
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS393_5.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      A       2           -
LGA    A       2      S       3           -
LGA    S       3      K       4           -
LGA    K       4      -       -           -
LGA    K       5      -       -           -
LGA    V       6      -       -           -
LGA    H       7      -       -           -
LGA    Q       8      -       -           -
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      K       5          4.023
LGA    M      17      V       6          2.632
LGA    D      18      H       7          3.372
LGA    V      19      Q       8          1.978
LGA    M      20      I       9          1.134
LGA    E      21      N      10          1.613
LGA    V      22      V      11          0.855
LGA    T      23      K      12          1.253
LGA    E      24      G      13          2.915
LGA    Q      25      F      14          2.810
LGA    T      26      F      15           #
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      V      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    K      27      E      30          3.709
LGA    E      28      Y      31          3.253
LGA    -       -      T      32           -
LGA    A      29      Y      33          2.264
LGA    E      30      D      34          5.222
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      -       -           -
LGA    D      34      -       -           -
LGA    F      35      F      35           #
LGA    K      36      K      36          4.382
LGA    E      37      E      37          2.890
LGA    I      38      I      38          3.709
LGA    L      39      L      39          1.420
LGA    S      40      S      40          1.421
LGA    E      41      E      41          2.868
LGA    F      42      F      42          2.834
LGA    N      43      N      43          3.198
LGA    G      44      G      44          2.586
LGA    K      45      K      45          2.256
LGA    N      46      N      46          3.806
LGA    V      47      V      47          4.528
LGA    S      48      S      48           #
LGA    I      49      I      49          4.969
LGA    T      50      T      50           #
LGA    V      51      V      51          4.891
LGA    K      52      K      52          1.219
LGA    E      53      E      53          3.654
LGA    E      54      E      54          2.732
LGA    N      55      N      55           #
LGA    E      56      E      56           -
LGA    L      57      L      57           -
LGA    P      58      P      58           -
LGA    V      59      V      59           -
LGA    K      60      K      60           -
LGA    G      61      G      61           -
LGA    V      62      V      62           -
LGA    E      63      E      63           -
LGA    M      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    D      67      -       -           -
LGA    P      68      -       -           -
LGA    L      69      -       -           -
LGA    E      70      -       -           -
LGA    H      71      -       -           -
LGA    H      72      -       -           -
LGA    H      73      -       -           -
LGA    H      74      -       -           -
LGA    H      75      -       -           -
LGA    H      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     31    3.15    58.06     30.664     0.954

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.157114 * X  +   0.882166 * Y  +  -0.443958 * Z  +   0.538329
  Y_new =  -0.831785 * X  +   0.360548 * Y  +   0.422064 * Z  + -12.933701
  Z_new =   0.532399 * X  +   0.302966 * Y  +   0.790420 * Z  +  -0.216997 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.366025   -2.775568  [ DEG:    20.9717   -159.0283 ]
  Theta =  -0.561432   -2.580161  [ DEG:   -32.1677   -147.8323 ]
  Phi   =  -1.384109    1.757484  [ DEG:   -79.3036    100.6964 ]
 
# 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_5                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS393_5.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   31   3.15   58.06  30.664
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS393_5
PFRMAT TS
TARGET T0309
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       5.703 -11.939  23.288  1.00 25.00           C
ATOM      2  CA  ALA     2       6.699 -11.219  19.633  1.00 25.00           C
ATOM      3  CA  SER     3       5.104 -11.622  16.191  1.00 25.00           C
ATOM      4  CA  LYS     4       4.127 -11.268  12.540  1.00 25.00           C
ATOM      5  CA  LYS     5       3.964 -10.719   8.757  1.00 25.00           C
ATOM      6  CA  VAL     6       1.569 -10.495   5.890  1.00 25.00           C
ATOM      7  CA  HIS     7       2.424 -13.954   4.710  1.00 25.00           C
ATOM      8  CA  GLN     8      -1.216 -14.962   4.972  1.00 25.00           C
ATOM      9  CA  ILE     9      -1.948 -17.824   2.578  1.00 25.00           C
ATOM     10  CA  ASN    10      -4.007 -20.462   0.745  1.00 25.00           C
ATOM     11  CA  VAL    11      -4.297 -22.938  -2.105  1.00 25.00           C
