
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0367TS168_2-D1
# Molecule2: number of CA atoms  123 (  996),  selected  123 , name T0367_D1.pdb
# PARAMETERS: T0367TS168_2-D1.T0367_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    D       2      -       -           -
LGA    E       3      -       -           -
LGA    L       4      -       -           -
LGA    E       5      -       -           -
LGA    L       6      -       -           -
LGA    R       7      -       -           -
LGA    I       8      -       -           -
LGA    R       9      -       -           -
LGA    K      10      -       -           -
LGA    A      11      -       -           -
LGA    E      12      -       -           -
LGA    K      13      -       -           -
LGA    L      14      -       -           -
LGA    V      15      -       -           -
LGA    Q      16      -       -           -
LGA    D      17      -       -           -
LGA    A      18      -       -           -
LGA    K      19      -       -           -
LGA    K      20      -       -           -
LGA    E      21      -       -           -
LGA    F      22      -       -           -
LGA    E      23      -       -           -
LGA    M      24      -       -           -
LGA    G      25      D       2          5.500
LGA    L      26      E       3          5.342
LGA    Y      27      -       -           -
LGA    E      28      L       4          3.224
LGA    R      29      E       5           #
LGA    C      30      L       6           #
LGA    C      31      R       7          4.047
LGA    S      32      I       8          1.282
LGA    T      33      R       9          4.790
LGA    A      34      K      10           #
LGA    Y      35      A      11          4.330
LGA    Y      36      E      12          1.214
LGA    -       -      K      13           -
LGA    A      37      L      14          4.332
LGA    M      38      V      15          4.786
LGA    F      39      -       -           -
LGA    H      40      Q      16          3.981
LGA    A      41      D      17           -
LGA    A      42      A      18           -
LGA    K      43      K      19           -
LGA    A      44      K      20           #
LGA    M      45      E      21           -
LGA    L      46      -       -           -
LGA    L      47      -       -           -
LGA    G      48      -       -           -
LGA    Y      49      -       -           -
LGA    G      50      F      22          5.494
LGA    R      51      E      23           #
LGA    D      52      M      24          5.106
LGA    S      53      G      25          4.656
LGA    -       -      L      26           -
LGA    -       -      Y      27           -
LGA    -       -      E      28           -
LGA    -       -      R      29           -
LGA    K      54      C      30          3.149
LGA    T      55      C      31           #
LGA    -       -      S      32           -
LGA    -       -      T      33           -
LGA    H      56      A      34          3.157
LGA    -       -      Y      35           -
LGA    -       -      Y      36           -
LGA    R      57      A      37          1.800
LGA    G      58      M      38          1.993
LGA    T      59      F      39          2.029
LGA    I      60      H      40          2.111
LGA    Y      61      A      41          2.196
LGA    L      62      A      42          2.787
LGA    I      63      K      43          3.049
LGA    W      64      A      44          3.062
LGA    E      65      M      45          3.602
LGA    C      66      -       -           -
LGA    R      67      L      46          1.176
LGA    E      68      L      47           -
LGA    -       -      G      48           -
LGA    -       -      Y      49           -
LGA    -       -      G      50           -
LGA    -       -      R      51           -
LGA    -       -      D      52           -
LGA    -       -      S      53           -
LGA    -       -      K      54           -
LGA    -       -      T      55           -
LGA    -       -      H      56           -
LGA    -       -      R      57           -
LGA    -       -      G      58           -
LGA    -       -      T      59           -
LGA    -       -      I      60           -
LGA    -       -      Y      61           -
LGA    -       -      L      62           -
LGA    -       -      I      63           -
LGA    -       -      W      64           -
LGA    -       -      E      65           -
