
#######################################################
#                                                     #
#                        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   86 (   86),  selected   86 , name T0292TS168_1-D1
# Molecule2: number of CA atoms   77 (  591),  selected   77 , name T0292_D1.pdb
# PARAMETERS: T0292TS168_1-D1.T0292_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1          3.669
LGA    R       2      R       2          1.301
LGA    A       3      A       3          2.278
LGA    E       4      E       4          1.968
LGA    D       5      D       5          1.769
LGA    Y       6      Y       6          4.045
LGA    E       7      E       7          2.079
LGA    V       8      V       8          2.158
LGA    L       9      L       9          1.625
LGA    Y      10      Y      10          1.026
LGA    T      11      T      11          1.047
LGA    I      12      I      12          0.944
LGA    G      13      G      13          1.319
LGA    T      14      T      14          3.137
LGA    G      15      G      15          2.742
LGA    S      16      S      16          3.423
LGA    Y      17      Y      17          2.784
LGA    G      18      G      18          2.810
LGA    R      19      R      19          1.683
LGA    C      20      C      20          1.289
LGA    Q      21      Q      21          1.719
LGA    K      22      K      22          1.760
LGA    I      23      I      23          1.719
LGA    R      24      R      24          1.412
LGA    R      25      R      25          0.941
LGA    K      26      K      26          1.291
LGA    S      27      S      27          2.430
LGA    D      28      D      28          2.364
LGA    G      29      G      29          1.237
LGA    K      30      K      30          0.828
LGA    I      31      I      31          0.616
LGA    L      32      L      32          1.323
LGA    V      33      V      33          1.372
LGA    W      34      W      34          0.285
LGA    K      35      K      35          0.838
LGA    E      36      E      36          0.333
LGA    L      37      L      37          0.665
LGA    D      38      D      38          2.427
LGA    Y      39      Y      39          3.102
LGA    G      40      G      40          2.120
LGA    S      41      S      41          3.986
LGA    M      42      M      42          3.305
LGA    T      43      T      43          2.313
LGA    E      44      -       -           -
LGA    A      45      -       -           -
LGA    E      46      -       -           -
LGA    K      47      -       -           -
LGA    Q      48      -       -           -
LGA    M      49      M      49          1.385
LGA    L      50      L      50          1.581
LGA    V      51      V      51          0.954
LGA    S      52      S      52          0.899
LGA    E      53      E      53          1.208
LGA    V      54      V      54          0.875
LGA    N      55      N      55          1.926
LGA    L      56      L      56          2.249
LGA    L      57      L      57          1.736
LGA    R      58      R      58          1.680
LGA    E      59      E      59          2.109
LGA    L      60      L      60          1.767
LGA    K      61      K      61          2.057
LGA    H      62      H      62          2.580
LGA    P      63      P      63          2.017
LGA    N      64      N      64          1.966
LGA    I      65      I      65          1.350
LGA    V      66      V      66          1.266
LGA    R      67      R      67          1.760
LGA    Y      68      Y      68          1.483
LGA    Y      69      Y      69          1.250
LGA    D      70      D      70          2.019
LGA    R      71      R      71          1.186
LGA    I      72      I      72          1.922
LGA    I      73      I      73          1.792
LGA    D      74      D      74          2.588
LGA    R      75      -       -           -
LGA    T      76      -       -           -
LGA    N      77      -       -           -
LGA    T      78      -       -           -
LGA    T      79      T      79          1.995
