
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0349TS550_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS550_5-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    V      11      L       5          4.022
LGA    L      12      R       6           -
LGA    L      13      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      S      14           -
LGA    S      14      A      15           #
LGA    A      15      V      16          2.643
LGA    V      16      G      17          3.000
LGA    G      17      A      18          2.334
LGA    A      18      -       -           -
LGA    L      19      L      19          1.375
LGA    L      20      L      20           #
LGA    D      21      D      21           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      G      22          3.456
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      A      23          4.446
LGA    V      29      D      24          3.778
LGA    P      45      I      25           #
LGA    R      46      G      26          3.548
LGA    R      47      H      27          4.893
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    V      48      V      50          2.903
LGA    L      49      H      51          3.023
LGA    V      50      E      52          2.250
LGA    H      51      D      53          3.717
LGA    -       -      D      54           -
LGA    E      52      L      55          1.726
LGA    D      53      A      56          0.721
LGA    D      54      G      57          0.293
LGA    L      55      A      58          1.391
LGA    A      56      R      59          1.242
LGA    G      57      R      60          0.602
LGA    A      58      L      61          1.144
LGA    R      59      L      62          1.429
LGA    R      60      T      63          0.745
LGA    L      61      D      64          1.605
LGA    -       -      A      65           -
LGA    L      62      G      66          1.087
LGA    T      63      L      67          2.025
LGA    D      64      A      68           #
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   57    5.0     26    2.61     7.69     33.009     0.958

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.530906 * X  +   0.653740 * Y  +   0.539224 * Z  + -20.941412
  Y_new =  -0.095546 * X  +   0.678425 * Y  +  -0.728431 * Z  + -35.964573
  Z_new =  -0.842027 * X  +   0.335207 * Y  +   0.422642 * Z  +  -7.388178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.670533   -2.471059  [ DEG:    38.4187   -141.5813 ]
  Theta =   1.001031    2.140562  [ DEG:    57.3548    122.6452 ]
  Phi   =  -0.178062    2.963530  [ DEG:   -10.2022    169.7978 ]
 
# 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: T0349TS550_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS550_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   57   5.0   26   2.61    7.69  33.009
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS550_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT 1ubf_A
ATOM      1  N   VAL    11       0.204   2.028  -0.522  1.00  0.00
ATOM      2  CA  VAL    11       1.066   2.409   0.580  1.00  0.00
ATOM      3  C   VAL    11       0.417   3.570   1.326  1.00  0.00
ATOM      4  O   VAL    11       0.020   3.414   2.475  1.00  0.00
ATOM      5  N   LEU    12       0.304   4.723   0.659  1.00  0.00
ATOM      6  CA  LEU    12      -0.289   5.922   1.257  1.00  0.00
