
#######################################################
#                                                     #
#                        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 T0340TS168_2
# Molecule2: number of CA atoms   90 (  685),  selected   90 , name T0340.pdb
# PARAMETERS: T0340TS168_2.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          1.852
LGA    L       3      L       3          1.352
LGA    R       4      R       4          1.643
LGA    P       5      P       5          1.882
LGA    R       6      R       6          2.286
LGA    L       7      L       7          2.506
LGA    C       8      C       8          0.259
LGA    H       9      H       9          0.677
LGA    L      10      L      10          0.992
LGA    R      11      R      11          1.082
LGA    K      12      K      12          1.170
LGA    G      13      G      13          1.846
LGA    P      14      P      14          2.701
LGA    Q      15      Q      15          2.269
LGA    G      16      G      16          0.941
LGA    Y      17      Y      17          1.472
LGA    G      18      G      18          1.442
LGA    F      19      F      19          1.329
LGA    N      20      N      20          1.837
LGA    L      21      L      21          0.208
LGA    H      22      H      22          0.177
LGA    S      23      S      23          1.779
LGA    D      24      D      24          3.264
LGA    K      25      K      25          3.303
LGA    S      26      S      26          5.594
LGA    R      27      R      27          2.481
LGA    P      28      P      28          2.002
LGA    G      29      G      29          0.687
LGA    Q      30      Q      30          1.635
LGA    Y      31      Y      31          1.386
LGA    I      32      I      32          1.489
LGA    R      33      R      33          1.607
LGA    S      34      S      34          1.409
LGA    V      35      V      35          0.925
LGA    D      36      D      36          0.691
LGA    P      37      P      37          2.188
LGA    G      38      G      38          2.834
LGA    S      39      S      39          2.415
LGA    P      40      P      40          2.374
LGA    A      41      A      41          0.914
LGA    A      42      A      42          0.680
LGA    R      43      R      43          0.931
LGA    S      44      S      44          1.734
LGA    G      45      G      45          0.629
LGA    L      46      L      46          1.293
LGA    R      47      R      47          1.408
LGA    A      48      A      48          1.224
LGA    Q      49      Q      49          1.283
LGA    D      50      D      50          1.329
LGA    R      51      R      51          1.696
LGA    L      52      L      52          1.746
LGA    I      53      I      53          1.141
LGA    E      54      E      54          1.246
LGA    V      55      V      55          0.936
LGA    N      56      N      56          0.766
LGA    G      57      G      57          3.666
LGA    Q      58      Q      58          2.969
LGA    N      59      N      59          1.648
LGA    V      60      V      60          0.764
LGA    E      61      E      61          0.966
LGA    G      62      G      62          1.375
LGA    L      63      L      63          2.640
LGA    R      64      R      64          2.787
LGA    H      65      H      65          1.721
LGA    A      66      A      66          1.385
LGA    E      67      E      67          1.389
LGA    V      68      V      68          1.427
LGA    V      69      V      69          1.145
LGA    A      70      A      70          0.964
LGA    S      71      S      71          0.957
LGA    I      72      I      72          1.028
LGA    K      73      K      73          0.890
LGA    A      74      A      74          0.628
LGA    R      75      R      75          1.487
LGA    E      76      E      76          1.866
LGA    D      77      D      77          2.420
LGA    E      78      E      78          2.101
LGA    A      79      A      79          0.302
LGA    R      80      R      80          1.736
LGA    L      81      L      81          1.910
LGA    L      82      L      82          1.235
LGA    V      83      V      83          1.637
