
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0283TS383_2-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS383_2-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    S       2      E       5          0.809
LGA    F       3      K       6          2.224
LGA    I       4      M       7          1.985
LGA    E       5      I       8          1.109
LGA    K       6      G       9          1.365
LGA    M       7      S      10          1.568
LGA    I       8      L      11          1.564
LGA    G       9      N      12          1.937
LGA    -       -      D      13           -
LGA    S      10      K      14          1.158
LGA    L      11      R      15          2.912
LGA    N      12      E      16          3.216
LGA    D      13      W      17          1.861
LGA    K      14      K      18          2.587
LGA    R      15      A      19          3.901
LGA    E      16      M      20          3.207
LGA    W      17      E      21          1.974
LGA    K      18      A      22          3.783
LGA    A      19      R      23          4.959
LGA    M      20      A      24          3.216
LGA    E      21      K      25          1.679
LGA    A      22      A      26          4.276
LGA    R      23      L      27          4.493
LGA    A      24      P      28          3.168
LGA    K      25      -       -           -
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      K      29          4.635
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    K      29      H      33          4.365
LGA    E      30      A      34           -
LGA    Y      31      Y      35           -
LGA    H      32      -       -           -
LGA    H      33      -       -           -
LGA    A      34      -       -           -
LGA    Y      35      K      36          3.413
LGA    K      36      -       -           -
LGA    A      37      A      37          3.602
LGA    I      38      I      38          2.990
LGA    Q      39      Q      39          1.453
LGA    K      40      K      40           #
LGA    Y      41      Y      41           #
LGA    T      44      M      42          2.643
LGA    S      45      W      43          2.260
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    G      46      G      47          3.644
LGA    G      47      P      48           #
LGA    P      48      T      49           #
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      -       -           -
LGA    F      58      -       -           -
LGA    G      59      -       -           -
LGA    G      60      D      50          1.378
LGA    I      61      W      51          1.475
LGA    L      62      Q      52          1.651
LGA    D      63      D      53          1.412
LGA    L      64      T      54          1.455
LGA    F      65      K      55          1.869
LGA    E      66      R      56          2.007
LGA    E      67      I      57          1.496
LGA    G      68      F      58          2.413
LGA    A      69      G      59          3.709
LGA    A      70      G      60          2.989
LGA    E      71      I      61          2.058
LGA    G      72      L      62          3.118
LGA    K      73      D      63          3.579
LGA    K      74      L      64          2.375
LGA    V      75      F      65          2.058
LGA    T      76      E      66          3.436
LGA    D      77      E      67          3.323
LGA    L      78      G      68          1.681
LGA    T      79      A      69          3.057
LGA    G      80      A      70          4.121
LGA    E      81      E      71          3.012
LGA    D      82      G      72           #
LGA    V      83      K      73           -
LGA    A      84      K      74           -
LGA    A      85      V      75           -
LGA    F      86      T      76           -
LGA    C      87      D      77           -
LGA    D      88      L      78           -
LGA    E      89      T      79           -
LGA    L      90      G      80           -
