
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0351TS599_2
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS599_2.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    L       3      L       3           -
LGA    Y       4      Y       4           -
LGA    D       5      D       5           -
LGA    A       6      -       -           -
LGA    I       7      -       -           -
LGA    M       8      -       -           -
LGA    Y       9      A       6           #
LGA    K      10      I       7          4.292
LGA    Y      11      M       8          4.655
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    P      12      Y      11          3.112
LGA    -       -      P      12           -
LGA    N      13      N      13          3.750
LGA    A      14      A      14          2.476
LGA    V      15      V      15           #
LGA    S      16      -       -           -
LGA    R      17      -       -           -
LGA    K      18      -       -           -
LGA    D      19      -       -           -
LGA    F      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      S      16           #
LGA    R      23      R      17           #
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    N      24      E      21          2.484
LGA    D      25      L      22          4.401
LGA    G      26      R      23           #
LGA    N      27      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    G      28      I      31           #
LGA    S      29      E      32           #
LGA    Y      30      K      33          4.963
LGA    I      31      W      34          2.675
LGA    E      32      N      35          4.402
LGA    K      33      L      36          2.397
LGA    W      34      R      37          4.335
LGA    -       -      A      38           -
LGA    N      35      P      39          2.990
LGA    L      36      L      40          3.155
LGA    R      37      P      41          1.606
LGA    A      38      T      42          2.290
LGA    P      39      Q      43          4.914
LGA    L      40      A      44          3.737
LGA    P      41      E      45           -
LGA    T      42      -       -           -
LGA    Q      43      -       -           -
LGA    A      44      -       -           -
LGA    E      45      -       -           -
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    T      48      -       -           -
LGA    W      49      -       -           -
LGA    W      50      -       -           -
LGA    E      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    K      55      -       -           -
LGA    N      56      -       -           -
LGA    P      57      -       -           -
LGA    P      58      -       -           -
LGA    Y      59      -       -           -
LGA    E      60      -       -           -
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    V      65      -       -           -
LGA    E      66      -       -           -
LGA    L      67      -       -           -
LGA    L      68      -       -           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      -       -           -
LGA    L      72      -       -           -
LGA    S      73      -       -           -
LGA    Q      74      -       -           -
LGA    E      75      -       -           -
LGA    K      76      -       -           -
LGA    L      77      -       -           -
LGA    A      78      -       -           -
LGA    R      79      -       -           -
LGA    K      80      -       -           -
LGA    Q      81      -       -           -
LGA    L      82      -       -           -
LGA    E      83      -       -           -
LGA    E      84      -       -           -
LGA    L      85      -       -           -
LGA    N      86      -       -           -
