
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0283TS168_3-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS168_3-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    S       2      S       2           -
LGA    F       3      F       3           -
LGA    I       4      I       4           -
LGA    E       5      E       5           -
LGA    K       6      K       6           -
LGA    M       7      M       7           -
LGA    I       8      I       8           -
LGA    G       9      -       -           -
LGA    S      10      -       -           -
LGA    L      11      -       -           -
LGA    N      12      -       -           -
LGA    D      13      -       -           -
LGA    K      14      -       -           -
LGA    R      15      -       -           -
LGA    E      16      -       -           -
LGA    W      17      -       -           -
LGA    K      18      -       -           -
LGA    A      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    A      22      -       -           -
LGA    R      23      -       -           -
LGA    A      24      -       -           -
LGA    K      25      -       -           -
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      -       -           -
LGA    K      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    H      32      -       -           -
LGA    H      33      -       -           -
LGA    A      34      -       -           -
LGA    Y      35      -       -           -
LGA    K      36      -       -           -
LGA    A      37      -       -           -
LGA    I      38      -       -           -
LGA    Q      39      -       -           -
LGA    K      40      G       9           #
LGA    -       -      S      10           -
LGA    Y      41      L      11           #
LGA    M      42      N      12          1.931
LGA    W      43      D      13           #
LGA    T      44      K      14          4.129
LGA    S      45      R      15          1.527
LGA    G      46      E      16          4.314
LGA    -       -      W      17           -
LGA    G      47      K      18           #
LGA    P      48      A      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      A      22           -
LGA    -       -      R      23           -
LGA    -       -      A      24           -
LGA    -       -      K      25           -
LGA    -       -      A      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      K      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    T      49      D      50          3.954
LGA    D      50      W      51          3.391
LGA    -       -      Q      52           -
LGA    W      51      D      53          0.850
LGA    Q      52      T      54          1.681
LGA    D      53      K      55          2.014
LGA    T      54      R      56          1.300
LGA    K      55      I      57          0.896
LGA    R      56      F      58          0.838
LGA    I      57      G      59          0.750
LGA    F      58      G      60          0.739
LGA    G      59      I      61          0.790
LGA    G      60      L      62          0.875
LGA    I      61      D      63          0.856
LGA    L      62      L      64          0.834
LGA    D      63      F      65          0.786
LGA    L      64      E      66          0.483
LGA    F      65      E      67          0.676
LGA    E      66      G      68          0.448
LGA    E      67      A      69          1.219
LGA    G      68      A      70          1.685
LGA    A      69      E      71          1.634
LGA    A      70      G      72          1.753
LGA    E      71      K      73          2.118
LGA    G      72      K      74          1.966
LGA    K      73      V      75          2.459
LGA    K      74      T      76          4.522
LGA    -       -      D      77           -
LGA    V      75      L      78          3.874
LGA    T      76      T      79          1.941
LGA    D      77      G      80          3.583
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    L      78      V      83          1.949
LGA    T      79      A      84          2.734
LGA    G      80      A      85           -
LGA    E      81      F      86           -
LGA    D      82      C      87          4.031
LGA    V      83      D      88          3.346
LGA    A      84      -       -           -
LGA    A      85      -       -           -
LGA    F      86      E      89          1.666
LGA    C      87      L      90          2.086
LGA    D      88      M      91          3.442