LGA    M      91      E      81           -
LGA    K      92      D      82           -
LGA    D      93      V      83           -
LGA    T      94      A      84           -
LGA    K      95      A      85           -
LGA    T      96      F      86           -
LGA    W      97      C      87           -
LGA    -       -      D      88           -
LGA    -       -      E      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      K      92           -
LGA    -       -      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    -       -      T      96           -
LGA    -       -      W      97           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   97    5.0     54    2.82    14.81     39.450     1.848

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.436423 * X  +  -0.626604 * Y  +   0.645680 * Z  +   7.436104
  Y_new =   0.646371 * X  +  -0.280861 * Y  +  -0.709452 * Z  +  61.563503
  Z_new =   0.625891 * X  +   0.726970 * Y  +   0.282444 * Z  + -61.644943 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.200223   -1.941370  [ DEG:    68.7677   -111.2323 ]
  Theta =  -0.676274   -2.465319  [ DEG:   -38.7476   -141.2524 ]
  Phi   =   0.976917   -2.164676  [ DEG:    55.9732   -124.0268 ]
 
# 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: T0283TS383_2-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS383_2-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   97   5.0   54   2.82   14.81  39.450
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS383_2-D1
PFRMAT TS
TARGET T0283
MODEL 2
PARENT 1n1qA
ATOM      1  CA  SER     2      24.767   8.464  16.976  1.00  0.00
ATOM      2  CA  PHE     3      25.129  12.099  15.811  1.00  0.00
ATOM      3  CA  ILE     4      28.758  11.694  14.665  1.00  0.00
ATOM      4  CA  GLU     5      27.311   9.024  12.429  1.00  0.00
ATOM      5  CA  LYS     6      24.196  10.824  11.224  1.00  0.00
ATOM      6  CA  MET     7      26.173  13.863  10.032  1.00  0.00
ATOM      7  CA  ILE     8      28.496  11.660   7.935  1.00  0.00
ATOM      8  CA  GLY     9      25.379  10.117   6.396  1.00  0.00
ATOM      9  CA  SER    10      27.769  15.246   4.097  1.00  0.00
ATOM     10  CA  LEU    11      27.999  12.176   1.841  1.00  0.00
ATOM     11  CA  ASN    12      24.576  13.202   0.597  1.00  0.00
ATOM     12  CA  ASP    13      25.608  16.831   0.031  1.00  0.00
ATOM     13  CA  LYS    14      28.605  15.620  -1.949  1.00  0.00
ATOM     14  CA  ARG    15      26.200  13.721  -4.226  1.00  0.00
ATOM     15  CA  GLU    16      23.792  16.650  -4.468  1.00  0.00
ATOM     16  CA  TRP    17      26.717  18.931  -5.284  1.00  0.00
ATOM     17  CA  LYS    18      27.661  16.665  -8.189  1.00  0.00
ATOM     18  CA  ALA    19      23.785  15.347  -9.738  1.00  0.00
ATOM     19  CA  MET    20      22.943  19.065  -9.608  1.00  0.00
ATOM     20  CA  GLU    21      26.118  20.136 -11.417  1.00  0.00
ATOM     21  CA  ALA    22      25.683  17.466 -14.070  1.00  0.00
ATOM     22  CA  ARG    23      22.067  18.457 -14.633  1.00  0.00
ATOM     23  CA  ALA    24      23.394  21.990 -15.247  1.00  0.00
ATOM     24  CA  LYS    25      25.750  20.565 -17.861  1.00  0.00
ATOM     25  CA  ALA    26      22.916  18.493 -19.348  1.00  0.00
ATOM     26  CA  LEU    27      20.900  21.636 -20.060  1.00  0.00
ATOM     27  CA  PRO    28      28.245  24.453 -12.893  1.00  0.00
ATOM     28  CA  LYS    29      29.555  26.449  -9.986  1.00  0.00
ATOM     29  CA  GLU    30      32.851  24.757  -9.294  1.00  0.00
ATOM     30  CA  TYR    31      35.000  26.805  -6.913  1.00  0.00
ATOM     31  CA  HIS    32      34.680  27.493  -3.203  1.00  0.00
ATOM     32  CA  HIS    33      34.761  31.226  -3.878  1.00  0.00
ATOM     33  CA  ALA    34      31.734  31.070  -6.185  1.00  0.00
ATOM     34  CA  TYR    35      29.946  28.654  -3.842  1.00  0.00
ATOM     35  CA  LYS    36      30.346  31.009  -0.890  1.00  0.00