LGA    V      84      V      84          0.713
LGA    G      85      G      85          0.614
LGA    P      86      P      86          1.187
LGA    S      87      S      87          2.008
LGA    T      88      T      88          3.242
LGA    R      89      R      89          2.831
LGA    L      90      L      90          6.818

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     89    1.95   100.00     88.801     4.351

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.513219 * X  +  -0.182324 * Y  +   0.838668 * Z  +  10.007858
  Y_new =  -0.309825 * X  +  -0.871925 * Y  +  -0.379151 * Z  +  25.820841
  Z_new =   0.800384 * X  +  -0.454428 * Y  +   0.391000 * Z  +   8.956898 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.860282    2.281310  [ DEG:   -49.2906    130.7094 ]
  Theta =  -0.927935   -2.213657  [ DEG:   -53.1668   -126.8332 ]
  Phi   =  -2.598464    0.543128  [ DEG:  -148.8810     31.1190 ]
 
# 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: T0340TS168_2                                  
REMARK     2: T0340.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS168_2.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   89   1.95  100.00  88.801
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS168_2
PFRMAT TS
TARGET T0340
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1      14.132  45.537   2.655  1.00 25.00           C
ATOM      2  CA  MET     2      14.303  45.164   6.452  1.00 25.00           C
ATOM      3  CA  LEU     3      15.109  41.540   5.631  1.00 25.00           C
ATOM      4  CA  ARG     4      15.927  39.455   8.707  1.00 25.00           C
ATOM      5  CA  PRO     5      13.271  37.535  10.523  1.00 25.00           C
ATOM      6  CA  ARG     6       9.697  37.329   9.294  1.00 25.00           C
ATOM      7  CA  LEU     7       8.954  34.729  12.008  1.00 25.00           C
ATOM      8  CA  CYS     8       7.052  31.808  13.573  1.00 25.00           C
ATOM      9  CA  HIS     9       6.002  30.982  17.196  1.00 25.00           C
ATOM     10  CA  LEU    10       3.738  28.104  16.133  1.00 25.00           C
ATOM     11  CA  ARG    11       1.699  26.821  19.079  1.00 25.00           C
ATOM     12  CA  LYS    12       1.625  23.040  18.978  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.762  21.361  19.523  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.238  17.675  20.259  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.085  16.338  16.684  1.00 25.00           C
ATOM     16  CA  GLY    16       0.826  17.341  14.370  1.00 25.00           C
ATOM     17  CA  TYR    17       2.456  20.815  14.261  1.00 25.00           C
ATOM     18  CA  GLY    18       1.029  21.409  10.774  1.00 25.00           C
ATOM     19  CA  PHE    19       3.734  20.956   8.083  1.00 25.00           C
ATOM     20  CA  ASN    20       5.439  18.251   6.023  1.00 25.00           C
ATOM     21  CA  LEU    21       8.761  20.015   5.406  1.00 25.00           C
ATOM     22  CA  HIS    22      10.761  19.500   2.247  1.00 25.00           C
ATOM     23  CA  SER    23      13.618  20.483   0.004  1.00 25.00           C
ATOM     24  CA  ASP    24      16.915  18.729  -0.641  1.00 25.00           C
ATOM     25  CA  LYS    25      18.784  17.073  -3.467  1.00 25.00           C
ATOM     26  CA  SER    26      21.939  19.200  -2.924  1.00 25.00           C
ATOM     27  CA  ARG    27      20.720  22.725  -2.014  1.00 25.00           C
ATOM     28  CA  PRO    28      21.749  23.366   1.591  1.00 25.00           C
ATOM     29  CA  GLY    29      18.089  24.209   2.350  1.00 25.00           C
ATOM     30  CA  GLN    30      16.051  22.876   5.281  1.00 25.00           C
ATOM     31  CA  TYR    31      12.872  24.053   3.619  1.00 25.00           C
ATOM     32  CA  ILE    32       9.274  25.081   4.539  1.00 25.00           C
ATOM     33  CA  ARG    33       6.685  23.396   2.331  1.00 25.00           C
ATOM     34  CA  SER    34       3.048  23.383   3.458  1.00 25.00           C
ATOM     35  CA  VAL    35       0.791  25.369   5.871  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.117  22.925   6.176  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.767  23.854   6.573  1.00 25.00           C
