
#######################################################
#                                                     #
#                        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 T0314TS599_5-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS599_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      M       1          4.771
LGA    S       2      S       2           #
LGA    I       3      I       3           #
LGA    T       4      T       4          3.911
LGA    S       5      S       5          3.490
LGA    T       6      T       6          1.147
LGA    D       7      D       7          0.718
LGA    I       8      I       8          0.923
LGA    C       9      C       9          1.484
LGA    Q      10      Q      10          0.939
LGA    A      11      A      11          0.402
LGA    A      12      A      12          1.841
LGA    D      13      D      13          2.909
LGA    A      14      -       -           -
LGA    L      15      A      14          2.553
LGA    K      16      L      15          2.978
LGA    G      17      -       -           -
LGA    F      18      K      16          1.518
LGA    V      19      G      17          2.703
LGA    G      20      F      18          3.424
LGA    F      21      V      19          2.985
LGA    N      22      G      20          3.010
LGA    R      23      F      21           #
LGA    K      24      N      22           #
LGA    T      25      R      23           #
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      R      27           -
LGA    G      26      Y      28          1.193
LGA    R      27      I      29          0.968
LGA    Y      28      V      30          0.801
LGA    I      29      R      31          3.056
LGA    V      30      F      32          2.948
LGA    R      31      S      33           #
LGA    F      32      E      34           -
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      D      35          4.943
LGA    T      47      S      36          3.465
LGA    P      48      F      37          3.793
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    T      49      D      43           #
LGA    -       -      D      44           -
LGA    -       -      S      45           -
LGA    -       -      I      46           -
LGA    S      50      T      47          4.650
LGA    E      51      P      48           #
LGA    F      52      T      49           -
LGA    V      53      S      50           -
LGA    W      54      E      51           -
LGA    S      55      F      52           -
LGA    S      56      V      53           -
LGA    V      57      W      54           -
LGA    R      58      S      55           -
LGA    D      59      S      56           -
LGA    D      60      V      57           -
LGA    V      61      R      58           -
LGA    M      62      D      59           -
LGA    R      63      D      60           -
LGA    L      64      V      61           -
LGA    G      65      M      62           -
LGA    R      66      R      63           -
LGA    E      67      L      64           -
LGA    Q      68      G      65           -
LGA    L      69      R      66           -
LGA    -       -      E      67           -
LGA    -       -      Q      68           -
LGA    -       -      L      69           -
LGA    -       -      Q      70           -
LGA    -       -      I      71           -
LGA    -       -      L      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    Q      70      Q      75          4.326
LGA    I      71      -       -           -
LGA    L      72      -       -           -
LGA    L      73      N      76           #
LGA    E      74      I      77          1.556
LGA    Q      75      N      78          3.054
LGA    N      76      E      79          1.356
LGA    I      77      R      80          4.388
LGA    -       -      L      81           -
LGA    N      78      N      82           #
LGA    E      79      I      83           #
LGA    R      80      G      84          5.545
LGA    L      81      E      85          4.320
LGA    N      82      P      86          5.360
LGA    I      83      L      87          3.483
LGA    G      84      L      88          3.030
LGA    E      85      V      89          2.149
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    P      86      R      92          4.605
LGA    L      87      R      93           -
LGA    L      88      -       -           -
LGA    V      89      Q      94          5.043
LGA    Y      90      D      95          4.531
LGA    -       -      L      96           -
LGA    L      91      P      97          5.499
LGA    R      92      E      98          1.598
LGA    R      93      I      99          4.134
LGA    Q      94      -       -           -
LGA    D      95      T     100          1.682
LGA    L      96      A     101          3.199
LGA    P      97      -       -           -
