
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS168_5-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS168_5-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1          1.720
LGA    Y       2      Y       2          2.080
LGA    V       3      V       3          1.324
LGA    D       4      D       4          1.364
LGA    P       5      P       5          1.137
LGA    H       6      H       6          2.942
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          1.290
LGA    H      16      H      16          1.339
LGA    E      17      E      17          3.043
LGA    F      18      F      18          1.560
LGA    A      19      A      19          1.249
LGA    K      20      K      20          1.990
LGA    E      21      E      21          3.579
LGA    L      22      L      22          2.258
LGA    D      23      D      23          3.830
LGA    A      24      A      24          3.965
LGA    T      25      -       -           -
LGA    N      26      T      25          1.536
LGA    I      27      -       -           -
LGA    S      28      N      26          2.245
LGA    I      29      I      27          4.933
LGA    D      30      S      28          4.949
LGA    K      31      I      29          5.222
LGA    V      32      D      30          0.998
LGA    V      33      K      31          0.753
LGA    G      34      V      32          2.526
LGA    A      35      V      33          1.937
LGA    G      36      G      34          3.768
LGA    E      37      A      35          2.041
LGA    F      38      G      36          2.682
LGA    -       -      E      37           -
LGA    -       -      F      38           -
LGA    -       -      G      39           -
LGA    G      39      E      40          0.762
LGA    E      40      V      41          2.305
LGA    V      41      C      42          2.709
LGA    C      42      S      43          2.063
LGA    S      43      G      44          2.209
LGA    G      44      R      45          2.986
LGA    R      45      L      46          2.224
LGA    L      46      K      47          3.456
LGA    K      47      L      48          2.541
LGA    L      48      P      49          4.825
LGA    P      49      -       -           -
LGA    S      50      S      50           #
LGA    K      51      K      51           #
LGA    -       -      K      52           -
LGA    K      52      E      53           #
LGA    E      53      I      54           -
LGA    I      54      S      55           -
LGA    S      55      -       -           -
LGA    V      56      V      56           #
LGA    A      57      A      57           #
LGA    I      58      I      58          3.357
LGA    K      59      K      59          1.313
LGA    T      60      T      60          1.241
LGA    L      61      L      61          1.590
LGA    K      62      K      62          1.278
LGA    V      63      V      63          1.344
LGA    G      64      G      64          3.026
LGA    Y      65      Y      65          2.190
LGA    T      66      T      66          1.857
LGA    E      67      E      67          0.990
LGA    K      68      K      68          0.922
LGA    Q      69      Q      69          0.408
LGA    R      70      R      70          0.204
LGA    R      71      R      71          0.351
LGA    D      72      D      72          0.522
LGA    F      73      F      73          0.436
LGA    L      74      L      74          1.265
LGA    G      75      G      75          1.190
LGA    E      76      E      76          1.694
LGA    A      77      A      77          1.702
LGA    S      78      S      78          2.024
LGA    I      79      I      79          2.628
LGA    M      80      M      80          2.603
LGA    G      81      G      81          2.764
LGA    Q      82      Q      82          3.779
LGA    F      83      F      83          3.286
LGA    D      84      D      84          2.569
LGA    H      85      H      85          2.430
LGA    P      86      P      86          1.421
LGA    N      87      N      87          2.691
LGA    I      88      I      88          3.020
LGA    I      89      I      89          2.220
LGA    R      90      R      90          1.120
LGA    L      91      L      91          0.964
LGA    E      92      E      92          1.169
LGA    G      93      G      93          1.231
LGA    V      94      V      94          1.553
LGA    V      95      V      95          1.388
LGA    T      96      T      96          1.666
LGA    K      97      K      97          3.002
LGA    S      98      S      98          4.478
LGA    K      99      K      99          1.054
LGA    P     100      P     100          1.179
LGA    V     101      V     101          1.158
LGA    M     102      M     102          1.249
LGA    I     103      I     103          1.267
LGA    V     104      V     104          1.587