LGA    E      69      C      66          3.852
LGA    L      70      R      67          2.121
LGA    G      71      E      68          2.855
LGA    -       -      E      69           -
LGA    -       -      L      70           -
LGA    L      72      G      71          3.704
LGA    S      73      L      72          2.502
LGA    D      74      S      73          2.150
LGA    -       -      D      74           -
LGA    D      75      D      75          3.366
LGA    D      76      D      76          3.376
LGA    C      77      C      77          3.235
LGA    S      78      S      78          2.452
LGA    K      79      K      79          1.851
LGA    L      80      L      80          2.547
LGA    S      81      S      81          2.650
LGA    R      82      R      82          2.062
LGA    A      83      A      83          2.030
LGA    F      84      F      84          2.390
LGA    D      85      D      85          2.571
LGA    L      86      L      86          2.584
LGA    R      87      R      87          2.826
LGA    E      88      E      88          3.441
LGA    E      89      E      89          3.822
LGA    S      90      S      90          3.365
LGA    D      91      D      91          1.901
LGA    Y      92      Y      92           -
LGA    G      93      G      93           -
LGA    I      94      I      94           -
LGA    Y      95      Y      95           -
LGA    K      96      K      96           -
LGA    E      97      E      97           -
LGA    V      98      V      98           -
LGA    S      99      S      99           -
LGA    K     100      K     100           -
LGA    D     101      D     101           -
LGA    L     102      L     102           -
LGA    A     103      A     103           -
LGA    I     104      I     104           -
LGA    K     105      K     105           -
LGA    I     106      I     106           -
LGA    L     107      L     107           -
LGA    K     108      K     108           -
LGA    D     109      D     109           -
LGA    A     110      A     110           -
LGA    E     111      E     111           -
LGA    I     112      I     112           -
LGA    F     113      F     113           -
LGA    V     114      V     114           -
LGA    Q     115      Q     115           -
LGA    K     116      K     116           -
LGA    A     117      A     117           -
LGA    K     118      K     118           -
LGA    N     119      N     119           -
LGA    A     120      A     120           -
LGA    V     121      V     121           -
LGA    N     122      N     122           -
LGA    K     123      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     49    3.30    34.69     25.748     1.443

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.472173 * X  +  -0.797796 * Y  +  -0.374933 * Z  +  46.697727
  Y_new =   0.853280 * X  +   0.306882 * Y  +   0.421588 * Z  +  34.324532
  Z_new =  -0.221281 * X  +  -0.518985 * Y  +   0.825644 * Z  +  34.438496 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.561171    2.580422  [ DEG:   -32.1527    147.8473 ]
  Theta =   0.223128    2.918465  [ DEG:    12.7843    167.2157 ]
  Phi   =   1.065375   -2.076217  [ DEG:    61.0415   -118.9585 ]
 
# 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: T0367TS168_2-D1                               
REMARK     2: T0367_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0367TS168_2-D1.T0367_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   49   3.30   34.69  25.748
REMARK  ---------------------------------------------------------- 
MOLECULE T0367TS168_2-D1
PFRMAT TS
TARGET T0367
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      86.980  39.372  49.346  1.00 25.00           C
ATOM      2  CA  ASP     2      83.204  40.074  49.466  1.00 25.00           C
ATOM      3  CA  GLU     3      82.692  36.280  49.356  1.00 25.00           C
ATOM      4  CA  LEU     4      79.719  36.588  51.753  1.00 25.00           C
ATOM      5  CA  GLU     5      78.205  39.339  49.561  1.00 25.00           C
ATOM      6  CA  LEU     6      78.643  37.139  46.456  1.00 25.00           C
ATOM      7  CA  ARG     7      76.946  34.216  48.258  1.00 25.00           C
ATOM      8  CA  ILE     8      74.038  36.495  49.267  1.00 25.00           C
ATOM      9  CA  ARG     9      73.685  37.691  45.646  1.00 25.00           C
ATOM     10  CA  LYS    10      73.656  34.060  44.425  1.00 25.00           C