LGA    E      98      Q     102          1.598
LGA    I      99      -       -           -
LGA    T     100      -       -           -
LGA    A     101      -       -           -
LGA    Q     102      R     103          3.476
LGA    R     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  103  103    5.0     48    3.28    25.00     27.527     1.420

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.663774 * X  +   0.667330 * Y  +   0.337750 * Z  +  20.004238
  Y_new =   0.731591 * X  +   0.485418 * Y  +   0.478690 * Z  +   5.547957
  Z_new =   0.155494 * X  +   0.564837 * Y  +  -0.810420 * Z  + -11.217524 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.532905   -0.608688  [ DEG:   145.1248    -34.8752 ]
  Theta =  -0.156128   -2.985465  [ DEG:    -8.9455   -171.0545 ]
  Phi   =   2.307631   -0.833962  [ DEG:   132.2175    -47.7825 ]
 
# 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: T0314TS599_5-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS599_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   48   3.28   25.00  27.527
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS599_5-D1
PFRMAT TS                                                                       
TARGET T0314                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       6.197   2.704   1.024  1.00  0.00              
ATOM      2  CA  SER     2       4.176   6.389   1.262  1.00  0.00              
ATOM      3  CA  ILE     3       2.783   9.785  -0.021  1.00  0.00              
ATOM      4  CA  THR     4       1.528  12.991  -1.912  1.00  0.00              
ATOM      5  CA  SER     5       2.118  13.043  -5.628  1.00  0.00              
ATOM      6  CA  THR     6       4.823  15.751  -5.260  1.00  0.00              
ATOM      7  CA  ASP     7       6.846  13.589  -2.903  1.00  0.00              
ATOM      8  CA  ILE     8       6.592  10.582  -5.292  1.00  0.00              
ATOM      9  CA  CYS     9       7.661  12.555  -8.378  1.00  0.00              
ATOM     10  CA  GLN    10      10.688  14.009  -6.544  1.00  0.00              
ATOM     11  CA  ALA    11      11.657  10.514  -5.254  1.00  0.00              
ATOM     12  CA  ALA    12      11.304   9.092  -8.720  1.00  0.00              
ATOM     13  CA  ASP    13      13.566  11.758 -10.224  1.00  0.00              
ATOM     14  CA  ALA    14      16.222  11.137  -7.561  1.00  0.00              
ATOM     15  CA  LEU    15      16.107   7.357  -8.056  1.00  0.00              
ATOM     16  CA  LYS    16      16.449   7.769 -11.783  1.00  0.00              
ATOM     17  CA  GLY    17      19.481   9.993 -11.379  1.00  0.00              
ATOM     18  CA  PHE    18      21.353   7.598  -8.994  1.00  0.00              
ATOM     19  CA  VAL    19      20.711   4.751 -11.412  1.00  0.00              
ATOM     20  CA  GLY    20      21.084   5.678 -15.054  1.00  0.00              
ATOM     21  CA  PHE    21      19.623   3.459 -17.718  1.00  0.00              
ATOM     22  CA  ASN    22      21.356   2.910 -20.989  1.00  0.00              
ATOM     23  CA  ARG    23      18.766   2.087 -23.536  1.00  0.00              
ATOM     24  CA  LYS    24      20.812   0.648 -26.344  1.00  0.00              
ATOM     25  CA  THR    25      22.543  -2.137 -24.526  1.00  0.00              
ATOM     26  CA  GLY    26      20.312  -2.913 -21.506  1.00  0.00              
ATOM     27  CA  ARG    27      23.039  -1.889 -19.112  1.00  0.00              
ATOM     28  CA  TYR    28      22.477   0.101 -15.883  1.00  0.00              
ATOM     29  CA  ILE    29      24.843   2.907 -15.143  1.00  0.00              
ATOM     30  CA  VAL    30      25.589   4.022 -11.633  1.00  0.00              
ATOM     31  CA  ARG    31      26.709   7.591 -11.084  1.00  0.00              
ATOM     32  CA  PHE    32      29.210   8.299  -8.386  1.00  0.00              
ATOM     33  CA  SER    33      30.511  11.809  -7.685  1.00  0.00              
ATOM     34  CA  GLU    34      34.297  11.443  -7.405  1.00  0.00              
ATOM     35  CA  ASP    35      34.453  11.659  -3.664  1.00  0.00              
ATOM     36  CA  SER    36      31.426   9.652  -2.638  1.00  0.00              
ATOM     37  CA  PHE    37      32.222   6.293  -4.267  1.00  0.00              
ATOM     38  CA  GLY    38      35.815   6.211  -5.441  1.00  0.00              
ATOM     39  CA  MET    39      36.414   3.696  -8.026  1.00  0.00              
ATOM     40  CA  ASP    40      38.611   1.262  -9.799  1.00  0.00              
ATOM     41  CA  VAL    41      37.521   0.742 -13.419  1.00  0.00              
ATOM     42  CA  ALA    42      38.656  -2.778 -14.359  1.00  0.00              
ATOM     43  CA  ASP    43      37.824  -4.532 -17.579  1.00  0.00              
ATOM     44  CA  ASP    44      34.414  -6.241 -17.202  1.00  0.00              
