
#######################################################
#                                                     #
#                        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 T0288TS393_1-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS393_1-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          6.587
LGA    P       4      P       4          3.387
LGA    G       5      G       5          1.602
LGA    K       6      K       6          1.612
LGA    V       7      V       7          1.195
LGA    T       8      T       8          2.202
LGA    L       9      L       9          2.100
LGA    Q      10      Q      10          2.087
LGA    K      11      K      11          2.078
LGA    D      12      D      12          3.115
LGA    A      13      A      13          1.479
LGA    Q      14      Q      14          1.186
LGA    N      15      N      15          4.263
LGA    L      16      L      16          0.980
LGA    I      17      I      17          0.847
LGA    G      18      G      18          1.475
LGA    I      19      I      19          1.427
LGA    S      20      S      20          1.711
LGA    I      21      I      21          0.904
LGA    G      22      G      22          0.879
LGA    G      23      G      23          0.867
LGA    G      24      G      24          0.456
LGA    A      25      A      25          4.767
LGA    Q      26      Q      26          0.893
LGA    Y      27      -       -           -
LGA    C      28      P      29          2.662
LGA    P      29      C      30          1.617
LGA    C      30      -       -           -
LGA    L      31      L      31          1.437
LGA    Y      32      Y      32          1.845
LGA    I      33      I      33          1.286
LGA    V      34      V      34          1.378
LGA    Q      35      Q      35          0.784
LGA    V      36      V      36          0.804
LGA    F      37      F      37          0.892
LGA    D      38      D      38          1.539
LGA    N      39      N      39          1.220
LGA    T      40      T      40          1.876
LGA    P      41      P      41          2.124
LGA    A      42      A      42          0.852
LGA    A      43      A      43          1.737
LGA    L      44      L      44          1.553
LGA    D      45      D      45          1.447
LGA    G      46      G      46          1.377
LGA    T      47      T      47          1.705
LGA    V      48      V      48          1.709
LGA    A      49      A      49          0.418
LGA    A      50      A      50          0.822
LGA    G      51      G      51          0.658
LGA    D      52      D      52          0.866
LGA    E      53      E      53          0.571
LGA    I      54      I      54          1.361
LGA    T      55      T      55          1.569
LGA    G      56      G      56          1.756
LGA    V      57      V      57          1.942
LGA    N      58      N      58          0.915
LGA    G      59      G      59          2.719
LGA    R      60      R      60          2.629
LGA    S      61      S      61          1.584
LGA    I      62      I      62          1.604
LGA    K      63      K      63          1.784
LGA    G      64      G      64          1.180
LGA    K      65      K      65          1.199
LGA    T      66      T      66          2.006
LGA    K      67      K      67          0.899
LGA    V      68      V      68          0.281
LGA    E      69      E      69          0.664
LGA    V      70      V      70          0.903
LGA    A      71      A      71          0.463
LGA    K      72      K      72          0.673
LGA    M      73      M      73          0.804
LGA    I      74      I      74          0.583
LGA    Q      75      Q      75          1.000
LGA    E      76      E      76          1.617
LGA    V      77      V      77          0.895
LGA    K      78      K      78          1.128
LGA    G      79      G      79          1.900
LGA    E      80      E      80          2.122
LGA    V      81      V      81          1.079
LGA    T      82      T      82          1.482
LGA    I      83      I      83          1.305
