
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS168_2-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS168_2-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      V       3          5.896
LGA    P       4      P       4          2.858
LGA    G       5      G       5          1.731
LGA    K       6      K       6          2.865
LGA    V       7      V       7          0.652
LGA    T       8      T       8          1.852
LGA    L       9      L       9          0.874
LGA    Q      10      Q      10          0.546
LGA    K      11      K      11          0.225
LGA    D      12      D      12          0.976
LGA    A      13      A      13          1.799
LGA    Q      14      Q      14          2.067
LGA    N      15      N      15          2.501
LGA    L      16      L      16          0.709
LGA    I      17      I      17          1.603
LGA    G      18      G      18          1.309
LGA    I      19      I      19          1.709
LGA    S      20      S      20          1.810
LGA    I      21      I      21          1.475
LGA    G      22      G      22          1.261
LGA    G      23      G      23          1.122
LGA    G      24      G      24          2.048
LGA    A      25      A      25          5.314
LGA    Q      26      -       -           -
LGA    Y      27      -       -           -
LGA    C      28      Q      26           #
LGA    P      29      P      29          2.628
LGA    C      30      C      30          1.365
LGA    L      31      L      31          1.177
LGA    Y      32      Y      32          1.424
LGA    I      33      I      33          0.274
LGA    V      34      V      34          0.577
LGA    Q      35      Q      35          0.668
LGA    V      36      V      36          0.385
LGA    F      37      F      37          1.804
LGA    D      38      D      38          0.608
LGA    N      39      N      39          0.732
LGA    T      40      T      40          0.851
LGA    P      41      P      41          1.292
LGA    A      42      A      42          1.486
LGA    A      43      A      43          1.496
LGA    L      44      L      44          1.559
LGA    D      45      D      45          1.256
LGA    G      46      G      46          1.728
LGA    T      47      T      47          1.631
LGA    V      48      V      48          0.972
LGA    A      49      A      49          1.055
LGA    A      50      A      50          1.538
LGA    G      51      G      51          1.329
LGA    D      52      D      52          0.787
LGA    E      53      E      53          1.454
LGA    I      54      I      54          1.623
LGA    T      55      T      55          2.159
LGA    G      56      G      56          3.296
LGA    V      57      V      57          1.572
LGA    N      58      N      58          1.217
LGA    G      59      G      59          1.972
LGA    R      60      R      60          1.063
LGA    S      61      S      61          0.452
LGA    I      62      I      62          0.950
LGA    K      63      K      63          2.459
LGA    G      64      G      64          2.158
LGA    K      65      K      65          2.462
LGA    T      66      T      66          0.930
LGA    K      67      K      67          0.935
LGA    V      68      V      68          1.526
LGA    E      69      E      69          0.838
LGA    V      70      V      70          0.452
LGA    A      71      A      71          1.078
LGA    K      72      K      72          0.820
LGA    M      73      M      73          0.681
LGA    I      74      I      74          1.420
LGA    Q      75      Q      75          0.981
LGA    E      76      E      76          0.916
LGA    V      77      V      77          1.448
LGA    K      78      K      78          0.989
LGA    G      79      G      79          3.055
LGA    E      80      E      80          1.313
LGA    V      81      V      81          0.864
LGA    T      82      T      82          0.773
LGA    I      83      I      83          0.923
LGA    H      84      H      84          0.941
LGA    Y      85      Y      85          0.627
