
#######################################################
#                                                     #
#                        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  103 (  103),  selected  103 , name T0314TS168_5-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS168_5-D1.T0314_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    -       -      I       3           -
LGA    -       -      T       4           -
LGA    M       1      S       5          1.794
LGA    S       2      T       6          0.866
LGA    I       3      D       7          3.986
LGA    T       4      I       8          3.742
LGA    S       5      C       9           -
LGA    T       6      Q      10           #
LGA    D       7      A      11          3.241
LGA    I       8      A      12          3.688
LGA    C       9      D      13          3.201
LGA    Q      10      A      14          0.632
LGA    A      11      L      15          3.652
LGA    A      12      -       -           -
LGA    D      13      -       -           -
LGA    A      14      K      16          4.131
LGA    L      15      G      17           #
LGA    K      16      -       -           -
LGA    G      17      -       -           -
LGA    F      18      F      18           #
LGA    V      19      V      19           #
LGA    G      20      -       -           -
LGA    F      21      G      20          4.433
LGA    N      22      F      21          0.755
LGA    R      23      N      22          3.957
LGA    K      24      -       -           -
LGA    T      25      R      23           #
LGA    G      26      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    R      27      R      27           #
LGA    Y      28      Y      28          5.212
LGA    I      29      I      29           -
LGA    -       -      V      30           -
LGA    -       -      R      31           -
LGA    -       -      F      32           -
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      D      43           -
LGA    -       -      D      44           -
LGA    -       -      S      45           -
LGA    -       -      I      46           -
LGA    -       -      T      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    V      30      F      52          4.280
LGA    R      31      V      53          4.138
LGA    F      32      W      54          3.872
LGA    S      33      S      55          4.650
LGA    E      34      S      56          1.233
LGA    -       -      V      57           -
LGA    -       -      R      58           -
LGA    -       -      D      59           -
LGA    -       -      D      60           -
LGA    -       -      V      61           -
LGA    D      35      M      62          2.406
LGA    S      36      R      63          3.659
LGA    F      37      L      64          1.683
LGA    G      38      G      65          3.417
LGA    M      39      R      66          0.924
LGA    D      40      E      67          4.082
LGA    V      41      -       -           -
LGA    A      42      -       -           -
LGA    D      43      -       -           -
LGA    D      44      -       -           -
LGA    S      45      -       -           -
LGA    I      46      -       -           -
LGA    T      47      -       -           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    S      50      -       -           -
LGA    E      51      -       -           -
LGA    F      52      Q      68          2.802
LGA    V      53      L      69          3.487
LGA    W      54      Q      70          3.308
LGA    -       -      I      71           -
LGA    S      55      L      72          1.844
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    S      56      Q      75          2.236
LGA    V      57      N      76          1.505
LGA    R      58      I      77          3.490
LGA    D      59      N      78          3.336
LGA    D      60      E      79          4.780
LGA    V      61      R      80          4.166
LGA    M      62      L      81          3.823
LGA    R      63      N      82          4.507
LGA    L      64      -       -           -
LGA    G      65      I      83           #
LGA    R      66      G      84           -
LGA    E      67      E      85           -
LGA    Q      68      P      86           -
LGA    L      69      L      87           -
LGA    Q      70      L      88           -
LGA    I      71      V      89           -
LGA    L      72      Y      90           -
LGA    L      73      L      91           -
LGA    E      74      R      92           -
LGA    Q      75      R      93           -
LGA    N      76      Q      94           -
LGA    I      77      D      95           -
LGA    N      78      L      96           -
LGA    E      79      P      97           -
LGA    R      80      E      98           -
LGA    L      81      I      99           -
LGA    N      82      T     100           -
LGA    I      83      A     101           -
