
#######################################################
#                                                     #
#                        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  106 (  106),  selected  106 , name T0366TS393_4
# Molecule2: number of CA atoms   84 (  589),  selected   84 , name T0366.pdb
# PARAMETERS: T0366TS393_4.T0366.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      -       -           -
LGA    E       2      -       -           -
LGA    N       3      -       -           -
LGA    L       4      -       -           -
LGA    Y       5      -       -           -
LGA    F       6      -       -           -
LGA    Q       7      -       -           -
LGA    S       8      -       -           -
LGA    M       9      -       -           -
LGA    G      10      -       -           -
LGA    L      11      L      11          1.479
LGA    R      12      R      12          1.839
LGA    T      13      T      13          0.510
LGA    V      14      V      14          1.342
LGA    E      15      E      15          1.703
LGA    M      16      M      16          3.008
LGA    K      17      -       -           -
LGA    K      18      K      17          1.072
LGA    G      19      K      18          3.292
LGA    P      20      -       -           -
LGA    T      21      -       -           -
LGA    D      22      -       -           -
LGA    S      23      S      23          1.815
LGA    L      24      L      24          2.237
LGA    G      25      G      25          2.266
LGA    I      26      I      26          1.745
LGA    S      27      S      27          1.679
LGA    I      28      I      28          2.578
LGA    A      29      A      29          1.686
LGA    G      30      G      30          1.429
LGA    G      31      G      31          1.064
LGA    V      32      V      32          2.814
LGA    G      33      G      33          2.969
LGA    S      34      S      34          3.064
LGA    P      35      P      35          2.959
LGA    L      36      L      36          3.694
LGA    G      37      G      37          4.235
LGA    D      38      D      38          2.475
LGA    V      39      V      39          2.797
LGA    P      40      P      40          1.078
LGA    I      41      I      41          4.639
LGA    F      42      F      42          1.577
LGA    I      43      I      43          0.608
LGA    A      44      A      44          1.854
LGA    M      45      M      45          1.772
LGA    M      46      M      46          2.162
LGA    H      47      H      47          1.389
LGA    P      48      P      48          1.972
LGA    T      49      T      49          0.863
LGA    G      50      G      50          1.109
LGA    V      51      V      51          1.346
LGA    A      52      A      52          1.769
LGA    A      53      A      53          1.584
LGA    Q      54      Q      54          2.008
LGA    T      55      T      55          2.582
LGA    Q      56      Q      56          2.084
LGA    K      57      K      57          0.540
LGA    L      58      L      58          0.543
LGA    R      59      R      59          1.140
LGA    V      60      V      60          0.677
LGA    G      61      G      61          1.100
LGA    D      62      D      62          1.360
LGA    R      63      R      63          1.637
LGA    I      64      I      64          1.788
LGA    V      65      V      65          2.670
LGA    T      66      T      66          2.062
LGA    I      67      I      67          1.577
LGA    C      68      C      68          0.883
LGA    G      69      G      69          1.879
LGA    T      70      T      70          1.347
LGA    S      71      S      71          4.061
