
#######################################################
#                                                     #
#                        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  102 (  102),  selected  102 , name T0300TS599_3
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300TS599_3.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D       7           -
LGA    A       2      K       8           -
LGA    S       3      T       9           -
LGA    K       4      Y      10           -
LGA    K       5      E      11           -
LGA    P       6      E      12           -
LGA    D       7      M      13           -
LGA    K       8      V      14           -
LGA    T       9      K      15           -
LGA    Y      10      E      16           -
LGA    E      11      V      17           -
LGA    E      12      E      18           -
LGA    M      13      R      19           -
LGA    V      14      L      20           -
LGA    K      15      K      21           -
LGA    E      16      L      22           -
LGA    V      17      E      23           -
LGA    E      18      N      24           -
LGA    R      19      -       -           -
LGA    L      20      -       -           -
LGA    K      21      -       -           -
LGA    L      22      -       -           -
LGA    E      23      -       -           -
LGA    N      24      -       -           -
LGA    K      25      -       -           -
LGA    T      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      -       -           -
LGA    Q      29      -       -           -
LGA    K      30      -       -           -
LGA    V      31      K      25          4.440
LGA    K      32      -       -           -
LGA    S      33      -       -           -
LGA    S      34      -       -           -
LGA    G      35      T      26          4.447
LGA    A      36      L      27          3.422
LGA    V      37      K      28           #
LGA    S      38      Q      29           -
LGA    S      39      K      30           -
LGA    D      40      V      31           -
LGA    D      41      S      39           -
LGA    S      42      D      40          5.094
LGA    I      43      D      41          1.864
LGA    L      44      S      42          4.096
LGA    T      45      I      43          2.379
LGA    A      46      L      44          2.393
LGA    A      47      T      45          3.140
LGA    -       -      A      46           -
LGA    K      48      A      47           #
LGA    R      49      K      48           #
LGA    E      50      R      49          2.957
LGA    S      51      E      50          4.193
LGA    I      52      S      51           #
LGA    I      53      I      52          4.713
LGA    V      54      I      53          1.520
LGA    -       -      V      54           -
LGA    S      55      S      55          2.034
LGA    S      56      S      56          2.202
LGA    S      57      S      57          3.049
LGA    R      58      R      58          2.205
LGA    A      59      A      59          0.302
LGA    L      60      L      60          1.242
LGA    G      61      G      61          1.610
LGA    A      62      A      62          1.218
LGA    V      63      V      63          1.324
LGA    A      64      A      64          1.617
LGA    M      65      M      65          1.248
LGA    R      66      R      66          1.409
LGA    K      67      K      67          1.556
LGA    I      68      I      68          0.710
LGA    E      69      E      69          0.960
LGA    A      70      A      70          1.780
LGA    K      71      K      71          1.310
LGA    V      72      V      72          0.514
LGA    R      73      R      73          1.533
LGA    S      74      S      74          2.028
LGA    R      75      R      75          1.235
LGA    A      76      A      76          0.838
LGA    A      77      A      77          1.877
LGA    K      78      K      78          2.045
LGA    A      79      A      79          2.943
LGA    V      80      V      80          2.402
LGA    T      81      T      81          2.983
LGA    E      82      E      82          2.922
LGA    Q      83      Q      83          2.492
LGA    E      84      E      84          1.632
LGA    L      85      L      85          0.796
LGA    T      86      T      86          1.507
LGA    S      87      S      87          0.974
LGA    L      88      L      88          1.242
LGA    L      89      L      89          1.982
LGA    Q      90      Q      90          1.050
LGA    S      91      S      91          1.640
LGA    L      92      L      92          2.748
LGA    T      93      T      93          2.813
LGA    L      94      L      94          4.815
LGA    R      95      R      95          4.926
LGA    V      96      V      96           #
LGA    D      97      D      97          4.598
