
#######################################################
#                                                     #
#                        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 T0361AL242_5-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected  158 , name T0361_D1.pdb
# PARAMETERS: T0361AL242_5-D1.T0361_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      E       6           -
LGA    -       -      D       7           -
LGA    -       -      D       8           -
LGA    -       -      V       9           -
LGA    -       -      L      10           -
LGA    -       -      E      11           -
LGA    -       -      Q      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      A      15           -
LGA    -       -      Q      16           -
LGA    -       -      D      17           -
LGA    L      41      N      18          3.701
LGA    F      42      L      19          0.939
LGA    V      43      F      20          2.112
LGA    -       -      S      21           -
LGA    -       -      F      22           -
LGA    D      44      M      23          1.575
LGA    N      45      K      24          1.966
LGA    D      46      T      25          2.476
LGA    E      47      A      26          2.264
LGA    E      48      H      27          2.176
LGA    I      49      S      28          1.857
LGA    V      50      I      29          0.782
LGA    E      51      L      30          1.566
LGA    Y      52      L      31          1.156
LGA    A      53      Q      32          0.724
LGA    V      54      G      33          2.084
LGA    K      55      I      34          2.483
LGA    P      56      R      35          0.934
LGA    -       -      Q      36           -
LGA    L      57      F      37          2.083
LGA    L      58      L      38          1.329
LGA    -       -      P      39           -
LGA    A      59      S      40          3.945
LGA    Q      60      L      41          4.437
LGA    S      61      F      42           #
LGA    G      62      V      43           -
LGA    -       -      D      44           -
LGA    -       -      N      45           -
LGA    -       -      D      46           -
LGA    -       -      E      47           -
LGA    -       -      E      48           -
LGA    -       -      I      49           -
LGA    -       -      V      50           -
LGA    -       -      E      51           -
LGA    -       -      Y      52           -
LGA    -       -      A      53           -
LGA    -       -      V      54           -
LGA    -       -      K      55           -
LGA    -       -      P      56           -
LGA    -       -      L      57           -
LGA    -       -      L      58           -
LGA    -       -      A      59           -
LGA    -       -      Q      60           -
LGA    -       -      S      61           -
LGA    -       -      G      62           -
LGA    -       -      P      63           -
LGA    -       -      L      64           -
LGA    -       -      D      65           -
LGA    -       -      D      66           -
LGA    -       -      I      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Y      75           -
LGA    P      63      A      76          4.363
LGA    -       -      L      77           -
LGA    -       -      G      78           -
LGA    L      64      K      79          4.792
LGA    D      65      M      80           -
LGA    -       -      D      81           -
LGA    -       -      K      82           -
LGA    -       -      W      83           -
LGA    -       -      L      84           -
LGA    -       -      Y      85           -
LGA    -       -      A      86           -
LGA    -       -      D      87           -
LGA    -       -      I      88           -
LGA    -       -      T      89           -
LGA    -       -      H      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      Q      93           -
LGA    -       -      Y      94           -
LGA    -       -      W      95           -
LGA    -       -      H      96           -
LGA    -       -      Y      97           -
LGA    -       -      L      98           -
LGA    -       -      N      99           -
LGA    -       -      E     100           -
LGA    -       -      Q     101           -
LGA    -       -      D     102           -
LGA    -       -      E     103           -
LGA    -       -      T     104           -
LGA    -       -      P     105           -
LGA    -       -      G     106           -
LGA    -       -      F     107           -
LGA    -       -      A     108           -
LGA    -       -      D     109           -
LGA    -       -      D     110           -
LGA    -       -      I     111           -
LGA    -       -      T     112           -
LGA    -       -      W     113           -
LGA    -       -      D     114           -
LGA    -       -      F     115           -
LGA    -       -      I     116           -
LGA    -       -      S     117           -
LGA    -       -      N     118           -
LGA    -       -      V     119           -
LGA    -       -      N     120           -
LGA    -       -      S     121           -
LGA    -       -      I     122           -
LGA    -       -      T     123           -
LGA    -       -      R     124           -