ATOM      7  C   LEU    12      -1.537   5.541   2.046  1.00  0.00
ATOM      8  O   LEU    12      -1.666   5.893   3.217  1.00  0.00
ATOM      9  N   LEU    13      -2.451   4.820   1.402  1.00  0.00
ATOM     10  CA  LEU    13      -3.664   4.400   2.079  1.00  0.00
ATOM     11  C   LEU    13      -3.377   3.555   3.303  1.00  0.00
ATOM     12  O   LEU    13      -4.055   3.675   4.315  1.00  0.00
ATOM     13  N   SER    14      -2.369   2.700   3.224  1.00  0.00
ATOM     14  CA  SER    14      -2.039   1.856   4.359  1.00  0.00
ATOM     15  C   SER    14      -1.570   2.693   5.582  1.00  0.00
ATOM     16  O   SER    14      -1.933   2.389   6.728  1.00  0.00
ATOM     17  N   ALA    15      -0.786   3.748   5.336  1.00  0.00
ATOM     18  CA  ALA    15      -0.276   4.627   6.400  1.00  0.00
ATOM     19  C   ALA    15      -1.377   5.345   7.153  1.00  0.00
ATOM     20  O   ALA    15      -1.308   5.493   8.370  1.00  0.00
ATOM     21  N   VAL    16      -2.382   5.809   6.420  1.00  0.00
ATOM     22  CA  VAL    16      -3.510   6.503   7.026  1.00  0.00
ATOM     23  C   VAL    16      -4.156   5.596   8.074  1.00  0.00
ATOM     24  O   VAL    16      -4.279   5.964   9.251  1.00  0.00
ATOM     25  N   GLY    17      -4.552   4.403   7.644  1.00  0.00
ATOM     26  CA  GLY    17      -5.161   3.466   8.552  1.00  0.00
ATOM     27  C   GLY    17      -4.286   3.343   9.779  1.00  0.00
ATOM     28  O   GLY    17      -4.746   3.568  10.887  1.00  0.00
ATOM     29  N   ALA    18      -3.021   3.001   9.580  1.00  0.00
ATOM     30  CA  ALA    18      -2.100   2.871  10.697  1.00  0.00
ATOM     31  C   ALA    18      -1.857   4.234  11.350  1.00  0.00
ATOM     32  O   ALA    18      -1.637   4.320  12.565  1.00  0.00
ATOM     33  N   LEU    19      -1.901   5.293  10.543  1.00  0.00
ATOM     34  CA  LEU    19      -1.665   6.638  11.042  1.00  0.00
ATOM     35  C   LEU    19      -2.684   7.095  12.066  1.00  0.00
ATOM     36  O   LEU    19      -2.374   7.905  12.945  1.00  0.00
ATOM     37  N   LEU    20      -3.898   6.568  11.963  1.00  0.00
ATOM     38  CA  LEU    20      -4.972   6.932  12.878  1.00  0.00
ATOM     39  C   LEU    20      -5.230   5.937  14.017  1.00  0.00
ATOM     40  O   LEU    20      -5.578   6.325  15.131  1.00  0.00
ATOM     41  N   ASP    21      -5.059   4.653  13.739  1.00  0.00
ATOM     42  CA  ASP    21      -5.302   3.650  14.758  1.00  0.00
ATOM     43  C   ASP    21      -4.170   3.659  15.774  1.00  0.00
ATOM     44  O   ASP    21      -4.194   2.925  16.758  1.00  0.00
ATOM     45  N   GLY    22      -4.935   4.181  14.153  1.00  0.00
ATOM     46  CA  GLY    22      -5.229   5.560  13.754  1.00  0.00
ATOM     47  C   GLY    22      -6.242   5.663  12.645  1.00  0.00
ATOM     48  O   GLY    22      -5.978   5.289  11.498  1.00  0.00
ATOM     49  N   ALA    23      -7.364   6.282  12.977  1.00  0.00
ATOM     50  CA  ALA    23      -8.409   6.456  12.005  1.00  0.00
ATOM     51  C   ALA    23      -8.733   7.920  11.789  1.00  0.00
ATOM     52  O   ALA    23      -8.741   8.721  12.741  1.00  0.00
ATOM     53  N   ASP    24      -8.896   8.268  10.508  1.00  0.00
ATOM     54  CA  ASP    24      -9.240   9.616  10.118  1.00  0.00
ATOM     55  C   ASP    24     -10.719   9.708   9.811  1.00  0.00
ATOM     56  O   ASP    24     -11.208   9.102   8.852  1.00  0.00