LGA    K      87      -       -           -
LGA    T      88      -       -           -
LGA    L      89      -       -           -
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      L      46          4.328
LGA    S     102      E      47          4.327
LGA    L     103      T      48          4.578
LGA    K     104      W      49          4.796
LGA    G     105      W      50          4.019
LGA    D     106      E      51          2.392
LGA    Y     107      E      52          1.364
LGA    A     108      L      53          1.562
LGA    E     109      Q      54          2.468
LGA    -       -      K      55           -
LGA    L     110      N      56          1.791
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117   56    5.0     28    3.55    14.29     29.057     0.767

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.771760 * X  +   0.507552 * Y  +   0.383116 * Z  +  -5.471052
  Y_new =   0.521666 * X  +   0.160774 * Y  +   0.837864 * Z  +  -7.501765
  Z_new =   0.363665 * X  +   0.846488 * Y  +  -0.388852 * Z  +  -2.059867 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.001415   -1.140177  [ DEG:   114.6727    -65.3273 ]
  Theta =  -0.372199   -2.769394  [ DEG:   -21.3254   -158.6746 ]
  Phi   =   2.547195   -0.594397  [ DEG:   145.9435    -34.0565 ]
 
# 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: T0351TS599_2                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS599_2.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117   56   5.0   28   3.55   14.29  29.057
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS599_2
PFRMAT TS                                                                       
TARGET T0351                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -4.678 -19.692   1.490  1.00  0.00              
ATOM      2  CA  ILE     2      -5.427 -17.257  -1.865  1.00  0.00              
ATOM      3  CA  LEU     3      -2.218 -14.835  -0.643  1.00  0.00              
ATOM      4  CA  TYR     4      -0.352 -15.910  -3.889  1.00  0.00              
ATOM      5  CA  ASP     5      -3.222 -15.179  -6.303  1.00  0.00              
ATOM      6  CA  ALA     6      -4.016 -12.058  -4.390  1.00  0.00              
ATOM      7  CA  ILE     7      -0.548 -10.514  -4.187  1.00  0.00              
ATOM      8  CA  MET     8      -0.425  -6.738  -4.850  1.00  0.00              
ATOM      9  CA  TYR     9       2.310  -4.797  -3.050  1.00  0.00              
ATOM     10  CA  LYS    10       1.745  -1.174  -2.221  1.00  0.00              
ATOM     11  CA  TYR    11       4.359   1.048  -0.754  1.00  0.00              
ATOM     12  CA  PRO    12       3.388   4.472   0.503  1.00  0.00              
ATOM     13  CA  ASN    13       6.011   6.790  -0.832  1.00  0.00              
ATOM     14  CA  ALA    14       7.377   8.225   2.359  1.00  0.00              
ATOM     15  CA  VAL    15       7.555   5.298   4.704  1.00  0.00              
ATOM     16  CA  SER    16      10.189   2.658   4.344  1.00  0.00              
ATOM     17  CA  ARG    17       9.317  -0.301   2.063  1.00  0.00              
ATOM     18  CA  LYS    18       9.208  -2.788   4.945  1.00  0.00              
ATOM     19  CA  ASP    19       6.454  -0.816   6.781  1.00  0.00              
ATOM     20  CA  PHE    20       4.221   0.567   4.028  1.00  0.00              
ATOM     21  CA  GLU    21       1.762   3.156   4.832  1.00  0.00              
ATOM     22  CA  LEU    22      -1.613   3.824   3.361  1.00  0.00              
ATOM     23  CA  ARG    23      -2.798   7.450   3.642  1.00  0.00              
ATOM     24  CA  ASN    24      -6.298   8.402   2.657  1.00  0.00              
ATOM     25  CA  ASP    25      -6.416  12.078   3.637  1.00  0.00              
