
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS393_3.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    A       2      -       -           -
LGA    S       3      -       -           -
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      A       2           #
LGA    F      15      S       3           #
LGA    D      16      K       4          1.873
LGA    M      17      K       5          1.690
LGA    D      18      V       6          3.477
LGA    V      19      H       7          3.822
LGA    M      20      Q       8          2.095
LGA    E      21      I       9          3.498
LGA    V      22      N      10          4.564
LGA    T      23      V      11          5.162
LGA    E      24      K      12           -
LGA    Q      25      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    T      26      V      22          3.004
LGA    K      27      T      23          4.410
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    E      28      D      34          3.139
LGA    A      29      F      35          3.628
LGA    E      30      K      36           -
LGA    Y      31      E      37           -
LGA    T      32      -       -           -
LGA    Y      33      -       -           -
LGA    D      34      -       -           -
LGA    F      35      I      38          3.695
LGA    K      36      L      39          0.892
LGA    E      37      S      40          2.700
LGA    I      38      E      41          3.954
LGA    L      39      F      42          3.164
LGA    S      40      N      43          1.811
LGA    E      41      G      44          4.568
LGA    F      42      K      45          2.747
LGA    N      43      N      46          2.994
LGA    G      44      -       -           -
LGA    K      45      -       -           -
LGA    N      46      V      47          1.983
LGA    V      47      S      48          2.410
LGA    S      48      I      49          3.176
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      -       -           -
LGA    M      64      -       -           -
LGA    A      65      T      50          4.986
LGA    G      66      V      51          5.569
LGA    D      67      K      52          3.916
LGA    P      68      E      53           #
LGA    L      69      E      54           #
LGA    E      70      -       -           -
LGA    H      71      -       -           -
LGA    H      72      N      55           #
LGA    H      73      E      56          4.004
LGA    H      74      L      57          2.466
LGA    H      75      P      58          1.734
LGA    H      76      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     30    3.43     3.33     28.298     0.850

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.455482 * X  +  -0.156841 * Y  +   0.876320 * Z  +  -4.267393
  Y_new =  -0.349912 * X  +  -0.873593 * Y  +  -0.338226 * Z  + -17.877829
  Z_new =   0.818595 * X  +  -0.460691 * Y  +   0.343026 * Z  +  -3.203167 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.930767    2.210826  [ DEG:   -53.3290    126.6710 ]
  Theta =  -0.958960   -2.182633  [ DEG:   -54.9444   -125.0556 ]
  Phi   =  -2.486531    0.655062  [ DEG:  -142.4677     37.5323 ]
 
# 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_3                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS393_3.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   30   3.43    3.33  28.298
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS393_3
PFRMAT TS
TARGET T0309
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1     -25.932  -9.619 -11.868  1.00 25.00           C
ATOM      2  CA  ALA     2     -22.160  -9.295 -12.318  1.00 25.00           C
ATOM      3  CA  SER     3     -19.645 -11.393 -10.386  1.00 25.00           C
ATOM      4  CA  LYS     4     -17.481 -14.251  -9.112  1.00 25.00           C
ATOM      5  CA  LYS     5     -15.053 -13.647  -6.323  1.00 25.00           C
ATOM      6  CA  VAL     6     -12.253 -14.635  -8.670  1.00 25.00           C
ATOM      7  CA  HIS     7     -11.761 -18.346  -7.856  1.00 25.00           C
ATOM      8  CA  GLN     8     -11.477 -20.430  -4.665  1.00 25.00           C
ATOM      9  CA  ILE     9      -9.492 -21.987  -1.742  1.00 25.00           C
ATOM     10  CA  ASN    10      -6.668 -22.276   0.803  1.00 25.00           C
ATOM     11  CA  VAL    11      -3.711 -23.563   2.825  1.00 25.00           C
ATOM     12  CA  LYS    12      -5.225 -24.272   6.218  1.00 25.00           C
ATOM     13  CA  GLY    13      -5.607 -26.083   9.559  1.00 25.00           C
ATOM     14  CA  PHE    14      -8.602 -27.767   7.961  1.00 25.00           C
ATOM     15  CA  PHE    15     -10.697 -24.573   8.027  1.00 25.00           C
ATOM     16  CA  ASP    16     -14.521 -24.429   8.465  1.00 25.00           C
