
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0350AL509_1
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350AL509_1.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    V      12      M       1           -
LGA    W      13      N       2           -
LGA    D      14      I       3           -
LGA    R      15      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    -       -      Q      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      N      28           -
LGA    Y      16      E      29           #
LGA    D      17      V      30          2.977
LGA    -       -      P      31           -
LGA    T      18      V      32          2.382
LGA    Q      19      H      33          1.069
LGA    I      20      Q      34          2.249
LGA    H      21      V      35          1.777
LGA    N      22      S      36          2.601
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    Q      23      N      39          0.674
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    K      24      E      42          5.870
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    V      30      H      57          2.181
LGA    P      31      L      58          0.744
LGA    V      32      K      59          0.568
LGA    H      33      F      60          0.837
LGA    Q      34      E      61          0.578
LGA    V      35      L      62          0.497
LGA    S      36      H      63          0.640
LGA    Y      37      D      64          1.476
LGA    -       -      K      65           -
LGA    T      38      L      66           #
LGA    N      39      -       -           -
LGA    A      41      -       -           -
LGA    E      42      N      67           #
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -
LGA    -       -      D     106           -
LGA    -       -      E     107           -
LGA    -       -      K     108           -
LGA    -       -      K     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25  109    5.0     16    2.17     0.00     12.442     0.706

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.294141 * X  +   0.954821 * Y  +  -0.042404 * Z  + -20.380253
  Y_new =  -0.707672 * X  +  -0.187755 * Y  +   0.681138 * Z  +  25.000156
  Z_new =   0.642403 * X  +   0.230358 * Y  +   0.730926 * Z  + -121.912720 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.305306   -2.836287  [ DEG:    17.4927   -162.5073 ]
  Theta =  -0.697630   -2.443963  [ DEG:   -39.9712   -140.0287 ]
  Phi   =  -1.964717    1.176876  [ DEG:  -112.5700     67.4300 ]
 
# 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: T0350AL509_1                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL509_1.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  109   5.0   16   2.17    0.00  12.442
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL509_1
REMARK Aligment from pdb entry: 1g8x_A
ATOM      1  N   VAL    12      -8.133  11.829 -23.928  1.00  0.00              
ATOM      2  CA  VAL    12      -8.562  10.442 -23.841  1.00  0.00              
ATOM      3  C   VAL    12      -7.404   9.501 -23.540  1.00  0.00              
ATOM      4  O   VAL    12      -7.609   8.409 -23.022  1.00  0.00              
ATOM      5  N   TRP    13      -6.182   9.912 -23.844  1.00  0.00              
ATOM      6  CA  TRP    13      -5.065   9.016 -23.605  1.00  0.00              
ATOM      7  C   TRP    13      -4.334   9.134 -22.285  1.00  0.00              
ATOM      8  O   TRP    13      -3.572   8.238 -21.937  1.00  0.00              
ATOM      9  N   ASP    14      -3.511   2.720 -20.444  1.00  0.00              
ATOM     10  CA  ASP    14      -2.434   1.770 -20.729  1.00  0.00              
ATOM     11  C   ASP    14      -2.472   1.269 -22.173  1.00  0.00              
ATOM     12  O   ASP    14      -3.537   1.165 -22.775  1.00  0.00              
ATOM     13  N   ARG    15      -1.301   0.944 -22.712  1.00  0.00              
ATOM     14  CA  ARG    15      -1.176   0.484 -24.090  1.00  0.00              
ATOM     15  C   ARG    15      -2.307  -0.397 -24.593  1.00  0.00              
ATOM     16  O   ARG    15      -2.839  -0.165 -25.688  1.00  0.00              
ATOM     17  N   TYR    16      -2.695  -1.392 -23.806  1.00  0.00              
ATOM     18  CA  TYR    16      -3.758  -2.296 -24.233  1.00  0.00              
ATOM     19  C   TYR    16      -5.167  -1.900 -23.770  1.00  0.00              
ATOM     20  O   TYR    16      -6.109  -2.670 -23.917  1.00  0.00              
ATOM     21  N   ASP    17      -5.304  -0.705 -23.205  1.00  0.00              
ATOM     22  CA  ASP    17      -6.605  -0.206 -22.751  1.00  0.00              
ATOM     23  C   ASP    17      -7.184   0.767 -23.777  1.00  0.00              
ATOM     24  O   ASP    17      -8.361   1.144 -23.703  1.00  0.00              
ATOM     25  N   THR    18      -6.351   1.190 -24.723  1.00  0.00              
ATOM     26  CA  THR    18      -6.801   2.091 -25.762  1.00  0.00              
ATOM     27  C   THR    18      -6.294   1.642 -27.108  1.00  0.00              
ATOM     28  O   THR    18      -5.414   0.799 -27.194  1.00  0.00              
ATOM     29  N   GLN    19      -6.868   2.220 -28.156  1.00  0.00              
ATOM     30  CA  GLN    19      -6.508   1.932 -29.535  1.00  0.00              
ATOM     31  C   GLN    19      -5.067   2.370 -29.795  1.00  0.00              
ATOM     32  O   GLN    19      -4.552   3.244 -29.108  1.00  0.00              