ATOM     45  CA  SER    45      32.897  -3.166 -15.626  1.00  0.00              
ATOM     46  CA  ILE    46      33.650  -0.144 -17.732  1.00  0.00              
ATOM     47  CA  THR    47      30.760   2.216 -17.937  1.00  0.00              
ATOM     48  CA  PRO    48      30.209   3.787 -21.383  1.00  0.00              
ATOM     49  CA  THR    49      26.464   4.263 -21.835  1.00  0.00              
ATOM     50  CA  SER    50      26.444   8.012 -22.414  1.00  0.00              
ATOM     51  CA  GLU    51      29.178   8.506 -19.805  1.00  0.00              
ATOM     52  CA  PHE    52      28.165   6.342 -16.963  1.00  0.00              
ATOM     53  CA  VAL    53      30.242   6.411 -13.835  1.00  0.00              
ATOM     54  CA  TRP    54      30.280   3.426 -11.659  1.00  0.00              
ATOM     55  CA  SER    55      31.007   3.624  -7.989  1.00  0.00              
ATOM     56  CA  SER    56      31.971   0.454  -6.094  1.00  0.00              
ATOM     57  CA  VAL    57      35.340   0.904  -4.463  1.00  0.00              
ATOM     58  CA  ARG    58      36.003  -2.690  -3.273  1.00  0.00              
ATOM     59  CA  ASP    59      39.768  -2.450  -2.936  1.00  0.00              
ATOM     60  CA  ASP    60      40.349  -1.501  -6.563  1.00  0.00              
ATOM     61  CA  VAL    61      38.326  -4.154  -8.286  1.00  0.00              
ATOM     62  CA  MET    62      35.910  -3.784 -11.115  1.00  0.00              
ATOM     63  CA  ARG    63      34.839  -6.895 -13.110  1.00  0.00              
ATOM     64  CA  LEU    64      31.116  -7.201 -13.609  1.00  0.00              
ATOM     65  CA  GLY    65      29.539  -8.934 -16.529  1.00  0.00              
ATOM     66  CA  ARG    66      26.447  -7.606 -18.199  1.00  0.00              
ATOM     67  CA  GLU    67      24.097 -10.118 -16.564  1.00  0.00              
ATOM     68  CA  GLN    68      25.559  -9.315 -13.126  1.00  0.00              
ATOM     69  CA  LEU    69      25.300  -5.545 -13.522  1.00  0.00              
ATOM     70  CA  GLN    70      21.666  -5.855 -14.632  1.00  0.00              
ATOM     71  CA  ILE    71      20.828  -7.952 -11.621  1.00  0.00              
ATOM     72  CA  LEU    72      22.451  -5.556  -9.112  1.00  0.00              
ATOM     73  CA  LEU    73      20.786  -2.493 -10.585  1.00  0.00              
ATOM     74  CA  GLU    74      17.102  -3.539 -10.789  1.00  0.00              
ATOM     75  CA  GLN    75      16.962  -4.751  -7.236  1.00  0.00              
ATOM     76  CA  ASN    76      18.875  -1.932  -5.665  1.00  0.00              
ATOM     77  CA  ILE    77      17.094   1.105  -7.199  1.00  0.00              
ATOM     78  CA  ASN    78      13.597  -0.155  -6.597  1.00  0.00              
ATOM     79  CA  GLU    79      14.376  -0.957  -2.949  1.00  0.00              
ATOM     80  CA  ARG    80      15.957   2.404  -2.010  1.00  0.00              
ATOM     81  CA  LEU    81      12.992   4.283  -3.491  1.00  0.00              
ATOM     82  CA  ASN    82       9.646   2.501  -2.853  1.00  0.00              
ATOM     83  CA  ILE    83       8.040   2.284  -6.250  1.00  0.00              
ATOM     84  CA  GLY    84       4.372   1.621  -5.975  1.00  0.00              
ATOM     85  CA  GLU    85       2.820   3.992  -8.557  1.00  0.00              
ATOM     86  CA  PRO    86       3.944   4.321 -12.128  1.00  0.00              
ATOM     87  CA  LEU    87       6.443   7.239 -12.266  1.00  0.00              
ATOM     88  CA  LEU    88       5.205   9.111 -15.324  1.00  0.00              
ATOM     89  CA  VAL    89       1.574   8.766 -14.179  1.00  0.00              
ATOM     90  CA  TYR    90       1.970   9.664 -10.474  1.00  0.00              
ATOM     91  CA  LEU    91       3.864  12.796 -11.695  1.00  0.00              
ATOM     92  CA  ARG    92       1.769  13.941 -14.674  1.00  0.00              
ATOM     93  CA  ARG    93       4.289  13.799 -17.540  1.00  0.00              
ATOM     94  CA  GLN    94       4.062  17.528 -18.238  1.00  0.00              
ATOM     95  CA  ASP    95       4.701  18.414 -14.590  1.00  0.00              
ATOM     96  CA  LEU    96       7.934  16.430 -14.267  1.00  0.00              
ATOM     97  CA  PRO    97       9.822  18.339 -17.001  1.00  0.00              
ATOM     98  CA  GLU    98       8.758  21.630 -15.380  1.00  0.00              
ATOM     99  CA  ILE    99       9.860  20.647 -11.853  1.00  0.00              
ATOM    100  CA  THR   100      13.232  19.536 -13.217  1.00  0.00              
ATOM    101  CA  ALA   101      13.620  22.839 -15.112  1.00  0.00              
ATOM    102  CA  GLN   102      12.811  25.190 -12.222  1.00  0.00              
ATOM    103  CA  ARG   103      15.291  23.463  -9.856  1.00  0.00              
TER                                                                             
END