LGA    N      86      N      86          0.593
LGA    K      87      K      87          0.192
LGA    L      88      L      88          2.041

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     83    1.71   100.00     88.250     4.580

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.309881 * X  +  -0.567595 * Y  +  -0.762765 * Z  +  27.687847
  Y_new =   0.494610 * X  +   0.588916 * Y  +  -0.639170 * Z  +  17.450378
  Z_new =   0.811994 * X  +  -0.575338 * Y  +   0.098245 * Z  +  13.231368 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.401668    1.739925  [ DEG:   -80.3096     99.6904 ]
  Theta =  -0.947561   -2.194032  [ DEG:   -54.2912   -125.7088 ]
  Phi   =   2.130484   -1.011109  [ DEG:   122.0677    -57.9323 ]
 
# 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: T0288TS168_2-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS168_2-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   83   1.71  100.00  88.250
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS168_2-D1
PFRMAT TS
TARGET T0288
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1      28.439   9.024  32.521  1.00 25.00           C
ATOM      2  CA  MET     2      25.790   9.450  29.869  1.00 25.00           C
ATOM      3  CA  VAL     3      26.279  11.809  26.990  1.00 25.00           C
ATOM      4  CA  PRO     4      24.292  13.295  24.130  1.00 25.00           C
ATOM      5  CA  GLY     5      23.629  17.007  23.639  1.00 25.00           C
ATOM      6  CA  LYS     6      20.674  18.744  21.965  1.00 25.00           C
ATOM      7  CA  VAL     7      20.851  20.182  18.466  1.00 25.00           C
ATOM      8  CA  THR     8      18.602  22.357  16.304  1.00 25.00           C
ATOM      9  CA  LEU     9      20.119  23.689  13.122  1.00 25.00           C
ATOM     10  CA  GLN    10      17.826  25.613  10.802  1.00 25.00           C
ATOM     11  CA  LYS    11      19.156  25.434   7.274  1.00 25.00           C
ATOM     12  CA  ASP    12      19.917  29.177   6.892  1.00 25.00           C
ATOM     13  CA  ALA    13      17.979  30.486   3.821  1.00 25.00           C
ATOM     14  CA  GLN    14      20.366  29.413   1.007  1.00 25.00           C
ATOM     15  CA  ASN    15      22.988  26.823   2.060  1.00 25.00           C
ATOM     16  CA  LEU    16      24.260  24.828   5.011  1.00 25.00           C
ATOM     17  CA  ILE    17      25.259  24.237   8.640  1.00 25.00           C
ATOM     18  CA  GLY    18      28.328  26.503   8.333  1.00 25.00           C
ATOM     19  CA  ILE    19      30.333  23.277   8.309  1.00 25.00           C
ATOM     20  CA  SER    20      33.273  21.448   6.647  1.00 25.00           C
ATOM     21  CA  ILE    21      33.477  17.776   7.676  1.00 25.00           C
ATOM     22  CA  GLY    22      36.710  15.809   8.034  1.00 25.00           C
ATOM     23  CA  GLY    23      37.069  12.231   9.122  1.00 25.00           C
ATOM     24  CA  GLY    24      35.313   8.964   9.782  1.00 25.00           C
ATOM     25  CA  ALA    25      36.099   6.098   7.406  1.00 25.00           C
ATOM     26  CA  GLN    26      38.337   3.859   9.518  1.00 25.00           C
ATOM     27  CA  TYR    27      40.143   6.713  11.159  1.00 25.00           C
ATOM     28  CA  CYS    28      37.952   5.705  14.154  1.00 25.00           C
ATOM     29  CA  PRO    29      34.284   4.664  13.787  1.00 25.00           C
ATOM     30  CA  CYS    30      33.253   8.257  14.700  1.00 25.00           C
ATOM     31  CA  LEU    31      32.120  11.347  12.850  1.00 25.00           C
ATOM     32  CA  TYR    32      33.313  14.982  12.348  1.00 25.00           C
ATOM     33  CA  ILE    33      32.609  18.619  13.346  1.00 25.00           C
ATOM     34  CA  VAL    34      35.454  20.613  11.942  1.00 25.00           C
ATOM     35  CA  GLN    35      35.141  24.415  11.445  1.00 25.00           C
ATOM     36  CA  VAL    36      31.792  25.965  12.365  1.00 25.00           C
ATOM     37  CA  PHE    37      32.455  29.604  11.476  1.00 25.00           C