ATOM     11  CA  ALA    11      70.959  33.189  47.000  1.00 25.00           C
ATOM     12  CA  GLU    12      68.865  36.185  45.857  1.00 25.00           C
ATOM     13  CA  LYS    13      69.230  35.080  42.209  1.00 25.00           C
ATOM     14  CA  LEU    14      68.137  31.532  43.149  1.00 25.00           C
ATOM     15  CA  VAL    15      65.092  32.933  45.001  1.00 25.00           C
ATOM     16  CA  GLN    16      64.183  35.059  41.949  1.00 25.00           C
ATOM     17  CA  ASP    17      64.484  31.983  39.686  1.00 25.00           C
ATOM     18  CA  ALA    18      62.230  29.990  42.056  1.00 25.00           C
ATOM     19  CA  LYS    19      59.652  32.823  42.025  1.00 25.00           C
ATOM     20  CA  LYS    20      59.742  32.895  38.197  1.00 25.00           C
ATOM     21  CA  GLU    21      59.229  29.102  38.088  1.00 25.00           C
ATOM     22  CA  PHE    22      56.257  29.409  40.484  1.00 25.00           C
ATOM     23  CA  GLU    23      54.742  32.160  38.292  1.00 25.00           C
ATOM     24  CA  MET    24      55.181  29.962  35.187  1.00 25.00           C
ATOM     25  CA  GLY    25      53.484  27.039  36.988  1.00 25.00           C
ATOM     26  CA  LEU    26      50.575  29.317  37.998  1.00 25.00           C
ATOM     27  CA  TYR    27      50.223  30.512  34.377  1.00 25.00           C
ATOM     28  CA  GLU    28      50.194  26.883  33.155  1.00 25.00           C
ATOM     29  CA  ARG    29      47.496  26.012  35.731  1.00 25.00           C
ATOM     30  CA  CYS    30      45.403  29.008  34.588  1.00 25.00           C
ATOM     31  CA  CYS    31      45.767  27.902  30.940  1.00 25.00           C
ATOM     32  CA  SER    32      44.675  24.354  31.879  1.00 25.00           C
ATOM     33  CA  THR    33      41.630  25.756  33.732  1.00 25.00           C
ATOM     34  CA  ALA    34      40.721  27.882  30.679  1.00 25.00           C
ATOM     35  CA  TYR    35      41.022  24.806  28.418  1.00 25.00           C
ATOM     36  CA  TYR    36      38.767  22.812  30.787  1.00 25.00           C
ATOM     37  CA  ALA    37      36.189  25.644  30.756  1.00 25.00           C
ATOM     38  CA  MET    38      36.280  25.718  26.928  1.00 25.00           C
ATOM     39  CA  PHE    39      35.767  21.924  26.818  1.00 25.00           C
ATOM     40  CA  HIS    40      32.794  22.232  29.215  1.00 25.00           C
ATOM     41  CA  ALA    41      31.280  24.983  27.022  1.00 25.00           C
ATOM     42  CA  ALA    42      31.718  22.783  23.918  1.00 25.00           C
ATOM     43  CA  LYS    43      30.021  19.860  25.719  1.00 25.00           C
ATOM     44  CA  ALA    44      27.113  22.139  26.729  1.00 25.00           C
ATOM     45  CA  MET    45      26.761  23.334  23.107  1.00 25.00           C
ATOM     46  CA  LEU    46      26.731  19.705  21.886  1.00 25.00           C
ATOM     47  CA  LEU    47      24.034  18.834  24.461  1.00 25.00           C
ATOM     48  CA  GLY    48      21.940  21.830  23.319  1.00 25.00           C
ATOM     49  CA  TYR    49      22.742  24.453  25.930  1.00 25.00           C
ATOM     50  CA  GLY    50      22.592  27.355  28.384  1.00 25.00           C
ATOM     51  CA  ARG    51      25.412  29.467  29.721  1.00 25.00           C
ATOM     52  CA  ASP    52      23.823  28.669  33.065  1.00 25.00           C
ATOM     53  CA  SER    53      25.182  28.111  36.542  1.00 25.00           C
ATOM     54  CA  LYS    54      28.657  28.698  35.022  1.00 25.00           C
ATOM     55  CA  THR    55      32.495  28.832  34.637  1.00 25.00           C
ATOM     56  CA  HIS    56      36.095  30.086  34.145  1.00 25.00           C
ATOM     57  CA  ARG    57      39.682  31.116  33.272  1.00 25.00           C
ATOM     58  CA  GLY    58      39.413  33.270  30.117  1.00 25.00           C
ATOM     59  CA  THR    59      42.185  35.569  31.420  1.00 25.00           C
ATOM     60  CA  ILE    60      44.401  32.530  32.141  1.00 25.00           C
ATOM     61  CA  TYR    61      43.767  31.200  28.606  1.00 25.00           C
ATOM     62  CA  LEU    62      44.681  34.615  27.132  1.00 25.00           C
ATOM     63  CA  ILE    63      47.906  34.672  29.197  1.00 25.00           C
ATOM     64  CA  TRP    64      48.781  31.151  27.972  1.00 25.00           C
ATOM     65  CA  GLU    65      48.161  32.230  24.350  1.00 25.00           C
ATOM     66  CA  CYS    66      50.410  35.290  24.851  1.00 25.00           C
ATOM     67  CA  ARG    67      53.158  33.061  26.317  1.00 25.00           C