LGA    -       -      N     125           -
LGA    -       -      A     126           -
LGA    -       -      T     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      D     130           -
LGA    -       -      A     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    -       -      A     134           -
LGA    -       -      M     135           -
LGA    -       -      K     136           -
LGA    -       -      E     145           -
LGA    -       -      A     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      S     149           -
LGA    -       -      G     150           -
LGA    -       -      M     151           -
LGA    -       -      V     152           -
LGA    -       -      K     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      L     156           -
LGA    -       -      T     157           -
LGA    -       -      L     158           -
LGA    -       -      A     159           -
LGA    -       -      V     160           -
LGA    -       -      T     161           -
LGA    -       -      T     162           -
LGA    -       -      T     163           -
LGA    -       -      L     164           -
LGA    -       -      K     165           -
LGA    -       -      E     166           -
LGA    -       -      L     167           -
LGA    -       -      T     168           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25  158    5.0     22    2.56     4.55     11.429     0.826

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.081052 * X  +  -0.810783 * Y  +   0.579709 * Z  +  14.583797
  Y_new =   0.967990 * X  +  -0.074584 * Y  +  -0.239653 * Z  +   1.587839
  Z_new =   0.237543 * X  +   0.580576 * Y  +   0.778784 * Z  +  18.100363 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.640609   -2.500984  [ DEG:    36.7042   -143.2958 ]
  Theta =  -0.239836   -2.901757  [ DEG:   -13.7416   -166.2584 ]
  Phi   =   1.487259   -1.654334  [ DEG:    85.2137    -94.7863 ]
 
# 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: T0361AL242_5-D1                               
REMARK     2: T0361_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0361AL242_5-D1.T0361_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  158   5.0   22   2.56    4.55  11.429
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL242_5-D1
REMARK Aligment from pdb entry: 2mlp
ATOM      1  N   LEU    41      -1.070  -7.826  31.688  1.00  0.00              
ATOM      2  CA  LEU    41      -0.787  -6.363  31.850  1.00  0.00              
ATOM      3  C   LEU    41       0.674  -6.009  31.378  1.00  0.00              
ATOM      4  O   LEU    41       1.649  -6.265  32.091  1.00  0.00              
ATOM      5  N   PHE    42       0.835  -5.475  30.148  1.00  0.00              
ATOM      6  CA  PHE    42       2.120  -5.536  29.373  1.00  0.00              
ATOM      7  C   PHE    42       2.161  -4.497  28.186  1.00  0.00              
ATOM      8  O   PHE    42       2.318  -3.293  28.414  1.00  0.00              
ATOM      9  N   VAL    43       1.954  -4.944  26.931  1.00  0.00              
ATOM     10  CA  VAL    43       1.706  -4.077  25.727  1.00  0.00              
ATOM     11  C   VAL    43       2.507  -2.719  25.726  1.00  0.00              
ATOM     12  O   VAL    43       1.979  -1.683  25.306  1.00  0.00              
ATOM     13  N   ASP    44       3.794  -2.724  26.129  1.00  0.00              
ATOM     14  CA  ASP    44       4.826  -1.703  25.737  1.00  0.00              
ATOM     15  C   ASP    44       4.472  -0.919  24.417  1.00  0.00              
ATOM     16  O   ASP    44       4.914  -1.298  23.324  1.00  0.00              
ATOM     17  N   ASN    45       3.729   0.202  24.507  1.00  0.00              
ATOM     18  CA  ASN    45       3.586   1.226  23.408  1.00  0.00              
ATOM     19  C   ASN    45       4.057   2.673  23.803  1.00  0.00              
ATOM     20  O   ASN    45       4.543   3.430  22.954  1.00  0.00              
ATOM     21  N   ASP    46       4.003   3.035  25.101  1.00  0.00              
ATOM     22  CA  ASP    46       4.901   4.087  25.688  1.00  0.00              
ATOM     23  C   ASP    46       6.419   3.642  25.727  1.00  0.00              
ATOM     24  O   ASP    46       7.291   4.345  26.244  1.00  0.00              
ATOM     25  N   GLU    47       6.741   2.486  25.111  1.00  0.00              
ATOM     26  CA  GLU    47       8.125   1.972  24.844  1.00  0.00              
ATOM     27  C   GLU    47       8.255   1.281  23.434  1.00  0.00              
ATOM     28  O   GLU    47       9.350   0.891  23.020  1.00  0.00              
ATOM     29  N   GLU    48       7.143   1.189  22.667  1.00  0.00              
ATOM     30  CA  GLU    48       7.143   0.765  21.224  1.00  0.00              
ATOM     31  C   GLU    48       7.715   1.859  20.245  1.00  0.00              
ATOM     32  O   GLU    48       8.172   1.548  19.143  1.00  0.00              
ATOM     33  N   ILE    49       7.623   3.151  20.621  1.00  0.00              
ATOM     34  CA  ILE    49       8.306   4.275  19.888  1.00  0.00              
ATOM     35  C   ILE    49       9.844   4.381  20.240  1.00  0.00              
ATOM     36  O   ILE    49      10.697   4.640  19.389  1.00  0.00              