ATOM     38  CA  ASP    38      30.080  32.495  11.667  1.00 25.00           C
ATOM     39  CA  ASN    39      26.881  34.422  11.044  1.00 25.00           C
ATOM     40  CA  THR    40      25.211  31.202   9.812  1.00 25.00           C
ATOM     41  CA  PRO    41      23.809  28.150  11.637  1.00 25.00           C
ATOM     42  CA  ALA    42      26.735  26.737  13.723  1.00 25.00           C
ATOM     43  CA  ALA    43      26.360  29.531  16.289  1.00 25.00           C
ATOM     44  CA  LEU    44      22.751  30.741  16.214  1.00 25.00           C
ATOM     45  CA  ASP    45      21.973  28.160  18.868  1.00 25.00           C
ATOM     46  CA  GLY    46      25.033  27.857  21.130  1.00 25.00           C
ATOM     47  CA  THR    47      25.602  24.567  19.341  1.00 25.00           C
ATOM     48  CA  VAL    48      28.035  21.670  18.801  1.00 25.00           C
ATOM     49  CA  ALA    49      31.174  23.844  18.290  1.00 25.00           C
ATOM     50  CA  ALA    50      34.748  23.406  16.958  1.00 25.00           C
ATOM     51  CA  GLY    51      35.657  19.711  17.203  1.00 25.00           C
ATOM     52  CA  ASP    52      32.529  18.119  18.768  1.00 25.00           C
ATOM     53  CA  GLU    53      31.155  15.068  16.958  1.00 25.00           C
ATOM     54  CA  ILE    54      28.636  14.645  14.129  1.00 25.00           C
ATOM     55  CA  THR    55      26.098  11.971  14.943  1.00 25.00           C
ATOM     56  CA  GLY    56      24.413  12.131  11.582  1.00 25.00           C
ATOM     57  CA  VAL    57      20.871  13.022  10.567  1.00 25.00           C
ATOM     58  CA  ASN    58      17.191  13.499  11.233  1.00 25.00           C
ATOM     59  CA  GLY    59      16.416  10.280  13.185  1.00 25.00           C
ATOM     60  CA  ARG    60      19.627   8.445  12.159  1.00 25.00           C
ATOM     61  CA  SER    61      22.696   7.002  13.883  1.00 25.00           C
ATOM     62  CA  ILE    62      26.039   7.406  12.055  1.00 25.00           C
ATOM     63  CA  LYS    63      28.571   5.460  14.136  1.00 25.00           C
ATOM     64  CA  GLY    64      28.989   2.848  11.441  1.00 25.00           C
ATOM     65  CA  LYS    65      30.190   5.100   8.554  1.00 25.00           C
ATOM     66  CA  THR    66      30.976   6.193   5.003  1.00 25.00           C
ATOM     67  CA  LYS    67      31.871   9.883   5.297  1.00 25.00           C
ATOM     68  CA  VAL    68      30.271  10.220   1.833  1.00 25.00           C
ATOM     69  CA  GLU    69      26.920   9.009   3.235  1.00 25.00           C
ATOM     70  CA  VAL    70      27.166  11.552   6.088  1.00 25.00           C
ATOM     71  CA  ALA    71      27.916  14.340   3.572  1.00 25.00           C
ATOM     72  CA  LYS    72      24.893  13.289   1.469  1.00 25.00           C
ATOM     73  CA  MET    73      22.677  13.325   4.593  1.00 25.00           C
ATOM     74  CA  ILE    74      23.954  16.824   5.487  1.00 25.00           C
ATOM     75  CA  GLN    75      23.210  18.031   1.930  1.00 25.00           C
ATOM     76  CA  GLU    76      19.675  16.574   2.147  1.00 25.00           C
ATOM     77  CA  VAL    77      17.944  17.239   5.527  1.00 25.00           C
ATOM     78  CA  LYS    78      16.015  19.963   3.688  1.00 25.00           C
ATOM     79  CA  GLY    79      13.896  20.230   6.814  1.00 25.00           C
ATOM     80  CA  GLU    80      15.830  20.834  10.017  1.00 25.00           C
ATOM     81  CA  VAL    81      18.643  18.379  10.676  1.00 25.00           C
ATOM     82  CA  THR    82      19.611  17.324  14.175  1.00 25.00           C
ATOM     83  CA  ILE    83      23.273  17.014  15.193  1.00 25.00           C
ATOM     84  CA  HIS    84      23.110  14.810  18.255  1.00 25.00           C
ATOM     85  CA  TYR    85      26.758  14.652  19.484  1.00 25.00           C
ATOM     86  CA  ASN    86      29.130  13.737  22.295  1.00 25.00           C
ATOM     87  CA  LYS    87      31.442  16.459  23.709  1.00 25.00           C
ATOM     88  CA  LEU    88      35.195  16.439  22.871  1.00 25.00           C
TER
END