ATOM     68  CA  GLU    68      52.864  30.688  23.326  1.00 25.00           C
ATOM     69  CA  GLU    69      53.127  33.654  20.916  1.00 25.00           C
ATOM     70  CA  LEU    70      50.014  35.493  19.805  1.00 25.00           C
ATOM     71  CA  GLY    71      49.230  33.305  16.786  1.00 25.00           C
ATOM     72  CA  LEU    72      46.417  32.030  19.047  1.00 25.00           C
ATOM     73  CA  SER    73      43.686  30.960  16.631  1.00 25.00           C
ATOM     74  CA  ASP    74      42.149  34.464  16.972  1.00 25.00           C
ATOM     75  CA  ASP    75      38.460  33.993  17.884  1.00 25.00           C
ATOM     76  CA  ASP    76      39.457  31.975  20.982  1.00 25.00           C
ATOM     77  CA  CYS    77      41.915  34.725  22.014  1.00 25.00           C
ATOM     78  CA  SER    78      39.178  37.368  21.578  1.00 25.00           C
ATOM     79  CA  LYS    79      36.784  35.279  23.717  1.00 25.00           C
ATOM     80  CA  LEU    80      39.467  34.941  26.430  1.00 25.00           C
ATOM     81  CA  SER    81      40.043  38.727  26.367  1.00 25.00           C
ATOM     82  CA  ARG    82      36.275  39.330  26.695  1.00 25.00           C
ATOM     83  CA  ALA    83      36.122  36.914  29.664  1.00 25.00           C
ATOM     84  CA  PHE    84      39.057  38.729  31.324  1.00 25.00           C
ATOM     85  CA  ASP    85      37.304  42.095  30.799  1.00 25.00           C
ATOM     86  CA  LEU    86      34.092  40.689  32.340  1.00 25.00           C
ATOM     87  CA  ARG    87      36.075  39.392  35.350  1.00 25.00           C
ATOM     88  CA  GLU    88      37.713  42.827  35.783  1.00 25.00           C
ATOM     89  CA  GLU    89      34.276  44.511  35.643  1.00 25.00           C
ATOM     90  CA  SER    90      32.264  41.978  37.671  1.00 25.00           C
ATOM     91  CA  ASP    91      32.477  40.458  41.149  1.00 25.00           C
ATOM     92  CA  TYR    92      34.490  38.064  43.230  1.00 25.00           C
ATOM     93  CA  GLY    93      32.325  39.183  46.102  1.00 25.00           C
ATOM     94  CA  ILE    94      33.905  38.951  49.556  1.00 25.00           C
ATOM     95  CA  TYR    95      32.668  36.101  51.753  1.00 25.00           C
ATOM     96  CA  LYS    96      35.123  33.622  53.143  1.00 25.00           C
ATOM     97  CA  GLU    97      37.397  30.524  52.978  1.00 25.00           C
ATOM     98  CA  VAL    98      40.544  28.974  51.443  1.00 25.00           C
ATOM     99  CA  SER    99      40.629  27.288  47.985  1.00 25.00           C
ATOM    100  CA  LYS   100      40.393  30.732  46.454  1.00 25.00           C
ATOM    101  CA  ASP   101      44.070  31.542  47.151  1.00 25.00           C
ATOM    102  CA  LEU   102      45.021  30.372  43.631  1.00 25.00           C
ATOM    103  CA  ALA   103      42.261  32.563  42.131  1.00 25.00           C
ATOM    104  CA  ILE   104      43.517  35.568  44.145  1.00 25.00           C
ATOM    105  CA  LYS   105      47.089  34.928  42.921  1.00 25.00           C
ATOM    106  CA  ILE   106      45.841  34.741  39.304  1.00 25.00           C
ATOM    107  CA  LEU   107      43.951  38.040  39.760  1.00 25.00           C
ATOM    108  CA  LYS   108      47.104  39.677  41.191  1.00 25.00           C
ATOM    109  CA  ASP   109      49.146  38.404  38.213  1.00 25.00           C
ATOM    110  CA  ALA   110      46.532  39.805  35.789  1.00 25.00           C
ATOM    111  CA  GLU   111      46.645  43.187  37.584  1.00 25.00           C
ATOM    112  CA  ILE   112      50.469  43.206  37.358  1.00 25.00           C
ATOM    113  CA  PHE   113      50.275  42.413  33.616  1.00 25.00           C
ATOM    114  CA  VAL   114      47.767  45.264  33.116  1.00 25.00           C
ATOM    115  CA  GLN   115      50.079  47.663  35.006  1.00 25.00           C
ATOM    116  CA  LYS   116      53.033  46.574  32.824  1.00 25.00           C
ATOM    117  CA  ALA   117      50.943  47.148  29.666  1.00 25.00           C
ATOM    118  CA  LYS   118      49.964  50.633  30.919  1.00 25.00           C
ATOM    119  CA  ASN   119      53.641  51.443  31.616  1.00 25.00           C
ATOM    120  CA  ALA   120      54.592  50.273  28.094  1.00 25.00           C
ATOM    121  CA  VAL   121      51.832  52.464  26.595  1.00 25.00           C
ATOM    122  CA  ASN   122      53.088  55.469  28.610  1.00 25.00           C
ATOM    123  CA  LYS   123      56.716  56.762  28.363  1.00 25.00           C
TER
END