LGA    H      84      H      84          0.489
LGA    Y      85      Y      85          1.539
LGA    N      86      N      86          0.882
LGA    K      87      K      87          0.533
LGA    L      88      L      88          0.890

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.78    97.62     89.244     4.475

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.816307 * X  +   0.458034 * Y  +   0.351919 * Z  +  27.514141
  Y_new =   0.541449 * X  +  -0.818980 * Y  +  -0.190011 * Z  +  17.405508
  Z_new =   0.201183 * X  +   0.345653 * Y  +  -0.916542 * Z  +  13.290710 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.780958   -0.360635  [ DEG:   159.3372    -20.6628 ]
  Theta =  -0.202565   -2.939027  [ DEG:   -11.6061   -168.3939 ]
  Phi   =   0.585662   -2.555931  [ DEG:    33.5560   -146.4440 ]
 
# 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: T0288TS393_1-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_1-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   84   1.78   97.62  89.244
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_1-D1
PFRMAT TS
TARGET T0288
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      22.578   7.449  31.540  1.00 25.00           C
ATOM      2  CA  MET     2      24.884  10.014  29.897  1.00 25.00           C
ATOM      3  CA  VAL     3      22.982  12.091  27.337  1.00 25.00           C
ATOM      4  CA  PRO     4      23.869  13.053  23.816  1.00 25.00           C
ATOM      5  CA  GLY     5      22.411  16.585  24.250  1.00 25.00           C
ATOM      6  CA  LYS     6      20.332  17.329  21.121  1.00 25.00           C
ATOM      7  CA  VAL     7      21.093  20.463  19.023  1.00 25.00           C
ATOM      8  CA  THR     8      18.110  22.032  17.322  1.00 25.00           C
ATOM      9  CA  LEU     9      20.625  23.565  14.827  1.00 25.00           C
ATOM     10  CA  GLN    10      17.927  24.983  12.497  1.00 25.00           C
ATOM     11  CA  LYS    11      18.885  26.249   9.103  1.00 25.00           C
ATOM     12  CA  ASP    12      16.981  28.099   6.318  1.00 25.00           C
ATOM     13  CA  ALA    13      19.143  30.151   3.958  1.00 25.00           C
ATOM     14  CA  GLN    14      21.283  28.260   1.443  1.00 25.00           C
ATOM     15  CA  ASN    15      24.046  27.871   3.945  1.00 25.00           C
ATOM     16  CA  LEU    16      23.107  24.449   5.263  1.00 25.00           C
ATOM     17  CA  ILE    17      24.100  23.960   8.931  1.00 25.00           C
ATOM     18  CA  GLY    18      27.550  25.155   7.802  1.00 25.00           C
ATOM     19  CA  ILE    19      29.435  21.996   8.975  1.00 25.00           C
ATOM     20  CA  SER    20      31.977  20.545   6.533  1.00 25.00           C
ATOM     21  CA  ILE    21      32.246  17.037   7.985  1.00 25.00           C
ATOM     22  CA  GLY    22      35.215  14.856   8.837  1.00 25.00           C
ATOM     23  CA  GLY    23      36.831  11.933  10.689  1.00 25.00           C
ATOM     24  CA  GLY    24      37.187   8.753   8.659  1.00 25.00           C
ATOM     25  CA  ALA    25      37.532   5.329   6.999  1.00 25.00           C
ATOM     26  CA  GLN    26      41.142   4.662   8.165  1.00 25.00           C
ATOM     27  CA  TYR    27      39.569   5.019  11.649  1.00 25.00           C
ATOM     28  CA  CYS    28      36.320   3.903  13.304  1.00 25.00           C
ATOM     29  CA  PRO    29      35.642   7.666  13.691  1.00 25.00           C
ATOM     30  CA  CYS    30      32.239   9.228  14.360  1.00 25.00           C
ATOM     31  CA  LEU    31      31.870  12.436  12.336  1.00 25.00           C
ATOM     32  CA  TYR    32      32.272  16.099  13.157  1.00 25.00           C
ATOM     33  CA  ILE    33      32.385  19.832  13.616  1.00 25.00           C
ATOM     34  CA  VAL    34      35.010  21.037  11.162  1.00 25.00           C
ATOM     35  CA  GLN    35      34.721  24.756  11.720  1.00 25.00           C
ATOM     36  CA  VAL    36      31.456  26.686  12.342  1.00 25.00           C
ATOM     37  CA  PHE    37      31.721  29.461   9.703  1.00 25.00           C
