
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0309TS393_1
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS393_1.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       2           -
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    -       -      K       5           -
LGA    M       1      V       6          2.426
LGA    A       2      H       7          0.950
LGA    S       3      Q       8          1.963
LGA    K       4      I       9          1.310
LGA    K       5      N      10          2.751
LGA    V       6      V      11          1.404
LGA    H       7      K      12           #
LGA    Q       8      G      13           #
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      -       -           -
LGA    M      17      -       -           -
LGA    D      18      -       -           -
LGA    V      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    V      22      F      14          0.957
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    Q      25      -       -           -
LGA    T      26      -       -           -
LGA    K      27      -       -           -
LGA    E      28      -       -           -
LGA    A      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      -       -           -
LGA    D      34      -       -           -
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      -       -           -
LGA    I      38      -       -           -
LGA    L      39      -       -           -
LGA    S      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      F      15           #
LGA    N      43      -       -           -
LGA    G      44      D      16           #
LGA    K      45      M      17          4.556
LGA    N      46      D      18          4.163
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    V      47      E      21          2.802
LGA    S      48      V      22          1.991
LGA    I      49      T      23          2.561
LGA    T      50      E      24          0.805
LGA    V      51      Q      25          4.773
LGA    K      52      T      26          1.713
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    N      55      -       -           -
LGA    E      56      -       -           -
LGA    L      57      -       -           -
LGA    P      58      K      27          2.989
LGA    V      59      E      28          4.414
LGA    K      60      -       -           -
LGA    G      61      -       -           -
LGA    V      62      A      29          3.407
LGA    E      63      E      30          2.287
LGA    M      64      Y      31          2.329
LGA    A      65      T      32          2.963
LGA    G      66      Y      33          3.164
LGA    D      67      D      34          4.284
LGA    P      68      F      35           -
LGA    L      69      K      36           -
LGA    E      70      E      37           -
LGA    H      71      I      38           -
LGA    H      72      L      39           -
LGA    H      73      S      40           -
LGA    H      74      E      41           -
LGA    H      75      F      42           -
LGA    H      76      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    -       -      T      50           -
LGA    -       -      V      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      N      55           -
LGA    -       -      E      56           -
LGA    -       -      L      57           -
LGA    -       -      P      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     23    2.90    13.04     24.543     0.767

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.278829 * X  +  -0.341224 * Y  +  -0.897675 * Z  +   0.671000
  Y_new =  -0.680908 * X  +   0.588920 * Y  +  -0.435358 * Z  +  -9.962831
  Z_new =   0.677213 * X  +   0.732625 * Y  +  -0.068134 * Z  + -13.793449 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.663529   -1.478063  [ DEG:    95.3132    -84.6868 ]
  Theta =  -0.743969   -2.397624  [ DEG:   -42.6263   -137.3737 ]
  Phi   =  -1.182131    1.959462  [ DEG:   -67.7311    112.2689 ]
 
# 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: T0309TS393_1                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS393_1.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76   62   5.0   23   2.90   13.04  24.543
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS393_1
PFRMAT TS
TARGET T0309
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1     -10.576 -22.139   1.923  1.00 25.00           C
ATOM      2  CA  ALA     2     -11.677 -19.180  -0.264  1.00 25.00           C
ATOM      3  CA  SER     3      -9.086 -18.243  -2.838  1.00 25.00           C
ATOM      4  CA  LYS     4      -5.992 -16.970  -4.623  1.00 25.00           C
ATOM      5  CA  LYS     5      -4.243 -17.000  -8.060  1.00 25.00           C
ATOM      6  CA  VAL     6      -1.155 -14.739  -8.262  1.00 25.00           C
ATOM      7  CA  HIS     7      -2.606 -11.584  -9.724  1.00 25.00           C
ATOM      8  CA  GLN     8      -1.453  -8.411 -11.499  1.00 25.00           C
ATOM      9  CA  ILE     9       0.386  -6.094 -13.879  1.00 25.00           C
ATOM     10  CA  ASN    10       2.378  -8.175 -16.397  1.00 25.00           C