LGA    V      98      V      98          4.220
LGA    S      99      S      99          2.711
LGA    M     100      M     100          4.534
LGA    E     101      E     101           -
LGA    E     102      E     102           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  102   89    5.0     58    2.68    79.31     49.031     2.089

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.002101 * X  +  -0.021788 * Y  +  -0.999760 * Z  +  38.523663
  Y_new =  -0.870940 * X  +   0.491309 * Y  +  -0.008877 * Z  + -20.354002
  Z_new =   0.491384 * X  +   0.870713 * Y  +  -0.020009 * Z  +  -4.715823 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.593772   -1.547821  [ DEG:    91.3164    -88.6836 ]
  Theta =  -0.513678   -2.627914  [ DEG:   -29.4316   -150.5684 ]
  Phi   =  -1.573209    1.568384  [ DEG:   -90.1382     89.8618 ]
 
# 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: T0300TS599_3                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300TS599_3.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  102   89   5.0   58   2.68   79.31  49.031
REMARK  ---------------------------------------------------------- 
MOLECULE T0300TS599_3
PFRMAT TS                                                                       
TARGET T0300                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      42.349 -39.412  -4.959  1.00  0.00              
ATOM      2  CA  ALA     2      45.277 -37.373  -5.350  1.00  0.00              
ATOM      3  CA  SER     3      41.832 -35.461  -3.866  1.00  0.00              
ATOM      4  CA  LYS     4      39.552 -33.637  -0.936  1.00  0.00              
ATOM      5  CA  LYS     5      37.690 -36.786  -0.100  1.00  0.00              
ATOM      6  CA  PRO     6      36.910 -38.345  -3.423  1.00  0.00              
ATOM      7  CA  ASP     7      38.059 -41.990  -3.066  1.00  0.00              
ATOM      8  CA  LYS     8      39.900 -42.605  -6.272  1.00  0.00              
ATOM      9  CA  THR     9      42.137 -45.162  -7.843  1.00  0.00              
ATOM     10  CA  TYR    10      45.422 -44.012  -9.481  1.00  0.00              
ATOM     11  CA  GLU    11      44.052 -44.939 -12.842  1.00  0.00              
ATOM     12  CA  GLU    12      40.779 -43.020 -12.333  1.00  0.00              
ATOM     13  CA  MET    13      42.653 -39.927 -11.179  1.00  0.00              
ATOM     14  CA  VAL    14      44.970 -40.085 -14.177  1.00  0.00              
ATOM     15  CA  LYS    15      41.914 -40.382 -16.477  1.00  0.00              
ATOM     16  CA  GLU    16      40.242 -37.410 -14.775  1.00  0.00              
ATOM     17  CA  VAL    17      43.443 -35.352 -15.235  1.00  0.00              
ATOM     18  CA  GLU    18      43.621 -36.323 -18.922  1.00  0.00              
ATOM     19  CA  ARG    19      40.011 -35.231 -19.371  1.00  0.00              
ATOM     20  CA  LEU    20      40.680 -31.901 -17.655  1.00  0.00              
ATOM     21  CA  LYS    21      43.710 -31.350 -19.906  1.00  0.00              
ATOM     22  CA  LEU    22      41.604 -32.009 -23.029  1.00  0.00              
ATOM     23  CA  GLU    23      38.889 -29.613 -21.799  1.00  0.00              
ATOM     24  CA  ASN    24      41.378 -26.842 -21.026  1.00  0.00              
ATOM     25  CA  LYS    25      42.904 -27.249 -24.488  1.00  0.00              
ATOM     26  CA  THR    26      39.452 -27.068 -26.103  1.00  0.00              
ATOM     27  CA  LEU    27      38.539 -23.887 -24.140  1.00  0.00              
ATOM     28  CA  LYS    28      41.830 -22.238 -25.055  1.00  0.00              
ATOM     29  CA  GLN    29      41.119 -23.012 -28.741  1.00  0.00              
ATOM     30  CA  LYS    30      37.620 -21.570 -28.494  1.00  0.00              
ATOM     31  CA  VAL    31      38.932 -18.396 -26.799  1.00  0.00              
ATOM     32  CA  LYS    32      41.567 -17.826 -29.427  1.00  0.00              
ATOM     33  CA  SER    33      39.061 -18.267 -32.264  1.00  0.00              
ATOM     34  CA  SER    34      36.389 -15.880 -30.938  1.00  0.00              
ATOM     35  CA  GLY    35      38.241 -12.997 -29.368  1.00  0.00              
ATOM     36  CA  ALA    36      36.370 -12.657 -26.119  1.00  0.00              
ATOM     37  CA  VAL    37      38.793 -12.668 -23.255  1.00  0.00              
ATOM     38  CA  SER    38      40.326  -9.624 -21.756  1.00  0.00              
ATOM     39  CA  SER    39      43.270  -8.037 -23.490  1.00  0.00              
ATOM     40  CA  ASP    40      46.205  -8.958 -21.315  1.00  0.00              
ATOM     41  CA  ASP    41      48.529 -10.320 -23.955  1.00  0.00              
ATOM     42  CA  SER    42      46.059 -11.296 -26.705  1.00  0.00              
ATOM     43  CA  ILE    43      45.905 -15.077 -26.124  1.00  0.00              
