
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0303TS393_1-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS393_1-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      18      S      18          2.353
LGA    L      19      L      19          3.569
LGA    P      20      P      20          3.162
LGA    D      21      D      21          2.630
LGA    L      22      L      22          2.770
LGA    A      23      A      23          2.962
LGA    L      24      L      24          2.232
LGA    S      25      S      25          1.573
LGA    I      26      I      26          2.745
LGA    N      27      N      27          2.788
LGA    S      28      S      28          1.266
LGA    A      29      A      29          1.271
LGA    L      30      L      30          2.257
LGA    K      31      K      31          1.929
LGA    D      32      D      32          0.766
LGA    V      33      V      33          2.322
LGA    N      34      N      34          1.343
LGA    L      35      L      35          3.611
LGA    P      36      P      36           -
LGA    Q      37      Q      37           -
LGA    A      38      -       -           -
LGA    S      39      -       -           -
LGA    E      40      A      38          5.808
LGA    N      41      S      39           -
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    -       -      L      42           -
LGA    L      42      V      43          3.993
LGA    V      43      -       -           -
LGA    M      44      M      44           #
LGA    T      45      T      45           -
LGA    W      46      W      46           #
LGA    I      47      I      47          1.250
LGA    G      48      G      48          3.714
LGA    N      49      N      49          5.297
LGA    G      50      G      50          4.941
LGA    A      51      A      51          4.970
LGA    D      52      D      52          4.693
LGA    V      53      -       -           -
LGA    L      54      V      53          1.212
LGA    S      55      L      54          5.652
LGA    Q      56      S      55           -
LGA    R      57      -       -           -
LGA    A      58      Q      56          3.924
LGA    V      59      R      57          4.467
LGA    D      60      A      58           -
LGA    W      61      V      59           -
LGA    A      62      D      60          4.461
LGA    C      63      W      61          3.228
LGA    T      64      -       -           -
LGA    Q      65      A      62          2.026
LGA    A      66      -       -           -
LGA    E      67      C      63          4.619
LGA    -       -      T      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      E      67           -
LGA    K      68      K      68          4.994
LGA    E      69      E      69           #
LGA    L      70      L      70          4.992
LGA    T      71      T      71          2.422
LGA    E      72      E      72          0.767
LGA    D      73      D      73          1.590
LGA    E      74      E      74          2.589
LGA    F      75      F      75          1.837
LGA    K      76      K      76          0.421
LGA    Y      77      Y      77          1.949
LGA    F      78      F      78          2.366
LGA    K      79      K      79          1.250
LGA    R      80      R      80          1.023
LGA    Q      81      Q      81          2.526
LGA    F      82      F      82          2.454
LGA    G      83      G      83          0.756
LGA    F      84      F      84          1.417
LGA    Y      85      Y      85          3.018
LGA    Y      86      Y      86          2.684
LGA    G      87      G      87          0.590
LGA    E      88      E      88          1.564
LGA    N      89      N      89          2.991
LGA    L      90      L      90          3.229
LGA    C      91      -       -           -
LGA    N      92      -       -           -
LGA    I      93      C      91          1.286
LGA    S      94      N      92          2.013
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   77    5.0     58    3.04    79.31     48.182     1.847

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.530179 * X  +  -0.067601 * Y  +  -0.845187 * Z  + -14.257635
  Y_new =   0.554956 * X  +  -0.725974 * Y  +   0.406185 * Z  +  83.910530
  Z_new =  -0.641042 * X  +  -0.684392 * Y  +  -0.347380 * Z  +  15.893931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.040485    1.101107  [ DEG:  -116.9112     63.0888 ]
  Theta =   0.695855    2.445738  [ DEG:    39.8696    140.1304 ]
  Phi   =   0.808227   -2.333365  [ DEG:    46.3080   -133.6920 ]
 
# 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: T0303TS393_1-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS393_1-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   77   5.0   58   3.04   79.31  48.182
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS393_1-D2
PFRMAT TS
TARGET T0303
MODEL 1
PARENT N/A
ATOM     18  CA  SER    18     -14.192  85.398  20.487  1.00 25.00           C
ATOM     19  CA  LEU    19     -13.659  89.222  20.463  1.00 25.00           C
ATOM     20  CA  PRO    20     -14.536  92.068  22.871  1.00 25.00           C
ATOM     21  CA  ASP    21     -12.763  90.232  25.726  1.00 25.00           C
ATOM     22  CA  LEU    22      -9.669  89.741  23.521  1.00 25.00           C
ATOM     23  CA  ALA    23      -9.685  93.464  22.627  1.00 25.00           C
ATOM     24  CA  LEU    24      -9.941  94.380  26.336  1.00 25.00           C
ATOM     25  CA  SER    25      -7.004  92.056  27.138  1.00 25.00           C
