
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS168_4-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          1.247
LGA    F       3      F       3          0.759
LGA    I       4      I       4          0.931
LGA    E       5      E       5          0.696
LGA    K       6      K       6          0.401
LGA    M       7      M       7          0.583
LGA    I       8      I       8          0.863
LGA    G       9      G       9          0.660
LGA    S      10      S      10          0.488
LGA    L      11      L      11          0.556
LGA    N      12      N      12          0.892
LGA    D      13      D      13          0.937
LGA    K      14      K      14          0.459
LGA    R      15      R      15          0.508
LGA    E      16      E      16          1.185
LGA    W      17      W      17          1.033
LGA    K      18      K      18          0.379
LGA    A      19      A      19          0.782
LGA    M      20      M      20          1.187
LGA    E      21      E      21          0.877
LGA    A      22      A      22          0.429
LGA    R      23      R      23          0.799
LGA    A      24      A      24          1.078
LGA    K      25      K      25          0.615
LGA    A      26      A      26          0.259
LGA    L      27      L      27          4.764
LGA    P      28      P      28           -
LGA    K      29      K      29           -
LGA    E      30      E      30           -
LGA    Y      31      Y      31           -
LGA    H      32      H      32           -
LGA    H      33      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    -       -      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    A      34      G      59          4.893
LGA    -       -      G      60           -
LGA    -       -      I      61           -
LGA    Y      35      L      62           #
LGA    K      36      D      63           #
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    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      L      64          1.724
LGA    F      58      F      65          4.343
LGA    G      59      E      66          3.487
LGA    G      60      E      67           #
LGA    I      61      G      68           #
LGA    L      62      -       -           -
LGA    D      63      A      69          4.145
LGA    L      64      A      70           -
LGA    F      65      E      71           -
LGA    E      66      G      72           -
LGA    E      67      K      73           -
LGA    G      68      -       -           -
LGA    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      -       -           -
LGA    G      72      -       -           -
LGA    K      73      -       -           -
LGA    K      74      K      74          3.024
LGA    V      75      V      75          2.008
LGA    T      76      -       -           -
LGA    D      77      -       -           -
LGA    L      78      T      76          2.003
LGA    T      79      D      77          2.511
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    D      82      -       -           -
LGA    V      83      L      78          4.995
LGA    A      84      T      79          2.555
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      D      82           -
LGA    -       -      V      83           -
LGA    A      85      A      84           #
LGA    F      86      A      85           #
LGA    C      87      F      86          3.700
LGA    D      88      C      87          2.280
LGA    E      89      D      88          2.803
LGA    L      90      E      89           #
LGA    M      91      L      90           #
LGA    K      92      -       -           -
LGA    D      93      M      91          4.464
LGA    T      94      K      92           -
LGA    K      95      D      93           -
LGA    -       -      T      94           -
LGA    -       -      K      95           -
LGA    T      96      T      96          4.480
LGA    W      97      W      97           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     42    2.37    71.43     34.231     1.703

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.660135 * X  +   0.606566 * Y  +   0.443057 * Z  +  19.182505