LGA    E      89      K      92          2.692
LGA    L      90      -       -           -
LGA    M      91      -       -           -
LGA    K      92      D      93          4.686
LGA    D      93      T      94           -
LGA    T      94      K      95           -
LGA    K      95      T      96           -
LGA    T      96      W      97           -
LGA    W      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     42    2.43     4.76     33.637     1.658

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.186654 * X  +  -0.307864 * Y  +   0.932942 * Z  +   7.518635
  Y_new =  -0.517367 * X  +   0.776477 * Y  +   0.359742 * Z  +  24.191866
  Z_new =  -0.835160 * X  +  -0.549820 * Y  +  -0.014346 * Z  +   4.207369 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.596882    1.544710  [ DEG:   -91.4946     88.5054 ]
  Theta =   0.988423    2.153170  [ DEG:    56.6325    123.3675 ]
  Phi   =  -1.224553    1.917040  [ DEG:   -70.1617    109.8383 ]
 
# 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: T0283TS168_3-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS168_3-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   42   2.43    4.76  33.637
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS168_3-D1
PFRMAT TS
TARGET T0283
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -0.141  10.641  21.146  1.00 25.00           C
ATOM      2  CA  SER     2      -3.321   8.792  20.165  1.00 25.00           C
ATOM      3  CA  PHE     3      -6.191   6.332  19.492  1.00 25.00           C
ATOM      4  CA  ILE     4      -4.824   4.792  16.263  1.00 25.00           C
ATOM      5  CA  GLU     5      -7.703   6.350  14.273  1.00 25.00           C
ATOM      6  CA  LYS     6      -6.990   9.760  15.865  1.00 25.00           C
ATOM      7  CA  MET     7      -3.281   9.428  14.973  1.00 25.00           C
ATOM      8  CA  ILE     8      -4.204   8.544  11.361  1.00 25.00           C
ATOM      9  CA  GLY     9      -6.514  11.592  11.180  1.00 25.00           C
ATOM     10  CA  SER    10      -3.710  13.829  12.525  1.00 25.00           C
ATOM     11  CA  LEU    11      -1.295  12.414   9.911  1.00 25.00           C
ATOM     12  CA  ASN    12      -3.859  13.080   7.145  1.00 25.00           C
ATOM     13  CA  ASP    13      -4.305  16.674   8.391  1.00 25.00           C
ATOM     14  CA  LYS    14      -0.507  17.170   8.395  1.00 25.00           C
ATOM     15  CA  ARG    15      -0.301  15.815   4.820  1.00 25.00           C
ATOM     16  CA  GLU    16      -3.092  18.199   3.728  1.00 25.00           C
ATOM     17  CA  TRP    17      -1.250  21.137   5.354  1.00 25.00           C
ATOM     18  CA  LYS    18       1.980  20.142   3.553  1.00 25.00           C
ATOM     19  CA  ALA    19       0.095  19.960   0.223  1.00 25.00           C
ATOM     20  CA  MET    20      -1.401  23.429   0.853  1.00 25.00           C
ATOM     21  CA  GLU    21       2.081  24.817   1.634  1.00 25.00           C
ATOM     22  CA  ALA    22       3.447  23.276  -1.595  1.00 25.00           C
ATOM     23  CA  ARG    23       0.568  24.835  -3.584  1.00 25.00           C
ATOM     24  CA  ALA    24       1.282  28.244  -1.992  1.00 25.00           C
ATOM     25  CA  LYS    25       4.991  27.912  -2.886  1.00 25.00           C
ATOM     26  CA  ALA    26       4.068  27.029  -6.496  1.00 25.00           C
ATOM     27  CA  LEU    27       6.215  23.917  -5.717  1.00 25.00           C
ATOM     28  CA  PRO    28       7.037  20.497  -4.167  1.00 25.00           C
ATOM     29  CA  LYS    29       5.805  19.194  -0.780  1.00 25.00           C
ATOM     30  CA  GLU    30       8.530  21.551   0.519  1.00 25.00           C
ATOM     31  CA  TYR    31       8.415  19.836   3.942  1.00 25.00           C
ATOM     32  CA  HIS    32       8.724  16.409   2.262  1.00 25.00           C
ATOM     33  CA  HIS    33      11.726  17.647   0.231  1.00 25.00           C
ATOM     34  CA  ALA    34      13.368  18.978   3.425  1.00 25.00           C
ATOM     35  CA  TYR    35      12.791  15.611   5.155  1.00 25.00           C
ATOM     36  CA  LYS    36      14.343  13.783   2.170  1.00 25.00           C
ATOM     37  CA  ALA    37      17.376  16.118   2.285  1.00 25.00           C
ATOM     38  CA  ILE    38      17.764  15.468   6.039  1.00 25.00           C
ATOM     39  CA  GLN    39      17.590  11.692   5.429  1.00 25.00           C
ATOM     40  CA  LYS    40      20.257  11.986   2.694  1.00 25.00           C