LGA    G      84      Q     102           -
LGA    E      85      -       -           -
LGA    P      86      -       -           -
LGA    L      87      -       -           -
LGA    L      88      -       -           -
LGA    V      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    R      92      -       -           -
LGA    R      93      -       -           -
LGA    Q      94      -       -           -
LGA    D      95      -       -           -
LGA    L      96      -       -           -
LGA    P      97      -       -           -
LGA    E      98      -       -           -
LGA    I      99      -       -           -
LGA    T     100      R     103           #
LGA    A     101      -       -           -
LGA    Q     102      -       -           -
LGA    R     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  103  103    5.0     37    3.40     8.11     19.263     1.058

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.392328 * X  +  -0.073857 * Y  +   0.916855 * Z  +  16.378962
  Y_new =   0.884181 * X  +  -0.305072 * Y  +   0.353772 * Z  +  13.192904
  Z_new =   0.253579 * X  +   0.949461 * Y  +   0.184992 * Z  + -12.533300 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.378369   -1.763224  [ DEG:    78.9747   -101.0253 ]
  Theta =  -0.256378   -2.885215  [ DEG:   -14.6894   -165.3106 ]
  Phi   =   1.988415   -1.153178  [ DEG:   113.9278    -66.0722 ]
 
# 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: T0314TS168_5-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS168_5-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  103  103   5.0   37   3.40    8.11  19.263
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS168_5-D1
PFRMAT TS
TARGET T0314
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       2.695  12.418  -3.788  1.00 25.00           C
ATOM      2  CA  SER     2       3.403  15.953  -4.943  1.00 25.00           C
ATOM      3  CA  ILE     3       6.763  15.590  -6.762  1.00 25.00           C
ATOM      4  CA  THR     4       7.885  14.117  -3.377  1.00 25.00           C
ATOM      5  CA  SER     5      10.647  12.597  -1.179  1.00 25.00           C
ATOM      6  CA  THR     6      14.086  10.918  -1.047  1.00 25.00           C
ATOM      7  CA  ASP     7      12.897   8.232  -3.504  1.00 25.00           C
ATOM      8  CA  ILE     8      11.571  10.941  -5.863  1.00 25.00           C
ATOM      9  CA  CYS     9      14.922  12.785  -5.668  1.00 25.00           C
ATOM     10  CA  GLN    10      16.785   9.534  -6.458  1.00 25.00           C
ATOM     11  CA  ALA    11      14.488   8.917  -9.460  1.00 25.00           C
ATOM     12  CA  ALA    12      15.123  12.482 -10.709  1.00 25.00           C
ATOM     13  CA  ASP    13      18.900  11.959 -10.355  1.00 25.00           C
ATOM     14  CA  ALA    14      18.654   8.675 -12.310  1.00 25.00           C
ATOM     15  CA  LEU    15      16.663  10.437 -15.066  1.00 25.00           C
ATOM     16  CA  LYS    16      18.106  13.835 -16.096  1.00 25.00           C
ATOM     17  CA  GLY    17      21.345  11.890 -16.306  1.00 25.00           C
ATOM     18  CA  PHE    18      20.634   8.943 -18.615  1.00 25.00           C
ATOM     19  CA  VAL    19      20.741   9.194 -22.434  1.00 25.00           C
ATOM     20  CA  GLY    20      22.145   5.858 -23.591  1.00 25.00           C
ATOM     21  CA  PHE    21      23.399   3.174 -26.035  1.00 25.00           C
ATOM     22  CA  ASN    22      22.813  -0.300 -24.567  1.00 25.00           C
ATOM     23  CA  ARG    23      26.230   0.295 -23.012  1.00 25.00           C
ATOM     24  CA  LYS    24      26.841  -2.723 -20.860  1.00 25.00           C
ATOM     25  CA  THR    25      23.759  -4.880 -21.045  1.00 25.00           C
ATOM     26  CA  GLY    26      22.082  -3.871 -17.781  1.00 25.00           C
ATOM     27  CA  ARG    27      18.761  -2.244 -18.679  1.00 25.00           C
ATOM     28  CA  TYR    28      16.358   0.246 -20.139  1.00 25.00           C
ATOM     29  CA  ILE    29      15.069   2.730 -22.778  1.00 25.00           C
ATOM     30  CA  VAL    30      16.933   5.295 -20.629  1.00 25.00           C
ATOM     31  CA  ARG    31      15.754   8.922 -20.122  1.00 25.00           C
ATOM     32  CA  PHE    32      13.580  11.571 -21.709  1.00 25.00           C
ATOM     33  CA  SER    33      15.281  14.787 -20.422  1.00 25.00           C
ATOM     34  CA  GLU    34      12.109  16.485 -21.752  1.00 25.00           C
ATOM     35  CA  ASP    35      10.283  15.184 -18.749  1.00 25.00           C
ATOM     36  CA  SER    36       9.034  11.584 -19.273  1.00 25.00           C
ATOM     37  CA  PHE    37       7.461  10.192 -16.103  1.00 25.00           C
ATOM     38  CA  GLY    38       4.593   8.019 -17.343  1.00 25.00           C
ATOM     39  CA  MET    39       6.887   5.078 -16.996  1.00 25.00           C
ATOM     40  CA  ASP    40       5.505   1.708 -15.966  1.00 25.00           C
ATOM     41  CA  VAL    41       5.981   0.847 -19.668  1.00 25.00           C