ATOM     57  N   ILE    25     -11.415  10.472  10.648  1.00  0.00
ATOM     58  CA  ILE    25     -12.844  10.711  10.508  1.00  0.00
ATOM     59  C   ILE    25     -12.987  12.224  10.468  1.00  0.00
ATOM     60  O   ILE    25     -12.359  12.914  11.268  1.00  0.00
ATOM     61  N   GLY    26     -13.750  12.734   9.501  1.00  0.00
ATOM     62  CA  GLY    26     -13.975  14.177   9.352  1.00  0.00
ATOM     63  C   GLY    26     -12.684  14.962   9.124  1.00  0.00
ATOM     64  O   GLY    26     -11.950  15.278  10.065  1.00  0.00
ATOM     65  N   HIS    27     -12.143  14.754   8.145  1.00  0.00
ATOM     66  CA  HIS    27     -10.966  15.545   7.792  1.00  0.00
ATOM     67  C   HIS    27      -9.682  15.069   8.451  1.00  0.00
ATOM     68  O   HIS    27      -9.315  15.510   9.545  1.00  0.00
ATOM     69  N   LEU    28      -8.998  14.162   7.767  1.00  0.00
ATOM     70  CA  LEU    28      -7.737  13.638   8.251  1.00  0.00
ATOM     71  C   LEU    28      -6.753  14.798   8.361  1.00  0.00
ATOM     72  O   LEU    28      -6.617  15.609   7.441  1.00  0.00
ATOM     73  N   VAL    29      -6.091  14.881   9.511  1.00  0.00
ATOM     74  CA  VAL    29      -5.119  15.934   9.772  1.00  0.00
ATOM     75  C   VAL    29      -3.939  15.435  10.619  1.00  0.00
ATOM     76  O   VAL    29      -4.116  14.988  11.752  1.00  0.00
ATOM    105  N   PRO    45      -5.259  10.353   0.771  1.00  0.00
ATOM    106  CA  PRO    45      -4.507   9.208   0.284  1.00  0.00
ATOM    107  C   PRO    45      -3.657   9.763  -0.849  1.00  0.00
ATOM    108  O   PRO    45      -2.488   9.400  -0.996  1.00  0.00
ATOM    109  N   ARG    46      -4.252  10.661  -1.636  1.00  0.00
ATOM    110  CA  ARG    46      -3.544  11.295  -2.741  1.00  0.00
ATOM    111  C   ARG    46      -2.633  12.381  -2.195  1.00  0.00
ATOM    112  O   ARG    46      -1.699  12.817  -2.867  1.00  0.00
ATOM    113  N   ARG    47      -2.907  12.819  -0.970  1.00  0.00
ATOM    114  CA  ARG    47      -2.068  13.825  -0.339  1.00  0.00
ATOM    115  C   ARG    47      -0.762  13.139   0.047  1.00  0.00
ATOM    116  O   ARG    47       0.329  13.688  -0.122  1.00  0.00
ATOM    117  N   VAL    48      -0.872  11.931   0.575  1.00  0.00
ATOM    118  CA  VAL    48       0.317  11.190   0.937  1.00  0.00
ATOM    119  C   VAL    48       1.018  10.779  -0.350  1.00  0.00
ATOM    120  O   VAL    48       2.235  10.898  -0.463  1.00  0.00
ATOM    121  N   LEU    49       0.236  10.323  -1.326  1.00  0.00
ATOM    122  CA  LEU    49       0.764   9.875  -2.616  1.00  0.00
ATOM    123  C   LEU    49       1.650  10.893  -3.335  1.00  0.00
ATOM    124  O   LEU    49       2.588  10.513  -4.036  1.00  0.00
ATOM    125  N   VAL    50       1.354  12.180  -3.165  1.00  0.00
ATOM    126  CA  VAL    50       2.140  13.239  -3.800  1.00  0.00
ATOM    127  C   VAL    50       3.104  13.931  -2.834  1.00  0.00
ATOM    128  O   VAL    50       3.857  14.829  -3.224  1.00  0.00
ATOM    129  N   HIS    51       3.071  13.513  -1.587  1.00  0.00
ATOM    130  CA  HIS    51       3.941  14.095  -0.577  1.00  0.00
ATOM    131  C   HIS    51       4.664  12.984   0.161  1.00  0.00
ATOM    132  O   HIS    51       4.268  12.587   1.250  1.00  0.00
ATOM    133  N   GLU    52       5.728  12.453  -0.449  1.00  0.00
ATOM    134  CA  GLU    52       6.532  11.374   0.121  1.00  0.00