  Y_new =   0.655078 * X  +   0.753516 * Y  +  -0.055563 * Z  +  24.140202
  Z_new =  -0.367553 * X  +   0.253558 * Y  +  -0.894770 * Z  +  -0.322127 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.865455   -0.276138  [ DEG:   164.1785    -15.8215 ]
  Theta =   0.376377    2.765216  [ DEG:    21.5648    158.4352 ]
  Phi   =   2.360039   -0.781553  [ DEG:   135.2203    -44.7797 ]
 
# 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_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS168_4-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   2.37   71.43  34.231
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS168_4-D1
PFRMAT TS
TARGET T0283
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      23.834  12.192  24.014  1.00 25.00           C
ATOM      2  CA  SER     2      26.353  10.627  21.688  1.00 25.00           C
ATOM      3  CA  PHE     3      29.447   8.910  20.226  1.00 25.00           C
ATOM      4  CA  ILE     4      28.024   6.378  17.731  1.00 25.00           C
ATOM      5  CA  GLU     5      24.818   8.449  17.419  1.00 25.00           C
ATOM      6  CA  LYS     6      26.892  11.609  16.802  1.00 25.00           C
ATOM      7  CA  MET     7      28.915   9.787  14.109  1.00 25.00           C
ATOM      8  CA  ILE     8      25.676   8.607  12.440  1.00 25.00           C
ATOM      9  CA  GLY     9      24.316  12.186  12.493  1.00 25.00           C
ATOM     10  CA  SER    10      27.564  13.470  10.924  1.00 25.00           C
ATOM     11  CA  LEU    11      27.334  10.792   8.195  1.00 25.00           C
ATOM     12  CA  ASN    12      23.703  11.785   7.492  1.00 25.00           C
ATOM     13  CA  ASP    13      24.732  15.465   7.245  1.00 25.00           C
ATOM     14  CA  LYS    14      27.543  14.541   4.814  1.00 25.00           C
ATOM     15  CA  ARG    15      25.075  12.528   2.686  1.00 25.00           C
ATOM     16  CA  GLU    16      22.658  15.499   2.636  1.00 25.00           C
ATOM     17  CA  TRP    17      25.503  17.827   1.561  1.00 25.00           C
ATOM     18  CA  LYS    18      26.468  15.395  -1.235  1.00 25.00           C
ATOM     19  CA  ALA    19      22.826  15.258  -2.409  1.00 25.00           C
ATOM     20  CA  MET    20      22.661  19.085  -2.425  1.00 25.00           C
ATOM     21  CA  GLU    21      25.899  19.240  -4.466  1.00 25.00           C
ATOM     22  CA  ALA    22      24.476  16.706  -6.961  1.00 25.00           C
ATOM     23  CA  ARG    23      21.270  18.779  -7.274  1.00 25.00           C
ATOM     24  CA  ALA    24      23.345  21.939  -7.890  1.00 25.00           C
ATOM     25  CA  LYS    25      25.367  20.116 -10.583  1.00 25.00           C
ATOM     26  CA  ALA    26      22.128  18.936 -12.253  1.00 25.00           C
ATOM     27  CA  LEU    27      18.429  18.288 -11.678  1.00 25.00           C
ATOM     28  CA  PRO    28      16.927  15.212  -9.936  1.00 25.00           C
ATOM     29  CA  LYS    29      16.263  12.377  -7.468  1.00 25.00           C
ATOM     30  CA  GLU    30      17.449  13.672  -4.064  1.00 25.00           C
ATOM     31  CA  TYR    31      16.935  17.282  -5.232  1.00 25.00           C
ATOM     32  CA  HIS    32      13.405  16.416  -6.438  1.00 25.00           C
ATOM     33  CA  HIS    33      12.623  14.787  -3.061  1.00 25.00           C
ATOM     34  CA  ALA    34      13.902  17.902  -1.236  1.00 25.00           C
ATOM     35  CA  TYR    35      11.717  20.130  -3.456  1.00 25.00           C
ATOM     36  CA  LYS    36       8.676  17.923  -2.719  1.00 25.00           C
ATOM     37  CA  ALA    37       9.395  18.143   1.037  1.00 25.00           C
ATOM     38  CA  ILE    38       9.665  21.955   0.786  1.00 25.00           C
ATOM     39  CA  GLN    39       6.329  22.093  -1.091  1.00 25.00           C
ATOM     40  CA  LYS    40       4.696  19.915   1.603  1.00 25.00           C
ATOM     41  CA  TYR    41       6.077  22.215   4.335  1.00 25.00           C
ATOM     42  CA  MET    42       4.709  25.276   2.484  1.00 25.00           C
ATOM     43  CA  TRP    43       1.281  23.594   2.186  1.00 25.00           C
ATOM     44  CA  THR    44       1.318  22.799   5.931  1.00 25.00           C
