
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0358TS393_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_2-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      G      10           #
LGA    R      14      -       -           -
LGA    R      15      P      11           #
LGA    Q      16      F      12           #
LGA    A      17      T      13           #
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    Q      18      A      17           #
LGA    A      19      Q      18           -
LGA    -       -      A      19           -
LGA    V      20      V      20          5.281
LGA    T      21      T      21          2.843
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    T      22      N      26          4.370
LGA    T      23      I      27          1.466
LGA    Y      24      T      28          4.104
LGA    S      25      -       -           -
LGA    N      26      L      29          2.450
LGA    I      27      E      30          4.519
LGA    T      28      D      31          3.186
LGA    L      29      D      32          3.313
LGA    E      30      Q      33          3.393
LGA    D      31      -       -           -
LGA    D      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    S      35      G      34          2.783
LGA    H      36      S      35          2.981
LGA    F      37      H      36          2.486
LGA    R      38      F      37          3.024
LGA    L      39      R      38          3.133
LGA    V      40      L      39          3.774
LGA    V      41      V      40          1.100
LGA    R      42      V      41          1.474
LGA    D      43      R      42          1.038
LGA    T      44      D      43          5.444
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    E      45      R      47          1.255
LGA    G      46      M      48          3.057
LGA    R      47      V      49          2.903
LGA    M      48      W      50          1.065
LGA    V      49      R      51          2.680
LGA    W      50      A      52          3.680
LGA    R      51      W      53          3.548
LGA    A      52      N      54          3.602
LGA    W      53      -       -           -
LGA    N      54      -       -           -
LGA    F      55      -       -           -
LGA    E      56      -       -           -
LGA    P      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      -       -           -
LGA    G      60      -       -           -
LGA    E      61      -       -           -
LGA    G      62      -       -           -
LGA    L      63      -       -           -
LGA    N      64      -       -           -
LGA    R      65      -       -           -
LGA    Y      66      F      55          2.850
LGA    I      67      E      56          2.444
LGA    R      68      P      57          2.683
LGA    T      69      D      58           -
LGA    S      70      A      59           -
LGA    G      71      G      60           -
LGA    I      72      E      61           -
LGA    R      73      G      62           -
LGA    T      74      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     31    3.17     9.68     28.972     0.948

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.394924 * X  +  -0.795003 * Y  +   0.460441 * Z  +   5.648959
  Y_new =  -0.111825 * X  +   0.539050 * Y  +   0.834818 * Z  +   6.780845
  Z_new =  -0.911883 * X  +   0.278200 * Y  +  -0.301784 * Z  +   2.486110 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.396835   -0.744757  [ DEG:   137.3286    -42.6715 ]
  Theta =   1.147849    1.993744  [ DEG:    65.7669    114.2331 ]
  Phi   =  -2.865660    0.275932  [ DEG:  -164.1902     15.8098 ]
 
# 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: T0358TS393_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_2-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   31   3.17    9.68  28.972
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_2-D1
PFRMAT TS
TARGET T0358
MODEL 2
PARENT N/A
ATOM     10  CA  GLY    10       4.839  -0.141  15.979  1.00 25.00           C
ATOM     11  CA  PRO    11       6.062  -2.657  13.403  1.00 25.00           C
ATOM     12  CA  PHE    12       7.988   0.222  11.805  1.00 25.00           C
ATOM     13  CA  THR    13       9.462  -1.215   8.625  1.00 25.00           C
ATOM     14  CA  ARG    14       9.197  -3.185   5.383  1.00 25.00           C
ATOM     15  CA  ARG    15       5.600  -3.503   6.656  1.00 25.00           C
ATOM     16  CA  GLN    16       4.636  -0.288   4.811  1.00 25.00           C