ATOM    135  C   GLU    52       7.167  11.878   1.405  1.00  0.00
ATOM    136  O   GLU    52       7.296  11.147   2.387  1.00  0.00
ATOM    137  N   ASP    53       7.566  13.144   1.368  1.00  0.00
ATOM    138  CA  ASP    53       8.182  13.826   2.499  1.00  0.00
ATOM    139  C   ASP    53       7.455  13.539   3.815  1.00  0.00
ATOM    140  O   ASP    53       7.991  12.859   4.690  1.00  0.00
ATOM    141  N   ASP    54       6.239  14.064   3.948  1.00  0.00
ATOM    142  CA  ASP    54       5.449  13.858   5.156  1.00  0.00
ATOM    143  C   ASP    54       5.188  12.354   5.318  1.00  0.00
ATOM    144  O   ASP    54       5.370  11.804   6.403  1.00  0.00
ATOM    145  N   LEU    55       4.803  11.701   4.220  1.00  0.00
ATOM    146  CA  LEU    55       4.523  10.265   4.177  1.00  0.00
ATOM    147  C   LEU    55       5.570   9.446   4.933  1.00  0.00
ATOM    148  O   LEU    55       5.233   8.694   5.858  1.00  0.00
ATOM    149  N   ALA    56       6.827   9.561   4.515  1.00  0.00
ATOM    150  CA  ALA    56       7.900   8.838   5.182  1.00  0.00
ATOM    151  C   ALA    56       7.740   9.040   6.679  1.00  0.00
ATOM    152  O   ALA    56       7.593   8.077   7.427  1.00  0.00
ATOM    153  N   GLY    57       7.723  10.304   7.102  1.00  0.00
ATOM    154  CA  GLY    57       7.588  10.642   8.516  1.00  0.00
ATOM    155  C   GLY    57       6.529   9.800   9.242  1.00  0.00
ATOM    156  O   GLY    57       6.813   9.235  10.306  1.00  0.00
ATOM    157  N   ALA    58       5.315   9.719   8.686  1.00  0.00
ATOM    158  CA  ALA    58       4.271   8.907   9.310  1.00  0.00
ATOM    159  C   ALA    58       4.806   7.480   9.347  1.00  0.00
ATOM    160  O   ALA    58       4.892   6.885  10.417  1.00  0.00
ATOM    161  N   ARG    59       5.181   6.937   8.190  1.00  0.00
ATOM    162  CA  ARG    59       5.720   5.579   8.155  1.00  0.00
ATOM    163  C   ARG    59       6.867   5.390   9.134  1.00  0.00
ATOM    164  O   ARG    59       7.004   4.339   9.763  1.00  0.00
ATOM    165  N   ARG    60       7.703   6.413   9.239  1.00  0.00
ATOM    166  CA  ARG    60       8.849   6.369  10.129  1.00  0.00
ATOM    167  C   ARG    60       8.337   6.202  11.559  1.00  0.00
ATOM    168  O   ARG    60       8.617   5.194  12.218  1.00  0.00
ATOM    169  N   LEU    61       7.562   7.183  12.023  1.00  0.00
ATOM    170  CA  LEU    61       6.998   7.153  13.374  1.00  0.00
ATOM    171  C   LEU    61       6.206   5.887  13.687  1.00  0.00
ATOM    172  O   LEU    61       6.235   5.382  14.816  1.00  0.00
ATOM    173  N   LEU    62       5.492   5.383  12.687  1.00  0.00
ATOM    174  CA  LEU    62       4.694   4.183  12.876  1.00  0.00
ATOM    175  C   LEU    62       5.610   2.989  13.175  1.00  0.00
ATOM    176  O   LEU    62       5.311   2.182  14.056  1.00  0.00
ATOM    177  N   THR    63       6.730   2.870  12.463  1.00  0.00
ATOM    178  CA  THR    63       7.636   1.756  12.738  1.00  0.00
ATOM    179  C   THR    63       8.336   1.882  14.085  1.00  0.00
ATOM    180  O   THR    63       8.538   0.881  14.767  1.00  0.00
ATOM    181  N   ASP    64       8.730   3.086  14.485  1.00  0.00
ATOM    182  CA  ASP    64       9.356   3.203  15.798  1.00  0.00
ATOM    183  C   ASP    64       8.354   2.777  16.846  1.00  0.00
ATOM    184  O   ASP    64       8.584   1.822  17.600  1.00  0.00
TER
END