LGA    L      80      L      80          0.569
LGA    Y      81      Y      81          0.494
LGA    I      82      I      82          0.877
LGA    V      83      V      83          2.446
LGA    M      84      M      84          1.684
LGA    E      85      E      85          0.803
LGA    Y      86      Y      86          0.836

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   86   77    5.0     77    1.93   100.00     87.651     3.784

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.442980 * X  +   0.050259 * Y  +   0.895122 * Z  +   6.081820
  Y_new =   0.819434 * X  +  -0.382366 * Y  +   0.426993 * Z  +  14.506542
  Z_new =   0.363725 * X  +   0.922643 * Y  +   0.128197 * Z  +  16.235325 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.432735   -1.708857  [ DEG:    82.0897    -97.9103 ]
  Theta =  -0.372263   -2.769329  [ DEG:   -21.3291   -158.6709 ]
  Phi   =   2.066388   -1.075204  [ DEG:   118.3953    -61.6047 ]
 
# 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: T0292TS168_1-D1                               
REMARK     2: T0292_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0292TS168_1-D1.T0292_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   86   77   5.0   77   1.93  100.00  87.651
REMARK  ---------------------------------------------------------- 
MOLECULE T0292TS168_1-D1
PFRMAT TS
TARGET T0292
MODEL 1
PARENT N/A
ATOM      1  CA  SER     1      -9.025  -8.781   4.140  1.00 25.00           C
ATOM      2  CA  ARG     2     -10.580  -7.164   7.244  1.00 25.00           C
ATOM      3  CA  ALA     3     -13.589  -4.937   7.806  1.00 25.00           C
ATOM      4  CA  GLU     4     -15.566  -7.984   9.026  1.00 25.00           C
ATOM      5  CA  ASP     5     -13.110  -7.728  11.943  1.00 25.00           C
ATOM      6  CA  TYR     6     -15.043  -6.428  15.021  1.00 25.00           C
ATOM      7  CA  GLU     7     -16.399  -2.880  14.692  1.00 25.00           C
ATOM      8  CA  VAL     8     -16.703   0.906  14.939  1.00 25.00           C
ATOM      9  CA  LEU     9     -15.940   3.153  17.886  1.00 25.00           C
ATOM     10  CA  TYR    10     -14.698   6.749  17.568  1.00 25.00           C
ATOM     11  CA  THR    11     -12.486   9.313  15.867  1.00 25.00           C
ATOM     12  CA  ILE    12      -9.483  10.007  18.124  1.00 25.00           C
ATOM     13  CA  GLY    13      -8.384  12.537  15.435  1.00 25.00           C
ATOM     14  CA  THR    14      -8.815  15.925  13.682  1.00 25.00           C
ATOM     15  CA  GLY    15      -6.296  14.996  10.973  1.00 25.00           C
ATOM     16  CA  SER    16      -4.668  16.627   7.896  1.00 25.00           C
ATOM     17  CA  TYR    17      -3.482  13.221   6.687  1.00 25.00           C
ATOM     18  CA  GLY    18      -6.356  10.902   7.630  1.00 25.00           C
ATOM     19  CA  ARG    19      -8.434   9.747  10.562  1.00 25.00           C
ATOM     20  CA  CYS    20      -8.266   7.537  13.603  1.00 25.00           C
ATOM     21  CA  GLN    21      -9.752   5.059  16.056  1.00 25.00           C
ATOM     22  CA  LYS    22     -10.244   2.415  18.699  1.00 25.00           C
ATOM     23  CA  ILE    23     -11.672   0.302  15.823  1.00 25.00           C
ATOM     24  CA  ARG    24     -11.722  -2.959  17.849  1.00 25.00           C
ATOM     25  CA  ARG    25      -9.908  -6.026  16.517  1.00 25.00           C
ATOM     26  CA  LYS    26     -10.870  -9.718  16.164  1.00 25.00           C
ATOM     27  CA  SER    27     -10.582 -12.797  18.392  1.00 25.00           C
ATOM     28  CA  ASP    28     -10.210 -10.587  21.431  1.00 25.00           C
ATOM     29  CA  GLY    29     -10.486  -6.759  21.773  1.00 25.00           C
ATOM     30  CA  LYS    30      -7.069  -5.519  20.673  1.00 25.00           C
ATOM     31  CA  ILE    31      -7.893  -1.847  21.251  1.00 25.00           C
ATOM     32  CA  LEU    32      -5.251  -1.391  18.481  1.00 25.00           C
ATOM     33  CA  VAL    33      -5.934   1.446  16.030  1.00 25.00           C
ATOM     34  CA  TRP    34      -6.311   2.937  12.571  1.00 25.00           C