ATOM     17  CA  ALA    17       6.235  -1.623   1.597  1.00 25.00           C
ATOM     18  CA  GLN    18       4.309  -4.912   1.977  1.00 25.00           C
ATOM     19  CA  ALA    19       1.045  -2.971   2.478  1.00 25.00           C
ATOM     20  CA  VAL    20       1.771  -0.894  -0.656  1.00 25.00           C
ATOM     21  CA  THR    21       2.448  -4.094  -2.649  1.00 25.00           C
ATOM     22  CA  THR    22      -0.847  -5.597  -1.403  1.00 25.00           C
ATOM     23  CA  THR    23      -2.714  -2.412  -2.424  1.00 25.00           C
ATOM     24  CA  TYR    24      -1.105  -2.552  -5.897  1.00 25.00           C
ATOM     25  CA  SER    25       1.517  -0.126  -7.097  1.00 25.00           C
ATOM     26  CA  ASN    26      -1.360   2.326  -7.336  1.00 25.00           C
ATOM     27  CA  ILE    27      -1.454   3.521  -3.757  1.00 25.00           C
ATOM     28  CA  THR    28      -3.203   6.777  -4.793  1.00 25.00           C
ATOM     29  CA  LEU    29      -3.456  10.623  -4.589  1.00 25.00           C
ATOM     30  CA  GLU    30      -3.331  14.307  -5.674  1.00 25.00           C
ATOM     31  CA  ASP    31      -5.937  13.072  -8.200  1.00 25.00           C
ATOM     32  CA  ASP    32      -9.062  11.715  -9.841  1.00 25.00           C
ATOM     33  CA  GLN    33      -7.493  12.282 -13.267  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.178  10.551 -12.446  1.00 25.00           C
ATOM     35  CA  SER    35      -1.198  10.948 -10.125  1.00 25.00           C
ATOM     36  CA  HIS    36       1.216  10.234  -7.225  1.00 25.00           C
ATOM     37  CA  PHE    37       1.880  10.095  -3.468  1.00 25.00           C
ATOM     38  CA  ARG    38      -0.428   8.468  -0.922  1.00 25.00           C
ATOM     39  CA  LEU    39      -2.799   7.039   1.617  1.00 25.00           C
ATOM     40  CA  VAL    40      -4.895   4.138   0.444  1.00 25.00           C
ATOM     41  CA  VAL    41      -5.757   0.431   0.422  1.00 25.00           C
ATOM     42  CA  ARG    42      -5.603  -2.356   3.009  1.00 25.00           C
ATOM     43  CA  ASP    43      -8.406  -4.646   2.003  1.00 25.00           C
ATOM     44  CA  THR    44     -11.667  -4.972  -0.009  1.00 25.00           C
ATOM     45  CA  GLU    45     -13.371  -4.625   3.405  1.00 25.00           C
ATOM     46  CA  GLY    46     -13.150  -1.149   5.041  1.00 25.00           C
ATOM     47  CA  ARG    47      -9.652   0.223   5.409  1.00 25.00           C
ATOM     48  CA  MET    48      -5.956   1.325   5.555  1.00 25.00           C
ATOM     49  CA  VAL    49      -2.458   1.613   4.006  1.00 25.00           C
ATOM     50  CA  TRP    50      -0.032   2.684   1.358  1.00 25.00           C
ATOM     51  CA  ARG    51       2.852   5.207   1.008  1.00 25.00           C
ATOM     52  CA  ALA    52       3.150   5.214  -2.783  1.00 25.00           C
ATOM     53  CA  TRP    53       5.015   1.974  -3.492  1.00 25.00           C
ATOM     54  CA  ASN    54       5.507   3.315  -6.955  1.00 25.00           C
ATOM     55  CA  PHE    55       5.519   4.990 -10.350  1.00 25.00           C
ATOM     56  CA  GLU    56       8.574   7.268 -10.730  1.00 25.00           C
ATOM     57  CA  PRO    57      10.562   4.025 -10.360  1.00 25.00           C
ATOM     58  CA  ASP    58      11.591   0.890  -8.354  1.00 25.00           C
ATOM     59  CA  ALA    59      11.383   2.168  -4.769  1.00 25.00           C
ATOM     60  CA  GLY    60      14.320   4.524  -4.213  1.00 25.00           C
ATOM     61  CA  GLU    61      11.748   7.191  -4.975  1.00 25.00           C
ATOM     62  CA  GLY    62       9.835  10.475  -5.443  1.00 25.00           C
ATOM     63  CA  LEU    63       6.784   8.979  -3.675  1.00 25.00           C
ATOM     64  CA  ASN    64       9.004   7.816  -0.778  1.00 25.00           C
ATOM     65  CA  ARG    65      10.529  11.319  -0.509  1.00 25.00           C
ATOM     66  CA  TYR    66       7.027  12.868  -0.456  1.00 25.00           C
ATOM     67  CA  ILE    67       5.964  10.430   2.300  1.00 25.00           C
ATOM     68  CA  ARG    68       9.082  11.330   4.333  1.00 25.00           C
ATOM     69  CA  THR    69       8.308  15.058   3.914  1.00 25.00           C
ATOM     70  CA  SER    70       8.088  17.700   1.167  1.00 25.00           C
ATOM     71  CA  GLY    71      11.330  19.657   1.285  1.00 25.00           C
ATOM     72  CA  ILE    72      12.517  17.794   4.402  1.00 25.00           C
ATOM     73  CA  ARG    73      14.870  20.772   5.056  1.00 25.00           C
ATOM     74  CA  THR    74      15.817  21.185   8.754  1.00 25.00           C
TER
END