ATOM     42  CA  ALA    42       6.886  -1.144 -22.803  1.00 25.00           C
ATOM     43  CA  ASP    43       4.068  -2.029 -25.288  1.00 25.00           C
ATOM     44  CA  ASP    44       4.192  -0.142 -28.598  1.00 25.00           C
ATOM     45  CA  SER    45       6.769   2.466 -29.620  1.00 25.00           C
ATOM     46  CA  ILE    46       9.740   2.742 -27.296  1.00 25.00           C
ATOM     47  CA  THR    47      10.483   6.107 -28.941  1.00 25.00           C
ATOM     48  CA  PRO    48      12.431   9.345 -29.230  1.00 25.00           C
ATOM     49  CA  THR    49      13.946  12.013 -26.953  1.00 25.00           C
ATOM     50  CA  SER    50      15.848   9.064 -25.365  1.00 25.00           C
ATOM     51  CA  GLU    51      12.652   7.241 -24.269  1.00 25.00           C
ATOM     52  CA  PHE    52      11.349   5.735 -21.018  1.00 25.00           C
ATOM     53  CA  VAL    53      12.356   2.977 -18.538  1.00 25.00           C
ATOM     54  CA  TRP    54      12.831  -0.061 -16.299  1.00 25.00           C
ATOM     55  CA  SER    55      16.264  -0.213 -14.651  1.00 25.00           C
ATOM     56  CA  SER    56      16.430  -3.827 -13.572  1.00 25.00           C
ATOM     57  CA  VAL    57      16.269  -6.664 -11.105  1.00 25.00           C
ATOM     58  CA  ARG    58      14.235  -4.377  -8.803  1.00 25.00           C
ATOM     59  CA  ASP    59      16.923  -4.676  -6.092  1.00 25.00           C
ATOM     60  CA  ASP    60      19.636  -3.806  -8.650  1.00 25.00           C
ATOM     61  CA  VAL    61      17.619  -0.755  -9.788  1.00 25.00           C
ATOM     62  CA  MET    62      17.220   0.369  -6.149  1.00 25.00           C
ATOM     63  CA  ARG    63      20.989  -0.018  -5.590  1.00 25.00           C
ATOM     64  CA  LEU    64      21.692   2.046  -8.738  1.00 25.00           C
ATOM     65  CA  GLY    65      19.291   4.769  -7.519  1.00 25.00           C
ATOM     66  CA  ARG    66      21.035   4.814  -4.109  1.00 25.00           C
ATOM     67  CA  GLU    67      24.443   5.128  -5.827  1.00 25.00           C
ATOM     68  CA  GLN    68      23.129   8.029  -7.955  1.00 25.00           C
ATOM     69  CA  LEU    69      21.791   9.761  -4.812  1.00 25.00           C
ATOM     70  CA  GLN    70      25.182   9.313  -3.091  1.00 25.00           C
ATOM     71  CA  ILE    71      26.956  10.791  -6.146  1.00 25.00           C
ATOM     72  CA  LEU    72      24.562  13.779  -6.121  1.00 25.00           C
ATOM     73  CA  LEU    73      25.232  14.317  -2.389  1.00 25.00           C
ATOM     74  CA  GLU    74      29.006  14.195  -3.025  1.00 25.00           C
ATOM     75  CA  GLN    75      28.638  16.754  -5.851  1.00 25.00           C
ATOM     76  CA  ASN    76      26.604  19.040  -3.548  1.00 25.00           C
ATOM     77  CA  ILE    77      29.292  18.742  -0.837  1.00 25.00           C
ATOM     78  CA  ASN    78      32.006  19.612  -3.396  1.00 25.00           C
ATOM     79  CA  GLU    79      29.989  22.663  -4.534  1.00 25.00           C
ATOM     80  CA  ARG    80      29.588  23.787  -0.895  1.00 25.00           C
ATOM     81  CA  LEU    81      33.357  23.400  -0.335  1.00 25.00           C
ATOM     82  CA  ASN    82      33.621  26.086  -2.996  1.00 25.00           C
ATOM     83  CA  ILE    83      30.578  27.910  -4.274  1.00 25.00           C
ATOM     84  CA  GLY    84      30.025  29.755  -7.601  1.00 25.00           C
ATOM     85  CA  GLU    85      26.983  27.607  -8.529  1.00 25.00           C
ATOM     86  CA  PRO    86      24.829  27.351 -11.685  1.00 25.00           C
ATOM     87  CA  LEU    87      22.165  25.407  -9.737  1.00 25.00           C
ATOM     88  CA  LEU    88      22.192  28.074  -6.990  1.00 25.00           C
ATOM     89  CA  VAL    89      21.795  30.826  -9.623  1.00 25.00           C
ATOM     90  CA  TYR    90      18.854  28.938 -11.188  1.00 25.00           C
ATOM     91  CA  LEU    91      17.220  28.577  -7.743  1.00 25.00           C
ATOM     92  CA  ARG    92      17.677  32.326  -7.106  1.00 25.00           C
ATOM     93  CA  ARG    93      16.099  33.121 -10.504  1.00 25.00           C
ATOM     94  CA  GLN    94      15.984  36.912 -10.801  1.00 25.00           C
ATOM     95  CA  ASP    95      14.490  39.020  -7.971  1.00 25.00           C
ATOM     96  CA  LEU    96      13.485  35.769  -6.258  1.00 25.00           C
ATOM     97  CA  PRO    97      10.142  34.353  -7.298  1.00 25.00           C
ATOM     98  CA  GLU    98       8.062  37.390  -8.352  1.00 25.00           C
ATOM     99  CA  ILE    99       8.011  36.131 -11.969  1.00 25.00           C
ATOM    100  CA  THR   100       6.883  32.672 -10.774  1.00 25.00           C
ATOM    101  CA  ALA   101       4.098  34.273  -8.689  1.00 25.00           C
ATOM    102  CA  GLN   102       2.966  36.317 -11.724  1.00 25.00           C
ATOM    103  CA  ARG   103       2.917  33.147 -13.871  1.00 25.00           C
TER
END
