
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0335TS168_5
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS168_5.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      -       -           -
LGA    S       3      -       -           -
LGA    N       4      I       2          5.756
LGA    -       -      S       3           -
LGA    A       5      N       4          1.365
LGA    -       -      A       5           -
LGA    K       6      K       6          2.966
LGA    I       7      I       7          2.106
LGA    A       8      A       8          1.224
LGA    R       9      R       9          2.733
LGA    I      10      I      10          2.826
LGA    N      11      N      11          1.509
LGA    E      12      E      12          2.103
LGA    L      13      L      13          3.729
LGA    A      14      A      14          2.597
LGA    A      15      A      15          1.366
LGA    K      16      K      16          3.408
LGA    A      17      A      17          4.114
LGA    K      18      K      18          1.543
LGA    A      19      A      19          2.891
LGA    G      20      G      20          1.524
LGA    V      21      V      21          1.094
LGA    I      22      I      22          1.882
LGA    T      23      T      23          0.838
LGA    E      24      E      24          1.544
LGA    E      25      E      25          0.670
LGA    E      26      E      26          0.917
LGA    K      27      K      27          1.227
LGA    A      28      A      28          0.937
LGA    E      29      E      29          0.901
LGA    Q      30      Q      30          1.482
LGA    Q      31      Q      31          1.564
LGA    K      32      K      32          1.733
LGA    L      33      L      33          1.369
LGA    R      34      R      34          1.365
LGA    Q      35      Q      35          0.657
LGA    E      36      E      36          1.320
LGA    Y      37      Y      37          1.782
LGA    L      38      L      38          0.928
LGA    K      39      K      39          1.361
LGA    G      40      G      40          2.393
LGA    F      41      F      41          0.658
LGA    R      42      -       -           -
LGA    S      43      -       -           -
LGA    S      44      R      42          1.936
LGA    M      45      -       -           -
LGA    K      46      -       -           -
LGA    N      47      -       -           -
LGA    T      48      -       -           -
LGA    L      49      -       -           -
LGA    K      50      -       -           -
LGA    S      51      -       -           -
LGA    V      52      -       -           -
LGA    K      53      -       -           -
LGA    I      54      -       -           -
LGA    I      55      -       -           -
LGA    D      56      -       -           -
LGA    P      57      -       -           -
LGA    E      58      -       -           -
LGA    G      59      -       -           -
LGA    N      60      -       -           -
LGA    D      61      -       -           -
LGA    V      62      -       -           -
LGA    T      63      -       -           -
LGA    P      64      -       -           -
LGA    E      65      -       -           -
LGA    K      66      -       -           -
LGA    L      67      -       -           -
LGA    K      68      -       -           -
LGA    R      69      -       -           -
LGA    E      70      -       -           -
LGA    Q      71      -       -           -
LGA    R      72      -       -           -
LGA    N      73      -       -           -
LGA    N      74      -       -           -
LGA    K      75      -       -           -
LGA    L      76      -       -           -
LGA    H      77      -       -           -
LGA    L      78      -       -           -
LGA    E      79      -       -           -
LGA    H      80      -       -           -
LGA    H      81      -       -           -
LGA    H      82      -       -           -
LGA    H      83      -       -           -
LGA    H      84      -       -           -
LGA    H      85      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   42    5.0     39    2.13    92.31     81.671     1.745

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.563336 * X  +   0.450078 * Y  +   0.692880 * Z  +   4.797042
  Y_new =   0.735360 * X  +   0.655458 * Y  +   0.172104 * Z  +   2.305432
  Z_new =  -0.376693 * X  +   0.606468 * Y  +  -0.700213 * Z  +  -6.433846 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.427814   -0.713779  [ DEG:   139.1035    -40.8965 ]
  Theta =   0.386224    2.755368  [ DEG:    22.1290    157.8710 ]
  Phi   =   2.224502   -0.917091  [ DEG:   127.4546    -52.5454 ]
 
# 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: T0335TS168_5                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_5.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   42   5.0   39   2.13   92.31  81.671
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_5
PFRMAT TS
TARGET T0335
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -7.470 -17.000 -14.439  1.00 25.00           C
ATOM      2  CA  ILE     2      -6.078 -14.635 -11.774  1.00 25.00           C
ATOM      3  CA  SER     3      -2.609 -13.159 -11.989  1.00 25.00           C
ATOM      4  CA  ASN     4      -1.463  -9.573 -11.138  1.00 25.00           C
ATOM      5  CA  ALA     5       0.225 -10.126  -7.744  1.00 25.00           C
ATOM      6  CA  LYS     6       1.462  -6.502  -7.742  1.00 25.00           C
ATOM      7  CA  ILE     7      -2.070  -5.269  -8.561  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.496  -7.382  -5.703  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.884  -5.941  -3.302  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.779  -2.390  -4.418  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.496  -3.124  -3.856  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.724  -4.482  -0.359  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.690  -1.337   0.440  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.584   0.868  -0.758  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.027  -1.104   1.434  1.00 25.00           C