LGA    T     105      T     105          1.492
LGA    E     106      E     106          1.464
LGA    Y     107      Y     107          2.961
LGA    M     108      M     108          3.015

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     89    2.36    77.53     62.014     3.613

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.343008 * X  +   0.804108 * Y  +   0.485547 * Z  +  -2.364188
  Y_new =  -0.673691 * X  +   0.149623 * Y  +  -0.723708 * Z  +   8.083252
  Z_new =  -0.654589 * X  +  -0.575346 * Y  +   0.490398 * Z  +  53.915722 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.864938    2.276654  [ DEG:   -49.5573    130.4427 ]
  Theta =   0.713638    2.427954  [ DEG:    40.8885    139.1115 ]
  Phi   =  -2.041735    1.099857  [ DEG:  -116.9828     63.0172 ]
 
# 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: T0291TS168_5-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS168_5-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   89   2.36   77.53  62.014
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS168_5-D1
PFRMAT TS
TARGET T0291
MODEL 5
PARENT N/A
ATOM      1  CA  THR     1      -1.816  31.870  47.606  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.002  29.085  49.008  1.00 25.00           C
ATOM      3  CA  VAL     3      -6.805  30.002  51.494  1.00 25.00           C
ATOM      4  CA  ASP     4      -8.224  28.745  54.826  1.00 25.00           C
ATOM      5  CA  PRO     5     -11.936  28.119  55.013  1.00 25.00           C
ATOM      6  CA  HIS     6     -13.863  29.655  57.925  1.00 25.00           C
ATOM      7  CA  THR     7     -13.400  33.379  57.352  1.00 25.00           C
ATOM      8  CA  TYR     8     -13.778  34.708  53.785  1.00 25.00           C
ATOM      9  CA  GLU     9     -16.709  36.590  55.149  1.00 25.00           C
ATOM     10  CA  ASP    10     -19.381  34.053  54.439  1.00 25.00           C
ATOM     11  CA  PRO    11     -17.934  30.595  53.899  1.00 25.00           C
ATOM     12  CA  THR    12     -20.580  27.982  52.983  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.053  29.625  49.556  1.00 25.00           C
ATOM     14  CA  ALA    14     -17.265  29.590  48.990  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.131  25.884  49.944  1.00 25.00           C
ATOM     16  CA  HIS    16     -19.988  25.129  47.508  1.00 25.00           C
ATOM     17  CA  GLU    17     -18.152  27.021  44.730  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.956  25.043  45.461  1.00 25.00           C
ATOM     19  CA  ALA    19     -16.925  21.761  45.314  1.00 25.00           C
ATOM     20  CA  LYS    20     -18.460  22.804  41.964  1.00 25.00           C
ATOM     21  CA  GLU    21     -21.049  20.805  40.025  1.00 25.00           C
ATOM     22  CA  LEU    22     -23.283  17.762  40.582  1.00 25.00           C
ATOM     23  CA  ASP    23     -26.877  18.563  41.464  1.00 25.00           C
ATOM     24  CA  ALA    24     -28.140  14.976  41.535  1.00 25.00           C
ATOM     25  CA  THR    25     -31.023  12.562  41.276  1.00 25.00           C
ATOM     26  CA  ASN    26     -28.513  10.096  39.875  1.00 25.00           C
ATOM     27  CA  ILE    27     -26.349  10.780  36.859  1.00 25.00           C
ATOM     28  CA  SER    28     -24.005   8.132  38.352  1.00 25.00           C
ATOM     29  CA  ILE    29     -20.588   6.856  37.090  1.00 25.00           C
ATOM     30  CA  ASP    30     -18.707   3.998  38.839  1.00 25.00           C
ATOM     31  CA  LYS    31     -18.642   0.876  41.062  1.00 25.00           C
ATOM     32  CA  VAL    32     -18.615  -0.872  44.416  1.00 25.00           C
ATOM     33  CA  VAL    33     -17.380  -1.514  47.963  1.00 25.00           C
ATOM     34  CA  GLY    34     -16.001  -0.280  51.314  1.00 25.00           C
ATOM     35  CA  ALA    35     -13.877   1.035  54.175  1.00 25.00           C
ATOM     36  CA  GLY    36     -14.498   3.416  57.124  1.00 25.00           C
ATOM     37  CA  GLU    37     -15.956   4.180  60.569  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.824   7.073  58.959  1.00 25.00           C
ATOM     39  CA  GLY    39     -19.546   4.704  56.606  1.00 25.00           C
ATOM     40  CA  GLU    40     -18.775   4.948  52.926  1.00 25.00           C
ATOM     41  CA  VAL    41     -15.384   5.169  51.214  1.00 25.00           C
ATOM     42  CA  CYS    42     -17.217   4.232  48.013  1.00 25.00           C
ATOM     43  CA  SER    43     -15.622   3.856  44.634  1.00 25.00           C
ATOM     44  CA  GLY    44     -15.275   6.357  41.732  1.00 25.00           C
ATOM     45  CA  ARG    45     -16.043   8.291  38.516  1.00 25.00           C
ATOM     46  CA  LEU    46     -17.058  11.748  37.167  1.00 25.00           C
ATOM     47  CA  LYS    47     -19.659  11.351  34.459  1.00 25.00           C