LGA    T      72      T      72          1.045
LGA    E      73      E      73          0.313
LGA    G      74      G      74          1.807
LGA    M      75      M      75          1.358
LGA    T      76      T      76          0.967
LGA    H      77      H      77          1.069
LGA    T      78      T      78          0.583
LGA    Q      79      Q      79          0.708
LGA    A      80      A      80          0.611
LGA    V      81      V      81          0.573
LGA    N      82      N      82          0.844
LGA    L      83      L      83          0.747
LGA    L      84      L      84          0.352
LGA    K      85      K      85          1.026
LGA    N      86      N      86          1.677
LGA    A      87      A      87          1.633
LGA    S      88      S      88          0.951
LGA    G      89      G      89          0.579
LGA    S      90      S      90          0.919
LGA    I      91      I      91          1.070
LGA    E      92      E      92          0.777
LGA    M      93      M      93          0.077
LGA    Q      94      Q      94          2.220
LGA    V      95      V      95          2.033
LGA    V      96      -       -           -
LGA    A      97      V      96          1.856
LGA    G      98      A      97          1.448
LGA    G      99      G      98          4.324
LGA    D     100      -       -           -
LGA    V     101      -       -           -
LGA    S     102      -       -           -
LGA    E     103      -       -           -
LGA    T     104      -       -           -
LGA    S     105      -       -           -
LGA    V     106      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  106   84    5.0     84    1.93    96.43     88.696     4.132

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.127277 * X  +  -0.907034 * Y  +  -0.401361 * Z  +  10.288471
  Y_new =  -0.892654 * X  +   0.071657 * Y  +  -0.445011 * Z  +  22.716026
  Z_new =   0.432400 * X  +   0.414916 * Y  +  -0.800547 * Z  +  12.096441 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.663420   -0.478173  [ DEG:   152.6027    -27.3973 ]
  Theta =  -0.447153   -2.694439  [ DEG:   -25.6200   -154.3800 ]
  Phi   =  -1.429168    1.712424  [ DEG:   -81.8853     98.1147 ]
 
# 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: T0366TS393_4                                  
REMARK     2: T0366.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0366TS393_4.T0366.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  106   84   5.0   84   1.93   96.43  88.696
REMARK  ---------------------------------------------------------- 
MOLECULE T0366TS393_4
PFRMAT TS
TARGET T0366
MODEL 4
PARENT N/A
ATOM      1  CA  THR     1      20.705  48.504  17.316  1.00 25.00           C
ATOM      2  CA  GLU     2      23.899  47.690  15.362  1.00 25.00           C
ATOM      3  CA  ASN     3      22.662  44.749  13.219  1.00 25.00           C
ATOM      4  CA  LEU     4      25.094  41.928  12.314  1.00 25.00           C
ATOM      5  CA  TYR     5      25.041  40.780   8.711  1.00 25.00           C
ATOM      6  CA  PHE     6      25.311  39.194   5.257  1.00 25.00           C
ATOM      7  CA  GLN     7      25.207  35.837   7.093  1.00 25.00           C
ATOM      8  CA  SER     8      23.026  32.963   8.280  1.00 25.00           C
ATOM      9  CA  MET     9      20.434  32.069  10.969  1.00 25.00           C
ATOM     10  CA  GLY    10      17.760  33.971  12.921  1.00 25.00           C
ATOM     11  CA  LEU    11      15.635  30.970  11.955  1.00 25.00           C
ATOM     12  CA  ARG    12      13.581  31.400   8.840  1.00 25.00           C
ATOM     13  CA  THR    13       9.940  31.099   7.922  1.00 25.00           C