ATOM     26  CA  GLY    26     -10.141  12.623   3.326  1.00  0.00              
ATOM     27  CA  ASN    27     -10.017  14.941   0.294  1.00  0.00              
ATOM     28  CA  GLY    28      -8.321  12.636  -2.220  1.00  0.00              
ATOM     29  CA  SER    29      -4.700  13.693  -1.832  1.00  0.00              
ATOM     30  CA  TYR    30      -2.645  10.600  -0.983  1.00  0.00              
ATOM     31  CA  ILE    31      -4.064   7.850  -3.219  1.00  0.00              
ATOM     32  CA  GLU    32      -4.554   9.844  -6.469  1.00  0.00              
ATOM     33  CA  LYS    33      -1.252  11.614  -6.159  1.00  0.00              
ATOM     34  CA  TRP    34       0.651   8.281  -5.768  1.00  0.00              
ATOM     35  CA  ASN    35      -1.095   6.103  -8.400  1.00  0.00              
ATOM     36  CA  LEU    36      -1.769   2.973  -6.393  1.00  0.00              
ATOM     37  CA  ARG    37      -2.129  -0.057  -8.574  1.00  0.00              
ATOM     38  CA  ALA    38      -3.438  -3.235  -7.021  1.00  0.00              
ATOM     39  CA  PRO    39      -3.465  -6.262  -9.287  1.00  0.00              
ATOM     40  CA  LEU    40      -6.989  -7.574  -9.402  1.00  0.00              
ATOM     41  CA  PRO    41      -7.007 -11.381  -9.074  1.00  0.00              
ATOM     42  CA  THR    42      -9.033 -12.683 -11.951  1.00  0.00              
ATOM     43  CA  GLN    43     -11.520 -15.427 -11.283  1.00  0.00              
ATOM     44  CA  ALA    44      -9.385 -17.833 -13.323  1.00  0.00              
ATOM     45  CA  GLU    45      -6.363 -17.328 -11.070  1.00  0.00              
ATOM     46  CA  LEU    46      -8.420 -17.917  -7.932  1.00  0.00              
ATOM     47  CA  GLU    47      -9.851 -21.143  -9.377  1.00  0.00              
ATOM     48  CA  THR    48      -6.380 -22.399 -10.362  1.00  0.00              
ATOM     49  CA  TRP    49      -5.057 -21.690  -6.874  1.00  0.00              
ATOM     50  CA  TRP    50      -7.977 -23.565  -5.300  1.00  0.00              
ATOM     51  CA  GLU    51      -7.483 -26.618  -7.511  1.00  0.00              
ATOM     52  CA  GLU    52      -3.778 -26.607  -6.607  1.00  0.00              
ATOM     53  CA  LEU    53      -4.795 -26.534  -2.956  1.00  0.00              
ATOM     54  CA  GLN    54      -7.232 -29.438  -3.215  1.00  0.00              
ATOM     55  CA  LYS    55      -4.474 -31.505  -4.882  1.00  0.00              
ATOM     56  CA  ASN    56      -1.718 -30.855  -2.368  1.00  0.00              
ATOM     57  CA  PRO    57      -1.328 -33.681   0.202  1.00  0.00              
ATOM     58  CA  PRO    58      -1.668 -31.910   3.496  1.00  0.00              
ATOM     59  CA  TYR    59      -4.352 -29.430   2.394  1.00  0.00              
ATOM     60  CA  GLU    60      -6.764 -31.918   0.813  1.00  0.00              
ATOM     61  CA  PRO    61      -8.133 -32.498   4.330  1.00  0.00              
ATOM     62  CA  PRO    62     -11.857 -31.878   4.401  1.00  0.00              
ATOM     63  CA  ASP    63     -11.947 -29.174   7.113  1.00  0.00              
ATOM     64  CA  GLN    64      -9.250 -26.842   5.746  1.00  0.00              
ATOM     65  CA  VAL    65     -10.000 -26.856   1.995  1.00  0.00              
ATOM     66  CA  GLU    66     -13.666 -26.185   2.540  1.00  0.00              
ATOM     67  CA  LEU    67     -13.119 -23.314   4.957  1.00  0.00              
ATOM     68  CA  LEU    68     -10.479 -21.787   2.726  1.00  0.00              
ATOM     69  CA  ALA    69     -12.682 -22.036  -0.400  1.00  0.00              
ATOM     70  CA  GLN    70     -15.541 -20.383   1.542  1.00  0.00              
ATOM     71  CA  GLU    71     -13.275 -17.584   2.785  1.00  0.00              
ATOM     72  CA  LEU    72     -11.953 -16.920  -0.759  1.00  0.00              