ATOM     45  CA  SER    45       2.262  26.371   6.828  1.00 25.00           C
ATOM     46  CA  GLY    46       1.435  28.789   4.075  1.00 25.00           C
ATOM     47  CA  GLY    47      -0.096  29.199   0.658  1.00 25.00           C
ATOM     48  CA  PRO    48       2.041  27.548  -2.024  1.00 25.00           C
ATOM     49  CA  THR    49       0.183  26.279  -5.093  1.00 25.00           C
ATOM     50  CA  ASP    50       1.513  22.808  -4.554  1.00 25.00           C
ATOM     51  CA  TRP    51       2.955  20.409  -7.191  1.00 25.00           C
ATOM     52  CA  GLN    52       3.111  23.545  -9.384  1.00 25.00           C
ATOM     53  CA  ASP    53       5.261  25.309  -6.753  1.00 25.00           C
ATOM     54  CA  THR    54       7.611  22.288  -6.611  1.00 25.00           C
ATOM     55  CA  LYS    55       7.896  22.299 -10.430  1.00 25.00           C
ATOM     56  CA  ARG    56       8.699  26.045 -10.383  1.00 25.00           C
ATOM     57  CA  ILE    57      11.386  25.459  -7.718  1.00 25.00           C
ATOM     58  CA  PHE    58      12.902  22.646  -9.828  1.00 25.00           C
ATOM     59  CA  GLY    59      12.940  24.935 -12.899  1.00 25.00           C
ATOM     60  CA  GLY    60      14.663  27.681 -10.859  1.00 25.00           C
ATOM     61  CA  ILE    61      17.279  25.165  -9.635  1.00 25.00           C
ATOM     62  CA  LEU    62      17.899  24.020 -13.237  1.00 25.00           C
ATOM     63  CA  ASP    63      18.320  27.661 -14.348  1.00 25.00           C
ATOM     64  CA  LEU    64      20.805  28.268 -11.499  1.00 25.00           C
ATOM     65  CA  PHE    65      22.772  25.144 -12.514  1.00 25.00           C
ATOM     66  CA  GLU    66      22.856  26.348 -16.149  1.00 25.00           C
ATOM     67  CA  GLU    67      24.111  29.782 -15.008  1.00 25.00           C
ATOM     68  CA  GLY    68      26.844  28.112 -12.908  1.00 25.00           C
ATOM     69  CA  ALA    69      27.891  25.986 -15.916  1.00 25.00           C
ATOM     70  CA  ALA    70      28.046  29.122 -18.110  1.00 25.00           C
ATOM     71  CA  GLU    71      25.369  30.890 -20.201  1.00 25.00           C
ATOM     72  CA  GLY    72      21.814  32.301 -20.613  1.00 25.00           C
ATOM     73  CA  LYS    73      20.330  32.886 -17.191  1.00 25.00           C
ATOM     74  CA  LYS    74      17.960  34.919 -14.922  1.00 25.00           C
ATOM     75  CA  VAL    75      18.428  33.865 -11.263  1.00 25.00           C
ATOM     76  CA  THR    76      19.125  35.442  -7.843  1.00 25.00           C
ATOM     77  CA  ASP    77      17.952  38.846  -9.147  1.00 25.00           C
ATOM     78  CA  LEU    78      14.750  37.249 -10.513  1.00 25.00           C
ATOM     79  CA  THR    79      11.206  36.045 -10.704  1.00 25.00           C
ATOM     80  CA  GLY    80       7.758  37.129  -9.389  1.00 25.00           C
ATOM     81  CA  GLU    81       8.636  39.747  -6.734  1.00 25.00           C
ATOM     82  CA  ASP    82       7.456  37.375  -3.969  1.00 25.00           C
ATOM     83  CA  VAL    83       9.589  34.556  -5.443  1.00 25.00           C
ATOM     84  CA  ALA    84      12.630  36.883  -5.556  1.00 25.00           C
ATOM     85  CA  ALA    85      12.042  37.869  -1.903  1.00 25.00           C
ATOM     86  CA  PHE    86      11.808  34.175  -0.918  1.00 25.00           C
ATOM     87  CA  CYS    87      15.078  33.448  -2.774  1.00 25.00           C
ATOM     88  CA  ASP    88      16.778  36.369  -0.974  1.00 25.00           C
ATOM     89  CA  GLU    89      15.518  35.057   2.397  1.00 25.00           C
ATOM     90  CA  LEU    90      16.857  31.567   1.567  1.00 25.00           C
ATOM     91  CA  MET    91      20.252  33.066   0.625  1.00 25.00           C
ATOM     92  CA  LYS    92      20.336  35.012   3.923  1.00 25.00           C
ATOM     93  CA  ASP    93      19.513  31.813   5.859  1.00 25.00           C
ATOM     94  CA  THR    94      22.317  29.954   4.029  1.00 25.00           C
ATOM     95  CA  LYS    95      24.768  32.774   4.868  1.00 25.00           C
ATOM     96  CA  THR    96      23.714  32.629   8.547  1.00 25.00           C
ATOM     97  CA  TRP    97      24.231  28.834   8.570  1.00 25.00           C
TER
END