ATOM     14  CA  VAL    14       8.672  27.857   6.381  1.00 25.00           C
ATOM     15  CA  GLU    15       5.388  28.461   4.558  1.00 25.00           C
ATOM     16  CA  MET    16       5.072  24.750   4.071  1.00 25.00           C
ATOM     17  CA  LYS    17       1.773  25.592   2.282  1.00 25.00           C
ATOM     18  CA  LYS    18      -1.295  23.349   2.755  1.00 25.00           C
ATOM     19  CA  GLY    19      -1.665  20.349   0.376  1.00 25.00           C
ATOM     20  CA  PRO    20      -5.371  20.482   1.078  1.00 25.00           C
ATOM     21  CA  THR    21      -5.635  16.652   0.675  1.00 25.00           C
ATOM     22  CA  ASP    22      -3.989  14.952   3.694  1.00 25.00           C
ATOM     23  CA  SER    23      -1.702  17.350   5.445  1.00 25.00           C
ATOM     24  CA  LEU    24       1.163  19.856   5.995  1.00 25.00           C
ATOM     25  CA  GLY    25       3.384  16.818   5.447  1.00 25.00           C
ATOM     26  CA  ILE    26       5.193  15.261   8.410  1.00 25.00           C
ATOM     27  CA  SER    27       6.024  12.794  11.105  1.00 25.00           C
ATOM     28  CA  ILE    28       5.869  14.871  14.266  1.00 25.00           C
ATOM     29  CA  ALA    29       8.743  13.829  16.575  1.00 25.00           C
ATOM     30  CA  GLY    30      11.390  13.511  19.313  1.00 25.00           C
ATOM     31  CA  GLY    31      10.672  16.051  22.131  1.00 25.00           C
ATOM     32  CA  VAL    32      10.875  14.575  25.639  1.00 25.00           C
ATOM     33  CA  GLY    33       9.443  11.107  26.276  1.00 25.00           C
ATOM     34  CA  SER    34      12.070   9.103  24.432  1.00 25.00           C
ATOM     35  CA  PRO    35      15.272  11.164  24.157  1.00 25.00           C
ATOM     36  CA  LEU    36      16.850  14.469  25.129  1.00 25.00           C
ATOM     37  CA  GLY    37      18.044  16.544  28.108  1.00 25.00           C
ATOM     38  CA  ASP    38      15.426  19.004  26.718  1.00 25.00           C
ATOM     39  CA  VAL    39      14.254  20.199  23.262  1.00 25.00           C
ATOM     40  CA  PRO    40      12.972  19.797  19.694  1.00 25.00           C
ATOM     41  CA  ILE    41      15.621  17.817  17.736  1.00 25.00           C
ATOM     42  CA  PHE    42      12.949  16.491  15.376  1.00 25.00           C
ATOM     43  CA  ILE    43      12.010  16.564  11.683  1.00 25.00           C
ATOM     44  CA  ALA    44      11.615  13.247   9.924  1.00 25.00           C
ATOM     45  CA  MET    45      10.124  11.310   7.063  1.00 25.00           C
ATOM     46  CA  MET    46      11.497  12.870   3.893  1.00 25.00           C
ATOM     47  CA  HIS    47       7.981  13.411   2.643  1.00 25.00           C
ATOM     48  CA  PRO    48       7.440  11.979  -0.883  1.00 25.00           C
ATOM     49  CA  THR    49       5.879  15.070  -2.538  1.00 25.00           C
ATOM     50  CA  GLY    50       3.528  15.173   0.452  1.00 25.00           C
ATOM     51  CA  VAL    51       4.639  18.834   0.669  1.00 25.00           C
ATOM     52  CA  ALA    52       8.060  20.043   1.832  1.00 25.00           C
ATOM     53  CA  ALA    53       9.853  17.892  -0.782  1.00 25.00           C
ATOM     54  CA  GLN    54       7.983  19.703  -3.590  1.00 25.00           C
ATOM     55  CA  THR    55       7.719  23.388  -2.807  1.00 25.00           C
ATOM     56  CA  GLN    56      10.459  25.042  -0.659  1.00 25.00           C
ATOM     57  CA  LYS    57      12.279  25.035   2.674  1.00 25.00           C
ATOM     58  CA  LEU    58      11.896  22.038   4.991  1.00 25.00           C
ATOM     59  CA  ARG    59      14.287  19.054   4.510  1.00 25.00           C
ATOM     60  CA  VAL    60      14.609  16.175   6.988  1.00 25.00           C