ATOM     73  CA  SER    73     -15.414 -16.830  -2.162  1.00  0.00              
ATOM     74  CA  GLN    74     -16.621 -14.349   0.489  1.00  0.00              
ATOM     75  CA  GLU    75     -13.608 -12.099  -0.129  1.00  0.00              
ATOM     76  CA  LYS    76     -14.150 -12.231  -3.884  1.00  0.00              
ATOM     77  CA  LEU    77     -17.884 -11.371  -3.501  1.00  0.00              
ATOM     78  CA  ALA    78     -17.060  -8.433  -1.258  1.00  0.00              
ATOM     79  CA  ARG    79     -14.502  -7.067  -3.714  1.00  0.00              
ATOM     80  CA  LYS    80     -17.065  -7.419  -6.539  1.00  0.00              
ATOM     81  CA  GLN    81     -19.788  -5.604  -4.593  1.00  0.00              
ATOM     82  CA  LEU    82     -17.375  -2.765  -3.715  1.00  0.00              
ATOM     83  CA  GLU    83     -16.388  -2.465  -7.408  1.00  0.00              
ATOM     84  CA  GLU    84     -20.025  -2.251  -8.459  1.00  0.00              
ATOM     85  CA  LEU    85     -20.563   0.493  -5.823  1.00  0.00              
ATOM     86  CA  ASN    86     -17.496   2.362  -7.053  1.00  0.00              
ATOM     87  CA  LYS    87     -18.756   2.275 -10.659  1.00  0.00              
ATOM     88  CA  THR    88     -22.224   3.612  -9.632  1.00  0.00              
ATOM     89  CA  LEU    89     -20.695   6.360  -7.639  1.00  0.00              
ATOM     90  CA  GLY    90     -18.414   7.177 -10.643  1.00  0.00              
ATOM     91  CA  ASN    91     -18.885  10.745  -9.993  1.00  0.00              
ATOM     92  CA  GLU    92     -18.089  10.264  -6.255  1.00  0.00              
ATOM     93  CA  LEU    93     -14.913   8.229  -7.029  1.00  0.00              
ATOM     94  CA  SER    94     -13.542  10.851  -9.428  1.00  0.00              
ATOM     95  CA  ASP    95     -14.116  13.629  -6.902  1.00  0.00              
ATOM     96  CA  ILE    96     -12.251  11.660  -4.193  1.00  0.00              
ATOM     97  CA  LYS    97      -9.101  10.715  -6.163  1.00  0.00              
ATOM     98  CA  LEU    98      -8.504   7.228  -5.010  1.00  0.00              
ATOM     99  CA  SER    99      -5.596   4.968  -5.786  1.00  0.00              
ATOM    100  CA  LEU   100      -5.860   1.389  -4.445  1.00  0.00              
ATOM    101  CA  LEU   101      -2.742  -0.322  -3.219  1.00  0.00              
ATOM    102  CA  SER   102      -3.197  -3.984  -2.436  1.00  0.00              
ATOM    103  CA  LEU   103      -1.023  -5.731   0.069  1.00  0.00              
ATOM    104  CA  LYS   104      -2.074  -9.284   0.687  1.00  0.00              
ATOM    105  CA  GLY   105      -1.525 -11.252   3.852  1.00  0.00              
ATOM    106  CA  ASP   106       1.799 -12.720   2.655  1.00  0.00              
ATOM    107  CA  TYR   107       3.260  -9.350   1.730  1.00  0.00              
ATOM    108  CA  ALA   108       2.603  -7.934   5.249  1.00  0.00              
ATOM    109  CA  GLU   109       4.414 -10.728   6.995  1.00  0.00              
ATOM    110  CA  LEU   110       7.520 -10.494   4.740  1.00  0.00              
ATOM    111  CA  GLU   111       7.972  -6.766   5.093  1.00  0.00              
ATOM    112  CA  HIS   112       7.721  -6.930   8.919  1.00  0.00              
ATOM    113  CA  HIS   113      10.289  -9.772   9.152  1.00  0.00              
ATOM    114  CA  HIS   114      12.924  -7.652   7.419  1.00  0.00              
ATOM    115  CA  HIS   115      13.493 -10.102   4.056  1.00  0.00              
ATOM    116  CA  HIS   116      16.821 -11.211   2.323  1.00  0.00              
ATOM    117  CA  HIS   117      15.046 -13.169  -0.810  1.00  0.00              
TER                                                                             
END