ATOM     41  CA  TYR    41      22.499  13.994   5.064  1.00 25.00           C
ATOM     42  CA  MET    42      22.048  11.335   7.783  1.00 25.00           C
ATOM     43  CA  TRP    43      22.957   8.584   5.279  1.00 25.00           C
ATOM     44  CA  THR    44      26.086  10.532   4.237  1.00 25.00           C
ATOM     45  CA  SER    45      25.206  12.339   1.033  1.00 25.00           C
ATOM     46  CA  GLY    46      26.181  15.958   1.714  1.00 25.00           C
ATOM     47  CA  GLY    47      26.468  18.401   4.648  1.00 25.00           C
ATOM     48  CA  PRO    48      25.558  21.832   6.000  1.00 25.00           C
ATOM     49  CA  THR    49      22.889  22.182   8.739  1.00 25.00           C
ATOM     50  CA  ASP    50      20.453  23.877  11.140  1.00 25.00           C
ATOM     51  CA  TRP    51      17.872  25.281   8.729  1.00 25.00           C
ATOM     52  CA  GLN    52      20.639  26.027   6.189  1.00 25.00           C
ATOM     53  CA  ASP    53      20.120  22.591   4.578  1.00 25.00           C
ATOM     54  CA  THR    54      16.350  23.232   4.367  1.00 25.00           C
ATOM     55  CA  LYS    55      16.996  26.640   2.741  1.00 25.00           C
ATOM     56  CA  ARG    56      19.358  25.009   0.206  1.00 25.00           C
ATOM     57  CA  ILE    57      16.709  22.363  -0.598  1.00 25.00           C
ATOM     58  CA  PHE    58      14.084  25.106  -1.094  1.00 25.00           C
ATOM     59  CA  GLY    59      16.462  26.994  -3.429  1.00 25.00           C
ATOM     60  CA  GLY    60      17.078  23.789  -5.433  1.00 25.00           C
ATOM     61  CA  ILE    61      13.303  23.208  -5.713  1.00 25.00           C
ATOM     62  CA  LEU    62      12.815  26.809  -6.922  1.00 25.00           C
ATOM     63  CA  ASP    63      15.576  26.334  -9.533  1.00 25.00           C
ATOM     64  CA  LEU    64      13.923  23.093 -10.727  1.00 25.00           C
ATOM     65  CA  PHE    65      10.552  24.888 -11.013  1.00 25.00           C
ATOM     66  CA  GLU    66      12.193  27.700 -13.029  1.00 25.00           C
ATOM     67  CA  GLU    67      13.811  25.122 -15.354  1.00 25.00           C
ATOM     68  CA  GLY    68      10.425  23.399 -15.840  1.00 25.00           C
ATOM     69  CA  ALA    69       8.800  26.770 -16.657  1.00 25.00           C
ATOM     70  CA  ALA    70      11.568  27.516 -19.198  1.00 25.00           C
ATOM     71  CA  GLU    71      14.272  29.727 -17.815  1.00 25.00           C
ATOM     72  CA  GLY    72      16.924  31.203 -15.585  1.00 25.00           C
ATOM     73  CA  LYS    73      18.398  30.543 -12.138  1.00 25.00           C
ATOM     74  CA  LYS    74      17.038  32.389  -9.102  1.00 25.00           C
ATOM     75  CA  VAL    75      14.562  33.415  -6.471  1.00 25.00           C
ATOM     76  CA  THR    76      13.313  36.586  -8.219  1.00 25.00           C
ATOM     77  CA  ASP    77      13.396  38.482  -4.893  1.00 25.00           C
ATOM     78  CA  LEU    78      16.974  37.269  -4.263  1.00 25.00           C
ATOM     79  CA  THR    79      20.324  36.711  -2.458  1.00 25.00           C
ATOM     80  CA  GLY    80      21.781  34.266   0.104  1.00 25.00           C
ATOM     81  CA  GLU    81      21.808  35.515   3.725  1.00 25.00           C
ATOM     82  CA  ASP    82      19.233  38.209   2.841  1.00 25.00           C
ATOM     83  CA  VAL    83      17.016  35.574   1.163  1.00 25.00           C
ATOM     84  CA  ALA    84      17.275  33.345   4.267  1.00 25.00           C
ATOM     85  CA  ALA    85      16.317  36.304   6.503  1.00 25.00           C
ATOM     86  CA  PHE    86      13.306  37.055   4.259  1.00 25.00           C
ATOM     87  CA  CYS    87      12.225  33.386   4.439  1.00 25.00           C
ATOM     88  CA  ASP    88      12.527  33.459   8.256  1.00 25.00           C
ATOM     89  CA  GLU    89      10.418  36.653   8.387  1.00 25.00           C
ATOM     90  CA  LEU    90       7.764  35.021   6.161  1.00 25.00           C
ATOM     91  CA  MET    91       7.709  31.944   8.439  1.00 25.00           C
ATOM     92  CA  LYS    92       7.297  34.194  11.511  1.00 25.00           C
ATOM     93  CA  ASP    93       4.410  36.040   9.801  1.00 25.00           C
ATOM     94  CA  THR    94       2.739  32.698   8.961  1.00 25.00           C
ATOM     95  CA  LYS    95       3.122  31.563  12.598  1.00 25.00           C
ATOM     96  CA  THR    96       1.575  34.850  13.812  1.00 25.00           C
ATOM     97  CA  TRP    97      -1.355  34.394  11.389  1.00 25.00           C
TER
END