ATOM     44  CA  LEU    44      46.567 -15.229 -22.432  1.00  0.00              
ATOM     45  CA  THR    45      50.059 -16.220 -21.469  1.00  0.00              
ATOM     46  CA  ALA    46      50.705 -18.485 -18.563  1.00  0.00              
ATOM     47  CA  ALA    47      51.840 -15.478 -16.470  1.00  0.00              
ATOM     48  CA  LYS    48      48.798 -13.418 -17.328  1.00  0.00              
ATOM     49  CA  ARG    49      46.521 -16.272 -16.436  1.00  0.00              
ATOM     50  CA  GLU    50      48.284 -16.803 -13.070  1.00  0.00              
ATOM     51  CA  SER    51      48.050 -13.062 -12.256  1.00  0.00              
ATOM     52  CA  ILE    52      44.342 -13.009 -13.164  1.00  0.00              
ATOM     53  CA  ILE    53      43.682 -16.088 -11.014  1.00  0.00              
ATOM     54  CA  VAL    54      45.513 -14.628  -7.996  1.00  0.00              
ATOM     55  CA  SER    55      43.575 -11.427  -8.346  1.00  0.00              
ATOM     56  CA  SER    56      40.237 -13.303  -8.537  1.00  0.00              
ATOM     57  CA  SER    57      41.101 -15.370  -5.424  1.00  0.00              
ATOM     58  CA  ARG    58      42.229 -12.301  -3.469  1.00  0.00              
ATOM     59  CA  ALA    59      38.958 -10.488  -4.333  1.00  0.00              
ATOM     60  CA  LEU    60      36.937 -13.531  -3.271  1.00  0.00              
ATOM     61  CA  GLY    61      38.850 -13.725   0.037  1.00  0.00              
ATOM     62  CA  ALA    62      38.021 -10.171   0.876  1.00  0.00              
ATOM     63  CA  VAL    63      34.282 -10.625   0.191  1.00  0.00              
ATOM     64  CA  ALA    64      34.191 -13.778   2.276  1.00  0.00              
ATOM     65  CA  MET    65      36.073 -12.162   5.159  1.00  0.00              
ATOM     66  CA  ARG    66      33.537  -9.336   5.343  1.00  0.00              
ATOM     67  CA  LYS    67      30.669 -11.854   5.372  1.00  0.00              
ATOM     68  CA  ILE    68      32.418 -13.790   8.122  1.00  0.00              
ATOM     69  CA  GLU    69      32.917 -10.630  10.187  1.00  0.00              
ATOM     70  CA  ALA    70      29.180 -10.168  10.112  1.00  0.00              
ATOM     71  CA  LYS    71      28.540 -13.735  11.190  1.00  0.00              
ATOM     72  CA  VAL    72      30.891 -13.686  14.080  1.00  0.00              
ATOM     73  CA  ARG    73      29.460 -10.454  15.327  1.00  0.00              
ATOM     74  CA  SER    74      25.851 -11.688  15.081  1.00  0.00              
ATOM     75  CA  ARG    75      26.534 -14.907  16.900  1.00  0.00              
ATOM     76  CA  ALA    76      28.258 -12.934  19.562  1.00  0.00              
ATOM     77  CA  ALA    77      25.693 -10.421  20.120  1.00  0.00              
ATOM     78  CA  LYS    78      22.974 -13.110  20.483  1.00  0.00              
ATOM     79  CA  ALA    79      24.976 -14.940  23.137  1.00  0.00              
ATOM     80  CA  VAL    80      25.666 -11.839  25.165  1.00  0.00              
ATOM     81  CA  THR    81      27.078 -12.089  28.729  1.00  0.00              
ATOM     82  CA  GLU    82      30.696 -10.932  29.130  1.00  0.00              
ATOM     83  CA  GLN    83      31.982 -14.455  29.966  1.00  0.00              
ATOM     84  CA  GLU    84      30.155 -15.830  26.983  1.00  0.00              
ATOM     85  CA  LEU    85      31.636 -13.090  24.690  1.00  0.00              
ATOM     86  CA  THR    86      35.159 -14.099  25.702  1.00  0.00              
ATOM     87  CA  SER    87      34.307 -17.730  24.925  1.00  0.00              
ATOM     88  CA  LEU    88      32.896 -16.756  21.492  1.00  0.00              
ATOM     89  CA  LEU    89      36.066 -14.727  20.733  1.00  0.00              
ATOM     90  CA  GLN    90      38.284 -17.660  21.599  1.00  0.00              
ATOM     91  CA  SER    91      36.281 -20.053  19.375  1.00  0.00              
ATOM     92  CA  LEU    92      35.917 -17.788  16.323  1.00  0.00              
ATOM     93  CA  THR    93      36.469 -19.631  13.034  1.00  0.00              
ATOM     94  CA  LEU    94      37.034 -17.422   9.997  1.00  0.00              
ATOM     95  CA  ARG    95      36.490 -18.859   6.575  1.00  0.00              
ATOM     96  CA  VAL    96      37.811 -17.102   3.523  1.00  0.00              
ATOM     97  CA  ASP    97      36.442 -18.245   0.187  1.00  0.00              
ATOM     98  CA  VAL    98      37.932 -17.546  -3.159  1.00  0.00              
ATOM     99  CA  SER    99      35.939 -18.720  -6.294  1.00  0.00              
ATOM    100  CA  MET   100      37.807 -18.840  -9.432  1.00  0.00              
ATOM    101  CA  GLU   101      39.425 -20.431 -12.208  1.00  0.00              
ATOM    102  CA  GLU   102      39.044 -18.844 -15.472  1.00  0.00              
TER                                                                             
END