ATOM     35  CA  LYS    35      -5.968   5.325   9.648  1.00 25.00           C
ATOM     36  CA  GLU    36      -8.765   6.025   7.185  1.00 25.00           C
ATOM     37  CA  LEU    37      -7.596   6.947   3.709  1.00 25.00           C
ATOM     38  CA  ASP    38     -11.086   7.624   2.330  1.00 25.00           C
ATOM     39  CA  TYR    39      -9.477   8.290  -1.021  1.00 25.00           C
ATOM     40  CA  GLY    40      -9.637   9.323  -4.728  1.00 25.00           C
ATOM     41  CA  SER    41      -8.601   7.511  -7.893  1.00 25.00           C
ATOM     42  CA  MET    42      -5.119   6.897  -6.390  1.00 25.00           C
ATOM     43  CA  THR    43      -3.230   7.966  -9.563  1.00 25.00           C
ATOM     44  CA  GLU    44      -1.307   4.744  -9.939  1.00 25.00           C
ATOM     45  CA  ALA    45       1.653   6.845  -8.711  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.186   8.108  -5.598  1.00 25.00           C
ATOM     47  CA  LYS    47      -0.816   4.500  -4.477  1.00 25.00           C
ATOM     48  CA  GLN    48       2.890   3.672  -4.977  1.00 25.00           C
ATOM     49  CA  MET    49       3.880   6.749  -2.923  1.00 25.00           C
ATOM     50  CA  LEU    50       1.479   5.690  -0.134  1.00 25.00           C
ATOM     51  CA  VAL    51       2.970   2.163  -0.155  1.00 25.00           C
ATOM     52  CA  SER    52       6.502   3.628   0.065  1.00 25.00           C
ATOM     53  CA  GLU    53       5.431   5.828   3.012  1.00 25.00           C
ATOM     54  CA  VAL    54       3.920   2.780   4.770  1.00 25.00           C
ATOM     55  CA  ASN    55       7.163   0.820   4.215  1.00 25.00           C
ATOM     56  CA  LEU    56       9.197   3.730   5.652  1.00 25.00           C
ATOM     57  CA  LEU    57       6.895   3.861   8.710  1.00 25.00           C
ATOM     58  CA  ARG    58       7.309   0.088   9.213  1.00 25.00           C
ATOM     59  CA  GLU    59      11.114   0.449   8.982  1.00 25.00           C
ATOM     60  CA  LEU    60      11.586   1.566  12.553  1.00 25.00           C
ATOM     61  CA  LYS    61      10.989  -0.310  15.788  1.00 25.00           C
ATOM     62  CA  HIS    62      12.375   2.064  18.440  1.00 25.00           C
ATOM     63  CA  PRO    63      10.332   2.156  21.685  1.00 25.00           C
ATOM     64  CA  ASN    64       9.773   5.799  20.643  1.00 25.00           C
ATOM     65  CA  ILE    65       7.403   5.238  17.717  1.00 25.00           C
ATOM     66  CA  VAL    66       4.122   3.300  17.452  1.00 25.00           C
ATOM     67  CA  ARG    67       4.607  -0.530  17.513  1.00 25.00           C
ATOM     68  CA  TYR    68       4.226  -0.102  13.735  1.00 25.00           C
ATOM     69  CA  TYR    69       1.189  -2.423  13.790  1.00 25.00           C
ATOM     70  CA  ASP    70       0.414  -2.709  10.077  1.00 25.00           C
ATOM     71  CA  ARG    71      -1.527  -3.072   6.826  1.00 25.00           C
ATOM     72  CA  ILE    72      -4.111  -2.607   4.115  1.00 25.00           C
ATOM     73  CA  ILE    73      -6.089  -3.293   0.992  1.00 25.00           C
ATOM     74  CA  ASP    74      -9.819  -3.850   0.205  1.00 25.00           C
ATOM     75  CA  ARG    75     -10.379  -3.598  -3.506  1.00 25.00           C
ATOM     76  CA  THR    76     -13.710  -2.056  -2.522  1.00 25.00           C
ATOM     77  CA  ASN    77     -13.514   1.341  -4.256  1.00 25.00           C
ATOM     78  CA  THR    78      -9.903   1.723  -3.377  1.00 25.00           C
ATOM     79  CA  THR    79      -8.657   3.267  -0.161  1.00 25.00           C
ATOM     80  CA  LEU    80      -6.505   2.073   2.710  1.00 25.00           C
ATOM     81  CA  TYR    81      -6.145   1.346   6.458  1.00 25.00           C
ATOM     82  CA  ILE    82      -2.649   1.945   7.802  1.00 25.00           C
ATOM     83  CA  VAL    83      -1.507   1.761  11.425  1.00 25.00           C
ATOM     84  CA  MET    84      -1.376   3.287  14.847  1.00 25.00           C
ATOM     85  CA  GLU    85      -0.391   1.087  17.728  1.00 25.00           C
ATOM     86  CA  TYR    86      -2.942   3.086  19.715  1.00 25.00           C
TER
END