ATOM     37  N   VAL    50      10.198   4.110  21.515  1.00  0.00              
ATOM     38  CA  VAL    50      11.567   3.673  21.953  1.00  0.00              
ATOM     39  C   VAL    50      12.120   2.511  21.035  1.00  0.00              
ATOM     40  O   VAL    50      13.325   2.422  20.781  1.00  0.00              
ATOM     41  N   GLU    51      11.232   1.629  20.533  1.00  0.00              
ATOM     42  CA  GLU    51      11.587   0.408  19.742  1.00  0.00              
ATOM     43  C   GLU    51      11.985   0.790  18.270  1.00  0.00              
ATOM     44  O   GLU    51      13.077   0.489  17.784  1.00  0.00              
ATOM     45  N   TYR    52      11.033   1.383  17.511  1.00  0.00              
ATOM     46  CA  TYR    52      11.206   1.728  16.061  1.00  0.00              
ATOM     47  C   TYR    52      12.209   2.908  15.811  1.00  0.00              
ATOM     48  O   TYR    52      12.801   3.067  14.744  1.00  0.00              
ATOM     49  N   ALA    53      12.326   3.829  16.806  1.00  0.00              
ATOM     50  CA  ALA    53      13.472   4.790  16.920  1.00  0.00              
ATOM     51  C   ALA    53      14.833   4.134  17.382  1.00  0.00              
ATOM     52  O   ALA    53      15.918   4.602  17.024  1.00  0.00              
ATOM     53  N   VAL    54      14.754   3.014  18.125  1.00  0.00              
ATOM     54  CA  VAL    54      15.905   2.065  18.290  1.00  0.00              
ATOM     55  C   VAL    54      16.260   1.396  16.899  1.00  0.00              
ATOM     56  O   VAL    54      17.437   1.152  16.629  1.00  0.00              
ATOM     57  N   LYS    55      15.242   1.204  16.041  1.00  0.00              
ATOM     58  CA  LYS    55      15.387   0.626  14.664  1.00  0.00              
ATOM     59  C   LYS    55      16.123   1.624  13.682  1.00  0.00              
ATOM     60  O   LYS    55      16.919   1.229  12.834  1.00  0.00              
ATOM     61  N   PRO    56      15.848   2.944  13.829  1.00  0.00              
ATOM     62  CA  PRO    56      16.751   4.063  13.404  1.00  0.00              
ATOM     63  C   PRO    56      18.244   3.931  13.927  1.00  0.00              
ATOM     64  O   PRO    56      19.161   4.504  13.342  1.00  0.00              
ATOM     65  N   LEU    57      18.404   3.250  15.077  1.00  0.00              
ATOM     66  CA  LEU    57      19.727   2.719  15.556  1.00  0.00              
ATOM     67  C   LEU    57      20.128   1.292  15.040  1.00  0.00              
ATOM     68  O   LEU    57      21.295   0.886  15.115  1.00  0.00              
ATOM     69  N   LEU    58      19.889   1.344  11.902  1.00  0.00              
ATOM     70  CA  LEU    58      20.650   2.314  11.059  1.00  0.00              
ATOM     71  C   LEU    58      21.908   2.917  11.784  1.00  0.00              
ATOM     72  O   LEU    58      22.978   3.154  11.218  1.00  0.00              
ATOM     73  N   ALA    59      21.780   3.172  13.114  1.00  0.00              
ATOM     74  CA  ALA    59      22.984   3.288  14.026  1.00  0.00              
ATOM     75  C   ALA    59      24.063   2.200  13.578  1.00  0.00              
ATOM     76  O   ALA    59      25.282   2.372  13.526  1.00  0.00              
ATOM     77  N   GLN    60      23.548   1.019  13.166  1.00  0.00              
ATOM     78  CA  GLN    60      24.167  -0.200  12.550  1.00  0.00              
ATOM     79  C   GLN    60      24.099  -0.164  10.970  1.00  0.00              
ATOM     80  O   GLN    60      25.055  -0.203  10.194  1.00  0.00              
ATOM     81  N   SER    61      22.852   0.022  10.453  1.00  0.00              
ATOM     82  CA  SER    61      22.253  -0.260   9.097  1.00  0.00              
ATOM     83  C   SER    61      22.404  -1.731   8.531  1.00  0.00              
ATOM     84  O   SER    61      21.614  -2.195   7.706  1.00  0.00              
ATOM     85  N   GLY    62      23.475  -2.424   8.950  1.00  0.00              
ATOM     86  CA  GLY    62      24.044  -3.623   8.247  1.00  0.00              
ATOM     87  C   GLY    62      25.364  -4.246   8.861  1.00  0.00              
ATOM     88  O   GLY    62      26.448  -3.754   8.530  1.00  0.00              
ATOM     89  N   PRO    63      25.370  -5.338   9.677  1.00  0.00              
ATOM     90  CA  PRO    63      26.552  -6.109  10.191  1.00  0.00              
ATOM     91  C   PRO    63      27.975  -5.712   9.660  1.00  0.00              
ATOM     92  O   PRO    63      28.678  -6.505   9.027  1.00  0.00              
ATOM     93  N   LEU    64      28.438  -4.495  10.004  1.00  0.00              
ATOM     94  CA  LEU    64      29.766  -3.893   9.632  1.00  0.00              
ATOM     95  C   LEU    64      30.398  -4.408   8.280  1.00  0.00              
ATOM     96  O   LEU    64      29.723  -4.830   7.338  1.00  0.00              
ATOM     97  N   ASP    65      31.742  -4.270   8.152  1.00  0.00              
ATOM     98  CA  ASP    65      32.569  -4.968   7.117  1.00  0.00              
ATOM     99  C   ASP    65      32.028  -6.367   6.649  1.00  0.00              
ATOM    100  O   ASP    65      31.173  -6.456   5.763  1.00  0.00              
END