ATOM     61  CA  GLY    61      17.098  16.381   9.833  1.00 25.00           C
ATOM     62  CA  ASP    62      16.208  20.065   9.826  1.00 25.00           C
ATOM     63  CA  ARG    63      15.600  20.678  13.517  1.00 25.00           C
ATOM     64  CA  ILE    64      12.244  21.887  14.771  1.00 25.00           C
ATOM     65  CA  VAL    65       9.719  24.242  16.389  1.00 25.00           C
ATOM     66  CA  THR    66       6.303  25.847  16.244  1.00 25.00           C
ATOM     67  CA  ILE    67       2.871  25.493  14.530  1.00 25.00           C
ATOM     68  CA  CYS    68       0.406  28.351  14.181  1.00 25.00           C
ATOM     69  CA  GLY    69       1.252  31.241  16.567  1.00 25.00           C
ATOM     70  CA  THR    70       2.588  29.638  19.795  1.00 25.00           C
ATOM     71  CA  SER    71       3.533  26.050  20.472  1.00 25.00           C
ATOM     72  CA  THR    72       7.009  24.691  21.342  1.00 25.00           C
ATOM     73  CA  GLU    73       9.870  25.428  23.685  1.00 25.00           C
ATOM     74  CA  GLY    74       9.807  22.323  25.854  1.00 25.00           C
ATOM     75  CA  MET    75       7.155  20.111  24.219  1.00 25.00           C
ATOM     76  CA  THR    76       5.756  16.597  24.849  1.00 25.00           C
ATOM     77  CA  HIS    77       5.721  16.066  21.057  1.00 25.00           C
ATOM     78  CA  THR    78       2.095  14.857  21.300  1.00 25.00           C
ATOM     79  CA  GLN    79       0.886  18.475  21.647  1.00 25.00           C
ATOM     80  CA  ALA    80       2.942  19.482  18.577  1.00 25.00           C
ATOM     81  CA  VAL    81       1.447  16.569  16.590  1.00 25.00           C
ATOM     82  CA  ASN    82      -2.079  17.628  17.643  1.00 25.00           C
ATOM     83  CA  LEU    83      -1.349  21.227  16.558  1.00 25.00           C
ATOM     84  CA  LEU    84      -0.065  19.973  13.175  1.00 25.00           C
ATOM     85  CA  LYS    85      -3.231  17.864  12.728  1.00 25.00           C
ATOM     86  CA  ASN    86      -5.404  20.905  13.560  1.00 25.00           C
ATOM     87  CA  ALA    87      -4.185  23.904  11.555  1.00 25.00           C
ATOM     88  CA  SER    88      -4.922  22.870   7.952  1.00 25.00           C
ATOM     89  CA  GLY    89      -5.936  26.353   6.630  1.00 25.00           C
ATOM     90  CA  SER    90      -2.283  27.388   7.043  1.00 25.00           C
ATOM     91  CA  ILE    91       0.076  25.341   9.247  1.00 25.00           C
ATOM     92  CA  GLU    92       3.070  27.684   9.354  1.00 25.00           C
ATOM     93  CA  MET    93       6.436  26.653  10.793  1.00 25.00           C
ATOM     94  CA  GLN    94       8.227  29.219  12.902  1.00 25.00           C
ATOM     95  CA  VAL    95      11.286  27.067  12.524  1.00 25.00           C
ATOM     96  CA  VAL    96      14.699  25.365  11.974  1.00 25.00           C
ATOM     97  CA  ALA    97      18.335  25.846  12.808  1.00 25.00           C
ATOM     98  CA  GLY    98      20.097  22.987  11.032  1.00 25.00           C
ATOM     99  CA  GLY    99      23.905  22.775  10.835  1.00 25.00           C
ATOM    100  CA  ASP   100      26.283  25.648  10.607  1.00 25.00           C
ATOM    101  CA  VAL   101      30.000  26.205  10.995  1.00 25.00           C
ATOM    102  CA  SER   102      31.154  24.716  14.274  1.00 25.00           C
ATOM    103  CA  GLU   103      34.440  25.899  15.858  1.00 25.00           C
ATOM    104  CA  THR   104      35.267  29.344  17.208  1.00 25.00           C
ATOM    105  CA  SER   105      35.645  29.015  20.979  1.00 25.00           C
ATOM    106  CA  VAL   106      32.955  31.644  21.140  1.00 25.00           C
TER
END