ATOM     11  CA  VAL    11       2.763  -5.632 -19.115  1.00 25.00           C
ATOM     12  CA  LYS    12       0.872  -3.357 -21.423  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.623  -1.142 -23.216  1.00 25.00           C
ATOM     14  CA  PHE    14       0.814   1.776 -23.198  1.00 25.00           C
ATOM     15  CA  PHE    15       3.631  -0.466 -24.462  1.00 25.00           C
ATOM     16  CA  ASP    16       5.793   1.779 -22.310  1.00 25.00           C
ATOM     17  CA  MET    17       3.934   0.168 -19.409  1.00 25.00           C
ATOM     18  CA  ASP    18       1.630   0.017 -16.431  1.00 25.00           C
ATOM     19  CA  VAL    19       3.872  -2.703 -15.048  1.00 25.00           C
ATOM     20  CA  MET    20       4.769  -4.466 -11.832  1.00 25.00           C
ATOM     21  CA  GLU    21       5.067  -8.277 -12.180  1.00 25.00           C
ATOM     22  CA  VAL    22       6.641 -11.791 -11.922  1.00 25.00           C
ATOM     23  CA  THR    23       6.047 -14.367  -9.133  1.00 25.00           C
ATOM     24  CA  GLU    24       6.208 -17.169  -6.522  1.00 25.00           C
ATOM     25  CA  GLN    25       6.047 -20.945  -6.666  1.00 25.00           C
ATOM     26  CA  THR    26       9.811 -20.959  -6.081  1.00 25.00           C
ATOM     27  CA  LYS    27      10.260 -23.050  -9.257  1.00 25.00           C
ATOM     28  CA  GLU    28      12.864 -20.510 -10.351  1.00 25.00           C
ATOM     29  CA  ALA    29      14.852 -19.153 -13.344  1.00 25.00           C
ATOM     30  CA  GLU    30      11.663 -20.113 -15.211  1.00 25.00           C
ATOM     31  CA  TYR    31       8.225 -20.075 -16.898  1.00 25.00           C
ATOM     32  CA  THR    32       7.133 -17.165 -14.660  1.00 25.00           C
ATOM     33  CA  TYR    33      10.328 -15.250 -15.547  1.00 25.00           C
ATOM     34  CA  ASP    34       8.663 -14.470 -18.873  1.00 25.00           C
ATOM     35  CA  PHE    35       7.738 -10.864 -18.367  1.00 25.00           C
ATOM     36  CA  LYS    36      11.512 -10.481 -17.840  1.00 25.00           C
ATOM     37  CA  GLU    37      11.221  -6.693 -18.328  1.00 25.00           C
ATOM     38  CA  ILE    38       8.357  -6.562 -15.788  1.00 25.00           C
ATOM     39  CA  LEU    39      10.453  -8.565 -13.285  1.00 25.00           C
ATOM     40  CA  SER    40      13.398  -6.171 -13.797  1.00 25.00           C
ATOM     41  CA  GLU    41      11.089  -3.169 -13.225  1.00 25.00           C
ATOM     42  CA  PHE    42       9.754  -4.776 -10.014  1.00 25.00           C
ATOM     43  CA  ASN    43      11.846  -2.407  -7.964  1.00 25.00           C
ATOM     44  CA  GLY    44       9.180  -1.061  -5.605  1.00 25.00           C
ATOM     45  CA  LYS    45       6.489  -1.283  -8.286  1.00 25.00           C
ATOM     46  CA  ASN    46       5.416  -4.550  -6.774  1.00 25.00           C
ATOM     47  CA  VAL    47       2.530  -6.829  -7.901  1.00 25.00           C
ATOM     48  CA  SER    48       2.376 -10.494  -9.006  1.00 25.00           C
ATOM     49  CA  ILE    49       1.668 -12.469 -12.230  1.00 25.00           C
ATOM     50  CA  THR    50       2.353 -13.595 -15.768  1.00 25.00           C
ATOM     51  CA  VAL    51      -0.886 -15.652 -16.185  1.00 25.00           C
ATOM     52  CA  LYS    52       0.939 -18.191 -18.405  1.00 25.00           C
ATOM     53  CA  GLU    53      -1.913 -20.219 -19.748  1.00 25.00           C
ATOM     54  CA  GLU    54      -4.666 -22.595 -21.000  1.00 25.00           C
ATOM     55  CA  ASN    55      -2.977 -22.201 -24.383  1.00 25.00           C
ATOM     56  CA  GLU    56      -5.377 -19.307 -24.963  1.00 25.00           C
ATOM     57  CA  LEU    57      -3.885 -16.497 -22.985  1.00 25.00           C
ATOM     58  CA  PRO    58      -0.559 -17.718 -24.317  1.00 25.00           C
ATOM     59  CA  VAL    59       3.128 -17.204 -23.411  1.00 25.00           C
ATOM     60  CA  LYS    60       3.257 -14.146 -25.701  1.00 25.00           C
ATOM     61  CA  GLY    61       1.276 -11.492 -23.717  1.00 25.00           C
ATOM     62  CA  VAL    62       0.847 -13.694 -20.634  1.00 25.00           C
ATOM     63  CA  GLU    63      -1.108 -11.205 -18.520  1.00 25.00           C
ATOM     64  CA  MET    64      -3.315 -11.144 -15.448  1.00 25.00           C
ATOM     65  CA  ALA    65      -5.107  -7.784 -15.158  1.00 25.00           C
ATOM     66  CA  GLY    66      -7.056  -9.485 -12.389  1.00 25.00           C
ATOM     67  CA  ASP    67      -7.661  -5.871 -11.305  1.00 25.00           C
ATOM     68  CA  PRO    68     -11.356  -6.668 -12.048  1.00 25.00           C
ATOM     69  CA  LEU    69     -14.125  -5.043 -14.153  1.00 25.00           C
ATOM     70  CA  GLU    70     -17.441  -3.707 -12.824  1.00 25.00           C
ATOM     71  CA  HIS    71     -19.041  -2.656  -9.491  1.00 25.00           C
ATOM     72  CA  HIS    72     -18.573  -1.309  -5.965  1.00 25.00           C
ATOM     73  CA  HIS    73     -17.222   2.006  -4.655  1.00 25.00           C
ATOM     74  CA  HIS    74     -17.490   5.231  -6.600  1.00 25.00           C
ATOM     75  CA  HIS    75     -16.699   8.807  -5.739  1.00 25.00           C
ATOM     76  CA  HIS    76     -13.597   8.590  -7.895  1.00 25.00           C
TER
END