ATOM     33  N   ILE    20      -4.391   1.756 -30.780  1.00  0.00              
ATOM     34  CA  ILE    20      -3.003   2.132 -31.094  1.00  0.00              
ATOM     35  C   ILE    20      -2.964   3.612 -31.469  1.00  0.00              
ATOM     36  O   ILE    20      -3.879   4.103 -32.124  1.00  0.00              
ATOM     37  N   HIS    21      -1.912   4.320 -31.067  1.00  0.00              
ATOM     38  CA  HIS    21      -1.813   5.748 -31.365  1.00  0.00              
ATOM     39  C   HIS    21      -0.471   6.322 -30.937  1.00  0.00              
ATOM     40  O   HIS    21       0.098   5.875 -29.941  1.00  0.00              
ATOM     41  N   ASN    22       0.042   7.324 -31.649  1.00  0.00              
ATOM     42  CA  ASN    22       1.317   7.864 -31.222  1.00  0.00              
ATOM     43  C   ASN    22       1.134   8.409 -29.798  1.00  0.00              
ATOM     44  O   ASN    22       2.072   8.378 -28.997  1.00  0.00              
ATOM     45  N   GLN    23      -0.074   8.881 -29.472  1.00  0.00              
ATOM     46  CA  GLN    23      -0.335   9.405 -28.127  1.00  0.00              
ATOM     47  C   GLN    23      -0.221   8.325 -27.018  1.00  0.00              
ATOM     48  O   GLN    23       0.226   8.600 -25.905  1.00  0.00              
ATOM     49  N   LYS    24      -0.617   7.096 -27.326  1.00  0.00              
ATOM     50  CA  LYS    24      -0.558   6.010 -26.355  1.00  0.00              
ATOM     51  C   LYS    24       0.883   5.671 -26.020  1.00  0.00              
ATOM     52  O   LYS    24       1.229   5.477 -24.859  1.00  0.00              
ATOM     53  N   VAL    30      11.076   5.910 -12.412  1.00  0.00              
ATOM     54  CA  VAL    30      12.120   6.878 -12.126  1.00  0.00              
ATOM     55  C   VAL    30      13.328   6.576 -12.990  1.00  0.00              
ATOM     56  O   VAL    30      14.476   6.647 -12.538  1.00  0.00              
ATOM     57  N   PRO    31      13.039   6.250 -14.248  1.00  0.00              
ATOM     58  CA  PRO    31      14.052   5.910 -15.240  1.00  0.00              
ATOM     59  C   PRO    31      13.820   6.657 -16.561  1.00  0.00              
ATOM     60  O   PRO    31      12.677   6.921 -16.939  1.00  0.00              
ATOM     61  N   VAL    32      14.906   7.002 -17.256  1.00  0.00              
ATOM     62  CA  VAL    32      14.813   7.719 -18.533  1.00  0.00              
ATOM     63  C   VAL    32      14.136   6.890 -19.608  1.00  0.00              
ATOM     64  O   VAL    32      14.262   5.663 -19.629  1.00  0.00              
ATOM     65  N   HIS    33      13.456   7.568 -20.526  1.00  0.00              
ATOM     66  CA  HIS    33      12.773   6.884 -21.618  1.00  0.00              
ATOM     67  C   HIS    33      13.262   7.423 -22.958  1.00  0.00              
ATOM     68  O   HIS    33      13.840   8.510 -23.033  1.00  0.00              
ATOM     69  N   GLN    34      13.051   6.653 -24.020  1.00  0.00              
ATOM     70  CA  GLN    34      13.421   7.124 -25.350  1.00  0.00              
ATOM     71  C   GLN    34      12.444   6.621 -26.383  1.00  0.00              
ATOM     72  O   GLN    34      11.955   5.487 -26.312  1.00  0.00              
ATOM     73  N   VAL    35      12.151   7.495 -27.335  1.00  0.00              
ATOM     74  CA  VAL    35      11.263   7.184 -28.442  1.00  0.00              
ATOM     75  C   VAL    35      12.068   7.185 -29.735  1.00  0.00              
ATOM     76  O   VAL    35      12.419   8.250 -30.249  1.00  0.00              
ATOM     77  N   SER    36      12.364   5.993 -30.245  1.00  0.00              
ATOM     78  CA  SER    36      13.121   5.843 -31.489  1.00  0.00              
ATOM     79  C   SER    36      12.168   5.700 -32.668  1.00  0.00              
ATOM     80  O   SER    36      11.552   4.652 -32.848  1.00  0.00              
ATOM     81  N   TYR    37      12.061   6.766 -33.466  1.00  0.00              
ATOM     82  CA  TYR    37      11.168   6.823 -34.635  1.00  0.00              
ATOM     83  C   TYR    37      11.902   6.754 -35.976  1.00  0.00              
ATOM     84  O   TYR    37      12.469   7.742 -36.417  1.00  0.00              
ATOM     85  N   THR    38      12.281   8.034 -46.190  1.00  0.00              
ATOM     86  CA  THR    38      12.045   9.449 -46.377  1.00  0.00              
ATOM     87  C   THR    38      10.604   9.678 -46.833  1.00  0.00              
ATOM     88  O   THR    38      10.199   9.199 -47.885  1.00  0.00              
ATOM     89  N   ASN    39       9.829  10.419 -46.060  1.00  0.00              
ATOM     90  CA  ASN    39       8.455  10.665 -46.451  1.00  0.00              
ATOM     91  C   ASN    39       7.492   9.694 -45.791  1.00  0.00              
ATOM     92  O   ASN    39       6.296   9.685 -46.066  1.00  0.00              
ATOM     93  N   ALA    41       8.009   8.869 -44.902  1.00  0.00              
ATOM     94  CA  ALA    41       7.162   7.907 -44.225  1.00  0.00              
ATOM     95  C   ALA    41       6.302   8.523 -43.112  1.00  0.00              
ATOM     96  O   ALA    41       5.289   7.941 -42.729  1.00  0.00              
ATOM     97  N   GLU    42       6.726   9.676 -42.583  1.00  0.00              
ATOM     98  CA  GLU    42       5.977  10.356 -41.533  1.00  0.00              
ATOM     99  C   GLU    42       6.681  10.482 -40.189  1.00  0.00              
ATOM    100  O   GLU    42       6.035  10.747 -39.170  1.00  0.00              
END