ATOM     17  CA  MET    17     -14.497 -22.631   5.073  1.00 25.00           C
ATOM     18  CA  ASP    18     -12.153 -19.624   5.157  1.00 25.00           C
ATOM     19  CA  VAL    19      -9.436 -18.113   2.898  1.00 25.00           C
ATOM     20  CA  MET    20      -8.511 -17.116  -0.654  1.00 25.00           C
ATOM     21  CA  GLU    21     -10.191 -15.662  -3.751  1.00 25.00           C
ATOM     22  CA  VAL    22      -7.556 -15.692  -6.454  1.00 25.00           C
ATOM     23  CA  THR    23      -6.201 -13.347  -9.066  1.00 25.00           C
ATOM     24  CA  GLU    24      -6.141 -10.255 -11.258  1.00 25.00           C
ATOM     25  CA  GLN    25      -3.189  -9.682 -13.535  1.00 25.00           C
ATOM     26  CA  THR    26       0.608 -10.002 -13.034  1.00 25.00           C
ATOM     27  CA  LYS    27       0.499  -6.165 -13.020  1.00 25.00           C
ATOM     28  CA  GLU    28      -1.007  -5.560  -9.579  1.00 25.00           C
ATOM     29  CA  ALA    29       0.578  -7.451  -6.648  1.00 25.00           C
ATOM     30  CA  GLU    30       1.906 -10.954  -7.349  1.00 25.00           C
ATOM     31  CA  TYR    31      -1.026 -13.268  -8.195  1.00 25.00           C
ATOM     32  CA  THR    32      -0.890 -14.766  -4.673  1.00 25.00           C
ATOM     33  CA  TYR    33      -0.891 -11.252  -3.150  1.00 25.00           C
ATOM     34  CA  ASP    34      -4.083 -10.370  -4.963  1.00 25.00           C
ATOM     35  CA  PHE    35      -6.452 -12.263  -2.586  1.00 25.00           C
ATOM     36  CA  LYS    36      -5.825  -9.176  -0.409  1.00 25.00           C
ATOM     37  CA  GLU    37      -9.595  -8.756   0.125  1.00 25.00           C
ATOM     38  CA  ILE    38      -9.889 -12.444   1.115  1.00 25.00           C
ATOM     39  CA  LEU    39      -6.995 -12.037   3.589  1.00 25.00           C
ATOM     40  CA  SER    40      -8.683  -8.945   5.092  1.00 25.00           C
ATOM     41  CA  GLU    41     -11.968 -10.880   5.448  1.00 25.00           C
ATOM     42  CA  PHE    42     -10.117 -13.755   7.174  1.00 25.00           C
ATOM     43  CA  ASN    43      -8.717 -11.328   9.739  1.00 25.00           C
ATOM     44  CA  GLY    44      -5.588  -9.158   9.742  1.00 25.00           C
ATOM     45  CA  LYS    45      -2.685 -11.094   8.102  1.00 25.00           C
ATOM     46  CA  ASN    46      -4.565 -14.318   7.333  1.00 25.00           C
ATOM     47  CA  VAL    47      -3.958 -16.237   4.125  1.00 25.00           C
ATOM     48  CA  SER    48      -2.379 -15.016   0.905  1.00 25.00           C
ATOM     49  CA  ILE    49      -3.641 -18.297  -0.516  1.00 25.00           C
ATOM     50  CA  THR    50      -5.208 -19.808  -3.608  1.00 25.00           C
ATOM     51  CA  VAL    51      -6.920 -21.514  -6.557  1.00 25.00           C
ATOM     52  CA  LYS    52      -5.699 -20.823 -10.063  1.00 25.00           C
ATOM     53  CA  GLU    53      -4.848 -23.434 -12.765  1.00 25.00           C
ATOM     54  CA  GLU    54      -3.424 -26.930 -13.102  1.00 25.00           C
ATOM     55  CA  ASN    55      -5.706 -29.918 -12.313  1.00 25.00           C
ATOM     56  CA  GLU    56      -8.186 -28.155 -14.663  1.00 25.00           C
ATOM     57  CA  LEU    57     -10.010 -25.819 -12.331  1.00 25.00           C
ATOM     58  CA  PRO    58     -12.437 -27.730 -10.065  1.00 25.00           C
ATOM     59  CA  VAL    59     -10.463 -26.263  -7.205  1.00 25.00           C
ATOM     60  CA  LYS    60      -7.623 -28.638  -6.412  1.00 25.00           C
ATOM     61  CA  GLY    61      -6.080 -25.978  -4.145  1.00 25.00           C
ATOM     62  CA  VAL    62      -3.666 -25.381  -7.065  1.00 25.00           C
ATOM     63  CA  GLU    63      -1.390 -22.712  -5.528  1.00 25.00           C
ATOM     64  CA  MET    64       0.510 -19.700  -6.875  1.00 25.00           C
ATOM     65  CA  ALA    65       1.474 -19.224  -3.209  1.00 25.00           C
ATOM     66  CA  GLY    66       2.523 -21.337  -0.153  1.00 25.00           C
ATOM     67  CA  ASP    67       4.921 -18.580   0.958  1.00 25.00           C
ATOM     68  CA  PRO    68       7.356 -21.117   2.457  1.00 25.00           C
ATOM     69  CA  LEU    69       9.202 -23.479   0.116  1.00 25.00           C
ATOM     70  CA  GLU    70      12.992 -23.803   0.112  1.00 25.00           C
ATOM     71  CA  HIS    71      16.740 -23.437   0.370  1.00 25.00           C
ATOM     72  CA  HIS    72      18.550 -23.710  -2.914  1.00 25.00           C
ATOM     73  CA  HIS    73      18.479 -22.445  -6.552  1.00 25.00           C
ATOM     74  CA  HIS    74      22.144 -23.007  -7.187  1.00 25.00           C
ATOM     75  CA  HIS    75      22.556 -21.096 -10.444  1.00 25.00           C
ATOM     76  CA  HIS    76      19.394 -22.872 -11.517  1.00 25.00           C
TER
END
