023  10.120  1.00 25.00           C
ATOM     37  CA  PHE    37      31.651  29.473  11.629  1.00 25.00           C
ATOM     38  CA  ASP    38      29.947  32.424   9.921  1.00 25.00           C
ATOM     39  CA  ASN    39      26.370  33.611  10.146  1.00 25.00           C
ATOM     40  CA  THR    40      25.371  30.153   9.050  1.00 25.00           C
ATOM     41  CA  PRO    41      22.979  28.706  11.608  1.00 25.00           C
ATOM     42  CA  ALA    42      25.146  26.268  13.502  1.00 25.00           C
ATOM     43  CA  ALA    43      27.762  28.692  14.897  1.00 25.00           C
ATOM     44  CA  LEU    44      25.089  31.411  15.255  1.00 25.00           C
ATOM     45  CA  ASP    45      23.596  29.057  17.902  1.00 25.00           C
ATOM     46  CA  GLY    46      26.448  27.441  19.901  1.00 25.00           C
ATOM     47  CA  THR    47      26.200  23.658  19.599  1.00 25.00           C
ATOM     48  CA  VAL    48      28.128  22.401  16.534  1.00 25.00           C
ATOM     49  CA  ALA    49      31.254  23.102  18.597  1.00 25.00           C
ATOM     50  CA  ALA    50      34.689  23.063  17.030  1.00 25.00           C
ATOM     51  CA  GLY    51      36.343  19.724  18.008  1.00 25.00           C
ATOM     52  CA  ASP    52      32.975  17.984  17.802  1.00 25.00           C
ATOM     53  CA  GLU    53      32.570  14.229  17.317  1.00 25.00           C
ATOM     54  CA  ILE    54      29.281  13.345  15.512  1.00 25.00           C
ATOM     55  CA  THR    55      26.460  10.973  16.480  1.00 25.00           C
ATOM     56  CA  GLY    56      23.577  11.173  14.032  1.00 25.00           C
ATOM     57  CA  VAL    57      21.601  11.572  10.824  1.00 25.00           C
ATOM     58  CA  ASN    58      18.276  13.103  11.811  1.00 25.00           C
ATOM     59  CA  GLY    59      16.396  10.697  14.043  1.00 25.00           C
ATOM     60  CA  ARG    60      18.302   8.003  12.134  1.00 25.00           C
ATOM     61  CA  SER    61      21.779   6.642  12.701  1.00 25.00           C
ATOM     62  CA  ILE    62      24.745   7.501  10.398  1.00 25.00           C
ATOM     63  CA  LYS    63      27.793   6.036  12.111  1.00 25.00           C
ATOM     64  CA  GLY    64      29.875   3.082  10.808  1.00 25.00           C
ATOM     65  CA  LYS    65      29.234   4.560   7.316  1.00 25.00           C
ATOM     66  CA  THR    66      31.968   7.132   7.677  1.00 25.00           C
ATOM     67  CA  LYS    67      32.106  10.762   6.459  1.00 25.00           C
ATOM     68  CA  VAL    68      31.001  11.325   2.836  1.00 25.00           C
ATOM     69  CA  GLU    69      27.606   9.724   3.597  1.00 25.00           C
ATOM     70  CA  VAL    70      27.204  11.975   6.669  1.00 25.00           C
ATOM     71  CA  ALA    71      28.053  15.054   4.554  1.00 25.00           C
ATOM     72  CA  LYS    72      25.474  13.992   1.929  1.00 25.00           C
ATOM     73  CA  MET    73      22.835  13.542   4.669  1.00 25.00           C
ATOM     74  CA  ILE    74      23.645  17.018   6.054  1.00 25.00           C
ATOM     75  CA  GLN    75      23.316  18.520   2.546  1.00 25.00           C
ATOM     76  CA  GLU    76      19.936  16.780   2.092  1.00 25.00           C
ATOM     77  CA  VAL    77      17.584  18.330   4.600  1.00 25.00           C
ATOM     78  CA  LYS    78      16.046  21.785   4.779  1.00 25.00           C
ATOM     79  CA  GLY    79      13.855  20.624   7.686  1.00 25.00           C
ATOM     80  CA  GLU    80      15.500  20.265  11.132  1.00 25.00           C
ATOM     81  CA  VAL    81      19.259  19.649  10.732  1.00 25.00           C
ATOM     82  CA  THR    82      19.575  17.975  14.137  1.00 25.00           C
ATOM     83  CA  ILE    83      23.342  17.377  13.944  1.00 25.00           C
ATOM     84  CA  HIS    84      24.865  15.826  17.135  1.00 25.00           C
ATOM     85  CA  TYR    85      27.620  16.356  19.726  1.00 25.00           C
ATOM     86  CA  ASN    86      29.642  13.636  21.495  1.00 25.00           C
ATOM     87  CA  LYS    87      31.830  16.513  22.679  1.00 25.00           C
ATOM     88  CA  LEU    88      35.248  15.955  24.251  1.00 25.00           C
ATOM     89  CA  GLN    89      36.337  15.667  27.853  1.00 25.00           C
ATOM     90  CA  TYR    90      39.845  14.456  28.460  1.00 25.00           C
ATOM     91  CA  TYR    91      41.633  11.587  30.306  1.00 25.00           C
ATOM     92  CA  LYS    92      42.649   9.102  32.941  1.00 25.00           C
ATOM     93  CA  VAL    93      45.890  11.095  33.148  1.00 25.00           C
TER
END
