
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0343AL242_1
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343AL242_1.T0343.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    -       -      T       2           -
LGA    -       -      W       3           -
LGA    -       -      R       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      I      19           -
LGA    -       -      V      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      D      26           -
LGA    -       -      C      27           -
LGA    -       -      P      28           -
LGA    V      78      C      29          4.833
LGA    K      79      E      30          2.576
LGA    L      80      -       -           -
LGA    V      81      P      31          0.815
LGA    S      82      I      32          1.842
LGA    L      83      P      33          2.676
LGA    D      84      P      34          0.302
LGA    G      85      T      35          3.003
LGA    P      86      L      36          4.109
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    -       -      N      54           -
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    A      87      W      64          3.122
LGA    P      88      A      65          4.397
LGA    -       -      I      66           -
LGA    -       -      E      67           -
LGA    -       -      V      68           -
LGA    P      89      L      69          3.007
LGA    K      90      E      70          0.928
LGA    -       -      R      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    V      91      D      74          2.906
LGA    M      92      G      75          1.249
LGA    K      93      E      76          3.036
LGA    R      94      N      77          1.490
LGA    L      95      V      78           -
LGA    S      96      K      79           -
LGA    L      97      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    -       -      M      92           -
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20   94    5.0     16    2.82     0.00     11.057     0.547

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.298105 * X  +   0.265499 * Y  +  -0.916866 * Z  +  54.165356
  Y_new =  -0.309085 * X  +  -0.935637 * Y  +  -0.170440 * Z  + 111.341354
  Z_new =  -0.903106 * X  +   0.232581 * Y  +   0.360980 * Z  +  17.228342 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.572361   -2.569232  [ DEG:    32.7938   -147.2061 ]
  Theta =   1.126948    2.014645  [ DEG:    64.5693    115.4307 ]
  Phi   =  -2.338113    0.803480  [ DEG:  -133.9640     46.0360 ]
 
# 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: T0343AL242_1                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343AL242_1.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   94   5.0   16   2.82    0.00  11.057
REMARK  ---------------------------------------------------------- 
MOLECULE T0343AL242_1
REMARK Aligment from pdb entry: 1pjm_A
ATOM      1  N   VAL    78      20.935  45.606   1.178  1.00  0.00              
ATOM      2  CA  VAL    78      21.227  44.512   2.153  1.00  0.00              
ATOM      3  C   VAL    78      20.293  44.600   3.367  1.00  0.00              
ATOM      4  O   VAL    78      19.788  45.678   3.707  1.00  0.00              
ATOM      5  N   LYS    79      20.062  43.465   4.020  1.00  0.00              
ATOM      6  CA  LYS    79      19.187  43.481   5.172  1.00  0.00              
ATOM      7  C   LYS    79      19.097  42.211   5.993  1.00  0.00              
ATOM      8  O   LYS    79      20.101  41.643   6.428  1.00  0.00              
ATOM      9  N   LEU    80      17.856  41.789   6.202  1.00  0.00              
ATOM     10  CA  LEU    80      17.518  40.620   6.994  1.00  0.00              
ATOM     11  C   LEU    80      18.248  39.343   6.613  1.00  0.00              
ATOM     12  O   LEU    80      18.282  38.960   5.445  1.00  0.00              
ATOM     13  N   VAL    81      18.822  38.685   7.612  1.00  0.00              
ATOM     14  CA  VAL    81      19.522  37.427   7.411  1.00  0.00              
ATOM     15  C   VAL    81      18.758  36.395   8.220  1.00  0.00              
ATOM     16  O   VAL    81      18.567  36.553   9.427  1.00  0.00              
ATOM     17  N   SER    82      18.307  35.344   7.545  1.00  0.00              
ATOM     18  CA  SER    82      17.521  34.298   8.195  1.00  0.00              
ATOM     19  C   SER    82      18.209  33.522   9.300  1.00  0.00              
ATOM     20  O   SER    82      19.442  33.444   9.357  1.00  0.00              
ATOM     21  N   LEU    83      17.380  32.971  10.185  1.00  0.00              
ATOM     22  CA  LEU    83      17.834  32.152  11.297  1.00  0.00              