ATOM     26  CA  ILE    26      -4.937  93.665  24.344  1.00 25.00           C
ATOM     27  CA  ASN    27      -5.759  97.148  25.708  1.00 25.00           C
ATOM     28  CA  SER    28      -4.710  96.047  29.222  1.00 25.00           C
ATOM     29  CA  ALA    29      -1.419  94.664  27.833  1.00 25.00           C
ATOM     30  CA  LEU    30      -0.781  97.963  25.996  1.00 25.00           C
ATOM     31  CA  LYS    31      -1.460  99.918  29.218  1.00 25.00           C
ATOM     32  CA  ASP    32       0.968  97.657  31.131  1.00 25.00           C
ATOM     33  CA  VAL    33       3.362  99.880  29.119  1.00 25.00           C
ATOM     34  CA  ASN    34       3.901 102.838  26.883  1.00 25.00           C
ATOM     35  CA  LEU    35       5.302 103.220  23.320  1.00 25.00           C
ATOM     36  CA  PRO    36       7.510 103.186  20.224  1.00 25.00           C
ATOM     37  CA  GLN    37       7.837  99.942  18.263  1.00 25.00           C
ATOM     38  CA  ALA    38       6.358  96.529  17.814  1.00 25.00           C
ATOM     39  CA  SER    39       3.150  94.778  16.829  1.00 25.00           C
ATOM     40  CA  GLU    40      -0.240  93.024  17.154  1.00 25.00           C
ATOM     41  CA  ASN    41      -0.142  91.019  20.414  1.00 25.00           C
ATOM     42  CA  LEU    42      -3.961  90.728  20.380  1.00 25.00           C
ATOM     43  CA  VAL    43      -3.861  89.522  16.746  1.00 25.00           C
ATOM     44  CA  MET    44      -1.205  86.918  17.658  1.00 25.00           C
ATOM     45  CA  THR    45      -3.355  85.716  20.590  1.00 25.00           C
ATOM     46  CA  TRP    46      -6.393  85.424  18.275  1.00 25.00           C
ATOM     47  CA  ILE    47      -4.315  83.414  15.763  1.00 25.00           C
ATOM     48  CA  GLY    48      -1.583  81.711  17.821  1.00 25.00           C
ATOM     49  CA  ASN    49       0.302  79.840  20.622  1.00 25.00           C
ATOM     50  CA  GLY    50       2.053  82.058  23.181  1.00 25.00           C
ATOM     51  CA  ALA    51       5.280  80.228  22.334  1.00 25.00           C
ATOM     52  CA  ASP    52       8.633  80.820  20.578  1.00 25.00           C
ATOM     53  CA  VAL    53       7.014  80.086  17.186  1.00 25.00           C
ATOM     54  CA  LEU    54       4.184  82.542  17.977  1.00 25.00           C
ATOM     55  CA  SER    55       6.746  85.218  18.952  1.00 25.00           C
ATOM     56  CA  GLN    56       8.645  84.626  15.680  1.00 25.00           C
ATOM     57  CA  ARG    57       5.384  84.950  13.698  1.00 25.00           C
ATOM     58  CA  ALA    58       4.576  88.223  15.516  1.00 25.00           C
ATOM     59  CA  VAL    59       8.078  89.556  14.723  1.00 25.00           C
ATOM     60  CA  ASP    60       7.629  88.613  11.038  1.00 25.00           C
ATOM     61  CA  TRP    61       4.243  90.401  10.969  1.00 25.00           C
ATOM     62  CA  ALA    62       5.828  93.516  12.534  1.00 25.00           C
ATOM     63  CA  CYS    63       3.860  96.741  12.326  1.00 25.00           C
ATOM     64  CA  THR    64       3.218  99.710  14.638  1.00 25.00           C
ATOM     65  CA  GLN    65       2.788  99.771  18.403  1.00 25.00           C
ATOM     66  CA  ALA    66       3.982  98.544  21.818  1.00 25.00           C
ATOM     67  CA  GLU    67       7.570  98.601  23.217  1.00 25.00           C
ATOM     68  CA  LYS    68      11.169  98.914  24.515  1.00 25.00           C
ATOM     69  CA  GLU    69      13.805  98.723  27.265  1.00 25.00           C
ATOM     70  CA  LEU    70      15.682  95.370  27.196  1.00 25.00           C
ATOM     71  CA  THR    71      14.196  93.437  24.242  1.00 25.00           C
ATOM     72  CA  GLU    72      14.167  90.225  26.327  1.00 25.00           C
ATOM     73  CA  ASP    73      12.416  92.069  29.190  1.00 25.00           C
ATOM     74  CA  GLU    74       9.805  93.438  26.744  1.00 25.00           C
ATOM     75  CA  PHE    75       9.216  89.914  25.365  1.00 25.00           C
ATOM     76  CA  LYS    76       8.783  88.566  28.924  1.00 25.00           C
ATOM     77  CA  TYR    77       6.276  91.354  29.700  1.00 25.00           C
ATOM     78  CA  PHE    78       4.332  90.530  26.505  1.00 25.00           C
ATOM     79  CA  LYS    79       4.267  86.824  27.471  1.00 25.00           C
ATOM     80  CA  ARG    80       2.986  87.732  30.964  1.00 25.00           C
ATOM     81  CA  GLN    81       0.247  89.919  29.419  1.00 25.00           C
ATOM     82  CA  PHE    82      -0.768  87.048  27.096  1.00 25.00           C
ATOM     83  CA  GLY    83      -0.925  84.655  30.082  1.00 25.00           C
ATOM     84  CA  PHE    84      -3.102  87.153  32.002  1.00 25.00           C
ATOM     85  CA  TYR    85      -5.437  87.474  28.982  1.00 25.00           C
ATOM     86  CA  TYR    86      -5.696  83.661  28.745  1.00 25.00           C
ATOM     87  CA  GLY    87      -6.519  83.460  32.479  1.00 25.00           C
ATOM     88  CA  GLU    88      -9.222  86.140  32.053  1.00 25.00           C
ATOM     89  CA  ASN    89     -10.707  84.207  29.100  1.00 25.00           C
ATOM     90  CA  LEU    90     -10.736  80.995  31.186  1.00 25.00           C
ATOM     91  CA  CYS    91     -12.488  82.840  34.048  1.00 25.00           C
ATOM     92  CA  ASN    92     -16.226  83.518  33.861  1.00 25.00           C
ATOM     93  CA  ILE    93     -15.583  83.417  30.106  1.00 25.00           C
ATOM     94  CA  SER    94     -16.614  86.232  27.810  1.00 25.00           C
TER
END