ATOM     36  CA  ALA    37      29.233  33.881  -3.089  1.00  0.00
ATOM     37  CA  ILE    38      26.016  32.259  -4.319  1.00  0.00
ATOM     38  CA  GLN    39      25.012  30.047  -1.381  1.00  0.00
ATOM     39  CA  LYS    40      22.149  31.135   0.874  1.00  0.00
ATOM     40  CA  TYR    41      23.404  28.675   3.479  1.00  0.00
ATOM     41  CA  THR    44      25.119  30.610   5.792  1.00  0.00
ATOM     42  CA  SER    45      26.348  31.042   6.429  1.00  0.00
ATOM     43  CA  GLY    46      25.757  30.084   6.199  1.00  0.00
ATOM     44  CA  GLY    47      28.871  28.250   7.439  1.00  0.00
ATOM     45  CA  PRO    48      29.124  26.809  10.939  1.00  0.00
ATOM     46  CA  THR    49      30.231  29.100  13.771  1.00  0.00
ATOM     47  CA  ASP    50      32.511  26.500  15.309  1.00  0.00
ATOM     48  CA  TRP    51      30.887  26.670  18.728  1.00  0.00
ATOM     49  CA  GLN    52      27.549  24.914  18.157  1.00  0.00
ATOM     50  CA  ASP    53      26.389  22.502  20.848  1.00  0.00
ATOM     51  CA  THR    54      25.087  19.106  19.695  1.00  0.00
ATOM     52  CA  LYS    55      21.492  20.333  19.882  1.00  0.00
ATOM     53  CA  ARG    56      22.330  23.553  18.046  1.00  0.00
ATOM     54  CA  ILE    57      23.948  21.491  15.278  1.00  0.00
ATOM     55  CA  PHE    58      20.770  19.453  14.780  1.00  0.00
ATOM     56  CA  GLY    59      18.694  22.616  15.048  1.00  0.00
ATOM     57  CA  GLY    60      20.978  24.273  12.485  1.00  0.00
ATOM     58  CA  ILE    61      20.491  21.436   9.988  1.00  0.00
ATOM     59  CA  LEU    62      16.747  21.697  10.539  1.00  0.00
ATOM     60  CA  ASP    63      16.886  25.436   9.788  1.00  0.00
ATOM     61  CA  LEU    64      19.034  24.922   6.685  1.00  0.00
ATOM     62  CA  PHE    65      16.935  22.068   5.303  1.00  0.00
ATOM     63  CA  GLU    66      13.775  24.082   5.920  1.00  0.00
ATOM     64  CA  GLU    67      15.293  26.997   3.999  1.00  0.00
ATOM     65  CA  GLY    68      16.295  24.676   1.139  1.00  0.00
ATOM     66  CA  ALA    69      12.800  23.173   0.952  1.00  0.00
ATOM     67  CA  ALA    70      11.449  26.665   0.375  1.00  0.00
ATOM     68  CA  GLU    71      14.080  27.427  -2.255  1.00  0.00
ATOM     69  CA  GLY    72      13.507  24.071  -3.939  1.00  0.00
ATOM     70  CA  LYS    73       9.794  24.832  -4.298  1.00  0.00
ATOM     71  CA  LYS    74      10.600  28.146  -5.991  1.00  0.00
ATOM     72  CA  VAL    75      13.220  26.603  -8.293  1.00  0.00
ATOM     73  CA  THR    76      10.882  23.787  -9.318  1.00  0.00
ATOM     74  CA  ASP    77       8.195  26.306 -10.235  1.00  0.00
ATOM     75  CA  LEU    78      10.675  28.184 -12.392  1.00  0.00
ATOM     76  CA  THR    79      11.863  24.959 -14.014  1.00  0.00
ATOM     77  CA  GLY    80       8.269  23.905 -14.657  1.00  0.00
ATOM     78  CA  GLU    81       7.550  27.262 -16.299  1.00  0.00
ATOM     79  CA  ASP    82      12.131  21.748 -17.837  1.00  0.00
ATOM     80  CA  VAL    83      15.080  19.553 -13.627  1.00  0.00
ATOM     81  CA  ALA    84      11.938  20.022 -11.538  1.00  0.00
ATOM     82  CA  ALA    85      11.812  16.285 -10.854  1.00  0.00
ATOM     83  CA  PHE    86      15.425  16.093  -9.648  1.00  0.00
ATOM     84  CA  CYS    87      14.865  19.071  -7.359  1.00  0.00
ATOM     85  CA  ASP    88      11.690  17.405  -6.080  1.00  0.00
ATOM     86  CA  GLU    89      13.622  14.252  -5.132  1.00  0.00
ATOM     87  CA  LEU    90      16.065  16.322  -3.042  1.00  0.00
ATOM     88  CA  MET    91      13.134  18.190  -1.477  1.00  0.00
ATOM     89  CA  LYS    92      11.260  15.026  -0.499  1.00  0.00
ATOM     90  CA  ASP    93      14.386  13.695   1.190  1.00  0.00
ATOM     91  CA  THR    94      14.925  16.894   3.171  1.00  0.00
ATOM     92  CA  LYS    95      11.330  16.947   4.381  1.00  0.00
ATOM     93  CA  THR    96      11.803  13.433   5.750  1.00  0.00
ATOM     94  CA  TRP    97      15.083  14.380   7.442  1.00  0.00
TER
END