ATOM     38  CA  ASP    38      31.224  33.204  10.162  1.00 25.00           C
ATOM     39  CA  ASN    39      27.669  34.576   9.753  1.00 25.00           C
ATOM     40  CA  THR    40      26.256  31.210   8.662  1.00 25.00           C
ATOM     41  CA  PRO    41      24.119  28.722  10.532  1.00 25.00           C
ATOM     42  CA  ALA    42      25.351  27.298  13.894  1.00 25.00           C
ATOM     43  CA  ALA    43      26.308  30.933  14.629  1.00 25.00           C
ATOM     44  CA  LEU    44      22.675  31.730  15.543  1.00 25.00           C
ATOM     45  CA  ASP    45      23.485  29.856  18.744  1.00 25.00           C
ATOM     46  CA  GLY    46      27.146  29.097  19.460  1.00 25.00           C
ATOM     47  CA  THR    47      26.816  25.267  19.752  1.00 25.00           C
ATOM     48  CA  VAL    48      28.484  23.231  16.996  1.00 25.00           C
ATOM     49  CA  ALA    49      31.861  22.856  18.668  1.00 25.00           C
ATOM     50  CA  ALA    50      35.286  22.317  17.137  1.00 25.00           C
ATOM     51  CA  GLY    51      35.353  18.586  17.808  1.00 25.00           C
ATOM     52  CA  ASP    52      31.844  17.201  18.074  1.00 25.00           C
ATOM     53  CA  GLU    53      31.796  13.398  17.803  1.00 25.00           C
ATOM     54  CA  ILE    54      28.343  12.827  16.382  1.00 25.00           C
ATOM     55  CA  THR    55      25.300  10.572  15.678  1.00 25.00           C
ATOM     56  CA  GLY    56      22.627  11.823  13.301  1.00 25.00           C
ATOM     57  CA  VAL    57      20.013  12.701  10.625  1.00 25.00           C
ATOM     58  CA  ASN    58      16.909  12.865  12.886  1.00 25.00           C
ATOM     59  CA  GLY    59      17.532   9.157  12.605  1.00 25.00           C
ATOM     60  CA  ARG    60      20.390   7.502  10.662  1.00 25.00           C
ATOM     61  CA  SER    61      23.541   6.675  12.561  1.00 25.00           C
ATOM     62  CA  ILE    62      26.920   7.682  11.182  1.00 25.00           C
ATOM     63  CA  LYS    63      28.782   4.974  13.131  1.00 25.00           C
ATOM     64  CA  GLY    64      29.560   2.779  10.082  1.00 25.00           C
ATOM     65  CA  LYS    65      29.400   5.389   7.284  1.00 25.00           C
ATOM     66  CA  THR    66      32.351   7.741   6.781  1.00 25.00           C
ATOM     67  CA  LYS    67      32.376  11.441   5.830  1.00 25.00           C
ATOM     68  CA  VAL    68      30.897  11.542   2.299  1.00 25.00           C
ATOM     69  CA  GLU    69      27.809   9.627   3.510  1.00 25.00           C
ATOM     70  CA  VAL    70      27.397  12.083   6.420  1.00 25.00           C
ATOM     71  CA  ALA    71      27.664  15.036   3.997  1.00 25.00           C
ATOM     72  CA  LYS    72      25.021  13.446   1.729  1.00 25.00           C
ATOM     73  CA  MET    73      22.709  12.936   4.738  1.00 25.00           C
ATOM     74  CA  ILE    74      23.192  16.595   5.761  1.00 25.00           C
ATOM     75  CA  GLN    75      22.373  17.726   2.196  1.00 25.00           C
ATOM     76  CA  GLU    76      19.211  15.566   2.210  1.00 25.00           C
ATOM     77  CA  VAL    77      17.814  17.945   4.910  1.00 25.00           C
ATOM     78  CA  LYS    78      16.208  21.074   3.418  1.00 25.00           C
ATOM     79  CA  GLY    79      15.694  22.239   7.021  1.00 25.00           C
ATOM     80  CA  GLU    80      15.022  20.239  10.186  1.00 25.00           C
ATOM     81  CA  VAL    81      18.529  19.395  11.388  1.00 25.00           C
ATOM     82  CA  THR    82      20.279  17.838  14.348  1.00 25.00           C
ATOM     83  CA  ILE    83      23.856  16.684  14.278  1.00 25.00           C
ATOM     84  CA  HIS    84      23.097  14.786  17.544  1.00 25.00           C
ATOM     85  CA  TYR    85      25.835  16.108  19.759  1.00 25.00           C
ATOM     86  CA  ASN    86      28.763  14.791  21.789  1.00 25.00           C
ATOM     87  CA  LYS    87      31.588  16.706  23.504  1.00 25.00           C
ATOM     88  CA  LEU    88      34.977  15.148  23.284  1.00 25.00           C
TER
END