ATOM     12  CA  LYS    12      -8.100 -22.977  -2.134  1.00 25.00           C
ATOM     13  CA  GLY    13     -10.977 -24.855  -3.683  1.00 25.00           C
ATOM     14  CA  PHE    14     -13.418 -22.081  -4.512  1.00 25.00           C
ATOM     15  CA  PHE    15     -12.425 -20.626  -1.173  1.00 25.00           C
ATOM     16  CA  ASP    16     -13.519 -23.133   1.521  1.00 25.00           C
ATOM     17  CA  MET    17     -10.159 -22.192   3.170  1.00 25.00           C
ATOM     18  CA  ASP    18      -9.951 -18.365   2.871  1.00 25.00           C
ATOM     19  CA  VAL    19      -8.279 -17.359  -0.428  1.00 25.00           C
ATOM     20  CA  MET    20      -6.117 -17.736  -3.510  1.00 25.00           C
ATOM     21  CA  GLU    21      -2.713 -18.923  -4.743  1.00 25.00           C
ATOM     22  CA  VAL    22      -2.269 -16.553  -7.716  1.00 25.00           C
ATOM     23  CA  THR    23       0.665 -15.578  -9.924  1.00 25.00           C
ATOM     24  CA  GLU    24       1.333 -14.821 -13.630  1.00 25.00           C
ATOM     25  CA  GLN    25       3.946 -12.039 -13.584  1.00 25.00           C
ATOM     26  CA  THR    26       2.321  -9.469 -15.865  1.00 25.00           C
ATOM     27  CA  LYS    27      -0.740 -11.436 -16.803  1.00 25.00           C
ATOM     28  CA  GLU    28      -3.551  -9.628 -15.065  1.00 25.00           C
ATOM     29  CA  ALA    29      -2.277  -7.606 -12.103  1.00 25.00           C
ATOM     30  CA  GLU    30       0.854  -7.771  -9.948  1.00 25.00           C
ATOM     31  CA  TYR    31       3.149  -9.038  -7.155  1.00 25.00           C
ATOM     32  CA  THR    32       0.127  -9.491  -4.846  1.00 25.00           C
ATOM     33  CA  TYR    33      -1.711 -11.431  -7.589  1.00 25.00           C
ATOM     34  CA  ASP    34      -5.297 -12.309  -8.275  1.00 25.00           C
ATOM     35  CA  PHE    35      -5.678 -12.695  -4.467  1.00 25.00           C
ATOM     36  CA  LYS    36      -4.943  -8.936  -4.536  1.00 25.00           C
ATOM     37  CA  GLU    37      -8.682  -8.175  -4.202  1.00 25.00           C
ATOM     38  CA  ILE    38      -8.930 -10.578  -1.230  1.00 25.00           C
ATOM     39  CA  LEU    39      -5.918  -8.885   0.422  1.00 25.00           C
ATOM     40  CA  SER    40      -7.528  -5.450  -0.106  1.00 25.00           C
ATOM     41  CA  GLU    41     -10.794  -6.716   1.445  1.00 25.00           C
ATOM     42  CA  PHE    42      -8.862  -8.091   4.452  1.00 25.00           C
ATOM     43  CA  ASN    43     -11.791  -6.523   6.359  1.00 25.00           C
ATOM     44  CA  GLY    44     -12.390  -9.344   8.906  1.00 25.00           C
ATOM     45  CA  LYS    45     -11.054 -12.058   6.647  1.00 25.00           C
ATOM     46  CA  ASN    46      -7.211 -12.290   6.912  1.00 25.00           C
ATOM     47  CA  VAL    47      -7.267 -13.263   3.202  1.00 25.00           C
ATOM     48  CA  SER    48      -4.370 -13.622   0.851  1.00 25.00           C
ATOM     49  CA  ILE    49      -1.047 -14.014  -1.047  1.00 25.00           C
ATOM     50  CA  THR    50       1.076 -15.162  -3.984  1.00 25.00           C
ATOM     51  CA  VAL    51       2.340 -18.741  -4.252  1.00 25.00           C
ATOM     52  CA  LYS    52       5.929 -18.844  -3.184  1.00 25.00           C
ATOM     53  CA  GLU    53       9.053 -17.938  -1.247  1.00 25.00           C
ATOM     54  CA  GLU    54      11.265 -19.642  -3.869  1.00 25.00           C
ATOM     55  CA  ASN    55      12.254 -23.170  -2.783  1.00 25.00           C
ATOM     56  CA  GLU    56      11.923 -22.184   0.935  1.00 25.00           C
ATOM     57  CA  LEU    57       8.211 -22.745   0.273  1.00 25.00           C
ATOM     58  CA  PRO    58       7.190 -25.724  -1.864  1.00 25.00           C
ATOM     59  CA  VAL    59       3.570 -24.629  -1.888  1.00 25.00           C
ATOM     60  CA  LYS    60       3.427 -23.570   1.778  1.00 25.00           C
ATOM     61  CA  GLY    61       2.838 -20.539   3.974  1.00 25.00           C
ATOM     62  CA  VAL    62       2.781 -18.394   0.812  1.00 25.00           C
ATOM     63  CA  GLU    63       4.450 -15.016   0.015  1.00 25.00           C
ATOM     64  CA  MET    64       3.408 -11.584  -1.351  1.00 25.00           C
ATOM     65  CA  ALA    65       1.863  -9.053   1.047  1.00 25.00           C
ATOM     66  CA  GLY    66       4.725  -6.848  -0.260  1.00 25.00           C
ATOM     67  CA  ASP    67       4.003  -4.181   2.355  1.00 25.00           C
ATOM     68  CA  PRO    68       6.989  -1.818   2.192  1.00 25.00           C
ATOM     69  CA  LEU    69       8.327  -1.017   5.629  1.00 25.00           C
ATOM     70  CA  GLU    70      10.320   2.127   5.075  1.00 25.00           C
ATOM     71  CA  HIS    71      13.367   4.264   5.795  1.00 25.00           C
ATOM     72  CA  HIS    72      15.200   2.285   3.160  1.00 25.00           C
ATOM     73  CA  HIS    73      17.996  -0.268   3.821  1.00 25.00           C
ATOM     74  CA  HIS    74      20.780  -2.743   4.748  1.00 25.00           C
ATOM     75  CA  HIS    75      23.338  -3.311   1.989  1.00 25.00           C
ATOM     76  CA  HIS    76      22.034  -0.064   0.565  1.00 25.00           C
TER
END