ATOM     48  CA  LEU    48     -22.267  13.773  35.950  1.00 25.00           C
ATOM     49  CA  PRO    49     -24.141  15.226  32.935  1.00 25.00           C
ATOM     50  CA  SER    50     -23.517  12.725  30.216  1.00 25.00           C
ATOM     51  CA  LYS    51     -24.270   9.130  29.071  1.00 25.00           C
ATOM     52  CA  LYS    52     -23.360   6.349  31.499  1.00 25.00           C
ATOM     53  CA  GLU    53     -24.093   3.676  34.105  1.00 25.00           C
ATOM     54  CA  ILE    54     -23.559   2.794  37.707  1.00 25.00           C
ATOM     55  CA  SER    55     -23.123   4.015  41.264  1.00 25.00           C
ATOM     56  CA  VAL    56     -20.666   6.543  42.764  1.00 25.00           C
ATOM     57  CA  ALA    57     -18.376   8.598  45.029  1.00 25.00           C
ATOM     58  CA  ILE    58     -19.991   9.239  48.477  1.00 25.00           C
ATOM     59  CA  LYS    59     -18.426  10.037  51.860  1.00 25.00           C
ATOM     60  CA  THR    60     -21.444   8.818  53.831  1.00 25.00           C
ATOM     61  CA  LEU    61     -20.966  10.965  56.908  1.00 25.00           C
ATOM     62  CA  LYS    62     -24.544  10.512  58.161  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.546   8.849  59.768  1.00 25.00           C
ATOM     64  CA  GLY    64     -26.989  10.297  63.259  1.00 25.00           C
ATOM     65  CA  TYR    65     -25.835  13.842  64.229  1.00 25.00           C
ATOM     66  CA  THR    66     -26.856  17.471  63.508  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.161  20.536  61.998  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.852  20.689  63.919  1.00 25.00           C
ATOM     69  CA  GLN    69     -20.816  17.306  62.452  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.676  18.542  58.930  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.603  21.710  59.509  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.653  19.588  60.719  1.00 25.00           C
ATOM     73  CA  PHE    73     -16.940  17.370  57.609  1.00 25.00           C
ATOM     74  CA  LEU    74     -16.980  20.476  55.369  1.00 25.00           C
ATOM     75  CA  GLY    75     -13.869  21.829  57.146  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.100  18.467  56.659  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.015  18.496  52.940  1.00 25.00           C
ATOM     78  CA  SER    78     -11.656  22.062  52.608  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.402  21.007  54.332  1.00 25.00           C
ATOM     80  CA  MET    80      -8.081  18.023  51.954  1.00 25.00           C
ATOM     81  CA  GLY    81      -8.636  20.327  48.946  1.00 25.00           C
ATOM     82  CA  GLN    82      -5.954  22.725  50.257  1.00 25.00           C
ATOM     83  CA  PHE    83      -2.883  21.239  48.490  1.00 25.00           C
ATOM     84  CA  ASP    84      -3.812  19.875  45.062  1.00 25.00           C
ATOM     85  CA  HIS    85      -0.484  18.034  44.834  1.00 25.00           C
ATOM     86  CA  PRO    86       0.542  15.211  42.547  1.00 25.00           C
ATOM     87  CA  ASN    87       0.843  11.742  43.975  1.00 25.00           C
ATOM     88  CA  ILE    88      -2.312  12.841  45.765  1.00 25.00           C
ATOM     89  CA  ILE    89      -5.994  12.050  45.578  1.00 25.00           C
ATOM     90  CA  ARG    90      -8.431  15.021  45.479  1.00 25.00           C
ATOM     91  CA  LEU    91     -12.057  16.117  44.859  1.00 25.00           C
ATOM     92  CA  GLU    92     -14.311  15.650  41.830  1.00 25.00           C
ATOM     93  CA  GLY    93     -17.449  16.280  43.937  1.00 25.00           C
ATOM     94  CA  VAL    94     -20.343  17.546  46.068  1.00 25.00           C
ATOM     95  CA  VAL    95     -23.874  17.333  47.386  1.00 25.00           C
ATOM     96  CA  THR    96     -25.583  20.131  49.411  1.00 25.00           C
ATOM     97  CA  LYS    97     -28.975  19.181  50.830  1.00 25.00           C
ATOM     98  CA  SER    98     -29.258  16.298  53.300  1.00 25.00           C
ATOM     99  CA  LYS    99     -29.192  13.247  50.944  1.00 25.00           C
ATOM    100  CA  PRO   100     -25.845  12.496  52.601  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.350  15.292  52.062  1.00 25.00           C
ATOM    102  CA  MET   102     -20.951  13.806  49.531  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.442  14.851  50.516  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.452  13.178  47.770  1.00 25.00           C
ATOM    105  CA  THR   105     -13.153  10.744  45.946  1.00 25.00           C
ATOM    106  CA  GLU   106     -10.839   9.720  43.143  1.00 25.00           C
ATOM    107  CA  TYR   107     -10.160   6.277  41.554  1.00 25.00           C
ATOM    108  CA  MET   108      -9.237   5.193  45.067  1.00 25.00           C
TER
END