ATOM     38  CA  GLY    38      -7.017  24.171  10.135  1.00 25.00           C
ATOM     39  CA  SER    39      -3.844  22.581  11.470  1.00 25.00           C
ATOM     40  CA  PRO    40      -2.926  26.086  12.550  1.00 25.00           C
ATOM     41  CA  ALA    41       0.619  26.524  11.170  1.00 25.00           C
ATOM     42  CA  ALA    42      -0.544  29.498   9.057  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.198  31.070  12.134  1.00 25.00           C
ATOM     44  CA  SER    44       1.218  32.507  13.032  1.00 25.00           C
ATOM     45  CA  GLY    45       3.412  32.635   9.961  1.00 25.00           C
ATOM     46  CA  LEU    46       4.354  30.435   6.942  1.00 25.00           C
ATOM     47  CA  ARG    47       3.699  30.872   3.234  1.00 25.00           C
ATOM     48  CA  ALA    48       3.691  27.738   1.011  1.00 25.00           C
ATOM     49  CA  GLN    49       7.174  28.247  -0.535  1.00 25.00           C
ATOM     50  CA  ASP    50       8.644  29.706   2.616  1.00 25.00           C
ATOM     51  CA  ARG    51      12.408  28.995   2.739  1.00 25.00           C
ATOM     52  CA  LEU    52      13.601  28.258   6.240  1.00 25.00           C
ATOM     53  CA  ILE    53      16.812  28.799   8.173  1.00 25.00           C
ATOM     54  CA  GLU    54      16.261  27.864  11.836  1.00 25.00           C
ATOM     55  CA  VAL    55      15.507  25.966  15.083  1.00 25.00           C
ATOM     56  CA  ASN    56      14.389  27.180  18.539  1.00 25.00           C
ATOM     57  CA  GLY    57      17.545  25.436  19.763  1.00 25.00           C
ATOM     58  CA  GLN    58      19.448  23.537  17.049  1.00 25.00           C
ATOM     59  CA  ASN    59      20.843  25.462  14.008  1.00 25.00           C
ATOM     60  CA  VAL    60      19.706  24.260  10.565  1.00 25.00           C
ATOM     61  CA  GLU    61      21.050  25.398   7.173  1.00 25.00           C
ATOM     62  CA  GLY    62      23.091  22.188   7.200  1.00 25.00           C
ATOM     63  CA  LEU    63      20.984  19.110   6.459  1.00 25.00           C
ATOM     64  CA  ARG    64      18.429  16.812   4.898  1.00 25.00           C
ATOM     65  CA  HIS    65      14.813  16.354   5.818  1.00 25.00           C
ATOM     66  CA  ALA    66      14.769  13.534   8.410  1.00 25.00           C
ATOM     67  CA  GLU    67      16.980  15.613  10.745  1.00 25.00           C
ATOM     68  CA  VAL    68      14.634  18.612  10.336  1.00 25.00           C
ATOM     69  CA  VAL    69      11.616  16.393  11.134  1.00 25.00           C
ATOM     70  CA  ALA    70      13.389  15.065  14.259  1.00 25.00           C
ATOM     71  CA  SER    71      14.169  18.647  15.367  1.00 25.00           C
ATOM     72  CA  ILE    72      10.504  19.632  14.850  1.00 25.00           C
ATOM     73  CA  LYS    73       9.376  16.608  16.914  1.00 25.00           C
ATOM     74  CA  ALA    74      11.811  17.575  19.707  1.00 25.00           C
ATOM     75  CA  ARG    75      10.073  20.610  21.324  1.00 25.00           C
ATOM     76  CA  GLU    76       6.491  20.058  22.331  1.00 25.00           C
ATOM     77  CA  ASP    77       5.630  23.451  23.810  1.00 25.00           C
ATOM     78  CA  GLU    78       6.701  25.768  20.970  1.00 25.00           C
ATOM     79  CA  ALA    79       8.455  25.010  17.759  1.00 25.00           C
ATOM     80  CA  ARG    80      10.142  27.551  15.528  1.00 25.00           C
ATOM     81  CA  LEU    81      10.827  27.459  11.809  1.00 25.00           C
ATOM     82  CA  LEU    82      12.283  30.959  11.228  1.00 25.00           C
ATOM     83  CA  VAL    83      11.313  32.619   7.960  1.00 25.00           C
ATOM     84  CA  VAL    84      13.299  33.464   4.828  1.00 25.00           C
ATOM     85  CA  GLY    85      11.253  33.899   1.717  1.00 25.00           C
ATOM     86  CA  PRO    86      12.075  33.629  -1.939  1.00 25.00           C
ATOM     87  CA  SER    87      14.583  35.953  -3.602  1.00 25.00           C
ATOM     88  CA  THR    88      15.886  36.598  -7.113  1.00 25.00           C
ATOM     89  CA  ARG    89      19.565  37.593  -6.950  1.00 25.00           C
ATOM     90  CA  LEU    90      22.351  37.878  -4.390  1.00 25.00           C
TER
END