ATOM     16  CA  LYS    16      -5.700  -0.684   4.447  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.480   3.081   3.784  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.298   3.293   3.577  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.607   1.393   6.888  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.362   1.065  10.634  1.00 25.00           C
ATOM     21  CA  VAL    21      -7.658   3.636  10.994  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.671   2.330   8.952  1.00 25.00           C
ATOM     23  CA  THR    23      -2.669   4.469  11.376  1.00 25.00           C
ATOM     24  CA  GLU    24       0.818   5.985  11.493  1.00 25.00           C
ATOM     25  CA  GLU    25       3.295   3.123  10.905  1.00 25.00           C
ATOM     26  CA  GLU    26       0.684   1.263   8.807  1.00 25.00           C
ATOM     27  CA  LYS    27       0.051   4.429   6.746  1.00 25.00           C
ATOM     28  CA  ALA    28       3.816   4.846   6.183  1.00 25.00           C
ATOM     29  CA  GLU    29       4.077   1.193   5.062  1.00 25.00           C
ATOM     30  CA  GLN    30       1.156   1.701   2.638  1.00 25.00           C
ATOM     31  CA  GLN    31       2.844   4.835   1.223  1.00 25.00           C
ATOM     32  CA  LYS    32       6.114   2.895   0.761  1.00 25.00           C
ATOM     33  CA  LEU    33       4.226   0.092  -1.041  1.00 25.00           C
ATOM     34  CA  ARG    34       2.547   2.663  -3.330  1.00 25.00           C
ATOM     35  CA  GLN    35       5.953   4.229  -4.110  1.00 25.00           C
ATOM     36  CA  GLU    36       7.384   0.773  -4.926  1.00 25.00           C
ATOM     37  CA  TYR    37       4.416   0.064  -7.240  1.00 25.00           C
ATOM     38  CA  LEU    38       4.951   3.424  -8.997  1.00 25.00           C
ATOM     39  CA  LYS    39       8.668   2.623  -9.450  1.00 25.00           C
ATOM     40  CA  GLY    40       7.778  -0.802 -10.913  1.00 25.00           C
ATOM     41  CA  PHE    41       5.304   0.845 -13.329  1.00 25.00           C
ATOM     42  CA  ARG    42       7.989   3.356 -14.405  1.00 25.00           C
ATOM     43  CA  SER    43      10.465   0.494 -14.992  1.00 25.00           C
ATOM     44  CA  SER    44       7.855  -1.366 -17.091  1.00 25.00           C
ATOM     45  CA  MET    45       7.221   1.800 -19.151  1.00 25.00           C
ATOM     46  CA  LYS    46      10.986   2.217 -19.714  1.00 25.00           C
ATOM     47  CA  ASN    47      11.247  -1.436 -20.835  1.00 25.00           C
ATOM     48  CA  THR    48       8.326  -0.927 -23.260  1.00 25.00           C
ATOM     49  CA  LEU    49      10.014   2.206 -24.674  1.00 25.00           C
ATOM     50  CA  LYS    50       6.829   3.938 -23.732  1.00 25.00           C
ATOM     51  CA  SER    51       3.452   3.684 -22.041  1.00 25.00           C
ATOM     52  CA  VAL    52       2.389   4.238 -18.403  1.00 25.00           C
ATOM     53  CA  LYS    53      -0.850   2.346 -17.668  1.00 25.00           C
ATOM     54  CA  ILE    54      -2.541   5.135 -15.602  1.00 25.00           C
ATOM     55  CA  ILE    55      -4.771   7.382 -13.479  1.00 25.00           C
ATOM     56  CA  ASP    56      -3.121  10.595 -14.679  1.00 25.00           C
ATOM     57  CA  PRO    57      -5.590  12.642 -12.676  1.00 25.00           C
ATOM     58  CA  GLU    58      -4.385  15.886 -14.292  1.00 25.00           C
ATOM     59  CA  GLY    59      -3.847  18.356 -11.469  1.00 25.00           C
ATOM     60  CA  ASN    60      -0.137  18.104 -12.348  1.00 25.00           C
ATOM     61  CA  ASP    61       0.979  14.809 -14.003  1.00 25.00           C
ATOM     62  CA  VAL    62       2.735  11.421 -13.585  1.00 25.00           C
ATOM     63  CA  THR    63       4.162  10.228 -16.914  1.00 25.00           C
ATOM     64  CA  PRO    64       7.508  11.887 -16.009  1.00 25.00           C
ATOM     65  CA  GLU    65       9.856  14.293 -14.176  1.00 25.00           C
ATOM     66  CA  LYS    66       9.565  12.187 -10.990  1.00 25.00           C
ATOM     67  CA  LEU    67      10.362   9.016 -12.984  1.00 25.00           C
ATOM     68  CA  LYS    68      13.419  10.728 -14.530  1.00 25.00           C
ATOM     69  CA  ARG    69      14.605  11.808 -11.052  1.00 25.00           C
ATOM     70  CA  GLU    70      14.180   8.226  -9.767  1.00 25.00           C
ATOM     71  CA  GLN    71      16.185   6.894 -12.744  1.00 25.00           C
ATOM     72  CA  ARG    72      18.957   9.443 -12.049  1.00 25.00           C
ATOM     73  CA  ASN    73      19.032   8.395  -8.366  1.00 25.00           C
ATOM     74  CA  ASN    74      19.278   4.713  -9.395  1.00 25.00           C
ATOM     75  CA  LYS    75      22.916   4.764 -10.504  1.00 25.00           C
ATOM     76  CA  LEU    76      23.710   4.049  -6.845  1.00 25.00           C
ATOM     77  CA  HIS    77      23.791   0.732  -5.046  1.00 25.00           C
ATOM     78  CA  LEU    78      23.290  -2.886  -5.954  1.00 25.00           C
ATOM     79  CA  GLU    79      21.067  -3.947  -3.073  1.00 25.00           C
ATOM     80  CA  HIS    80      20.370  -1.974   0.065  1.00 25.00           C
ATOM     81  CA  HIS    81      17.532  -4.351   1.101  1.00 25.00           C
ATOM     82  CA  HIS    82      15.362  -4.502   4.263  1.00 25.00           C
ATOM     83  CA  HIS    83      17.477  -1.721   5.768  1.00 25.00           C
ATOM     84  CA  HIS    84      14.977  -1.944   8.663  1.00 25.00           C
ATOM     85  CA  HIS    85      12.960  -4.879  10.098  1.00 25.00           C
TER
END