ATOM     23  C   LEU    83      18.270  30.861  10.649  1.00  0.00              
ATOM     24  O   LEU    83      17.434  30.069  10.188  1.00  0.00              
ATOM     25  N   ASP    84      19.574  30.662  10.563  1.00  0.00              
ATOM     26  CA  ASP    84      20.072  29.452   9.948  1.00  0.00              
ATOM     27  C   ASP    84      21.233  28.827  10.688  1.00  0.00              
ATOM     28  O   ASP    84      22.163  29.506  11.131  1.00  0.00              
ATOM     29  N   GLY    85      21.144  27.508  10.823  1.00  0.00              
ATOM     30  CA  GLY    85      22.138  26.741  11.544  1.00  0.00              
ATOM     31  C   GLY    85      21.403  26.138  12.727  1.00  0.00              
ATOM     32  O   GLY    85      20.244  26.486  12.979  1.00  0.00              
ATOM     33  N   PRO    86      22.067  25.244  13.450  1.00  0.00              
ATOM     34  CA  PRO    86      21.475  24.581  14.612  1.00  0.00              
ATOM     35  C   PRO    86      20.912  25.534  15.680  1.00  0.00              
ATOM     36  O   PRO    86      20.434  26.629  15.374  1.00  0.00              
ATOM     37  N   ALA    87      20.953  25.090  16.934  1.00  0.00              
ATOM     38  CA  ALA    87      20.481  25.886  18.064  1.00  0.00              
ATOM     39  C   ALA    87      21.186  25.341  19.315  1.00  0.00              
ATOM     40  O   ALA    87      21.891  26.081  20.005  1.00  0.00              
ATOM     41  N   PRO    88      21.009  24.035  19.624  1.00  0.00              
ATOM     42  CA  PRO    88      20.206  23.032  18.906  1.00  0.00              
ATOM     43  C   PRO    88      18.790  22.984  19.496  1.00  0.00              
ATOM     44  O   PRO    88      18.620  22.999  20.717  1.00  0.00              
ATOM     45  N   PRO    89      17.757  22.926  18.637  1.00  0.00              
ATOM     46  CA  PRO    89      16.375  22.880  19.132  1.00  0.00              
ATOM     47  C   PRO    89      16.026  21.600  19.907  1.00  0.00              
ATOM     48  O   PRO    89      16.851  20.687  20.033  1.00  0.00              
ATOM     49  N   LYS    90      14.803  21.555  20.433  1.00  0.00              
ATOM     50  CA  LYS    90      14.318  20.395  21.182  1.00  0.00              
ATOM     51  C   LYS    90      14.614  19.077  20.461  1.00  0.00              
ATOM     52  O   LYS    90      14.866  19.059  19.256  1.00  0.00              
ATOM     53  N   VAL    91      14.615  17.954  21.200  1.00  0.00              
ATOM     54  CA  VAL    91      14.872  16.684  20.512  1.00  0.00              
ATOM     55  C   VAL    91      13.608  16.402  19.692  1.00  0.00              
ATOM     56  O   VAL    91      12.503  16.747  20.107  1.00  0.00              
ATOM     57  N   MET    92      13.769  15.800  18.525  1.00  0.00              
ATOM     58  CA  MET    92      12.624  15.496  17.683  1.00  0.00              
ATOM     59  C   MET    92      11.676  14.494  18.363  1.00  0.00              
ATOM     60  O   MET    92      10.452  14.620  18.271  1.00  0.00              
ATOM     61  N   LYS    93      12.245  13.514  19.060  1.00  0.00              
ATOM     62  CA  LYS    93      11.448  12.481  19.702  1.00  0.00              
ATOM     63  C   LYS    93      11.744  12.302  21.192  1.00  0.00              
ATOM     64  O   LYS    93      12.729  12.839  21.705  1.00  0.00              
ATOM     65  N   ARG    94      10.875  11.551  21.874  1.00  0.00              
ATOM     66  CA  ARG    94      10.996  11.284  23.313  1.00  0.00              
ATOM     67  C   ARG    94      10.685   9.838  23.666  1.00  0.00              
ATOM     68  O   ARG    94       9.590   9.333  23.391  1.00  0.00              
ATOM     69  N   LEU    95      11.641   9.175  24.302  1.00  0.00              
ATOM     70  CA  LEU    95      11.464   7.791  24.728  1.00  0.00              
ATOM     71  C   LEU    95      10.839   7.865  26.122  1.00  0.00              
ATOM     72  O   LEU    95      11.235   8.695  26.938  1.00  0.00              
ATOM     73  N   SER    96       9.853   7.018  26.389  1.00  0.00              
ATOM     74  CA  SER    96       9.240   7.035  27.704  1.00  0.00              
ATOM     75  C   SER    96       9.931   6.041  28.645  1.00  0.00              
ATOM     76  O   SER    96       9.892   4.835  28.426  1.00  0.00              
ATOM     77  N   LEU    97      10.590   6.557  29.678  1.00  0.00              
ATOM     78  CA  LEU    97      11.274   5.702  30.633  1.00  0.00              
ATOM     79  C   LEU    97      10.299   5.210  31.682  1.00  0.00              
ATOM     80  O   LEU    97      10.463   4.078  32.197  1.00  0.00              
END
