
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0361AL381_5
# Molecule2: number of CA atoms  166 ( 1335),  selected  166 , name T0361.pdb
# PARAMETERS: T0361AL381_5.T0361.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    P      39      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    -       -      N      18           -
LGA    -       -      L      19           -
LGA    -       -      F      20           -
LGA    -       -      S      21           -
LGA    -       -      F      22           -
LGA    -       -      M      23           -
LGA    -       -      K      24           -
LGA    -       -      T      25           -
LGA    -       -      A      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      I      29           -
LGA    -       -      L      30           -
LGA    -       -      L      31           -
LGA    -       -      Q      32           -
LGA    -       -      G      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      Q      36           -
LGA    -       -      F      37           -
LGA    -       -      L      38           -
LGA    -       -      P      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      F      42           -
LGA    -       -      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    S      40      D      66          4.250
LGA    L      41      I      67          2.827
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    F      42      A      70          2.225
LGA    V      43      L      71          3.053
LGA    D      44      R      72           #
LGA    N      45      L      73           #
LGA    -       -      I      74           -
LGA    D      46      Y      75          2.497
LGA    -       -      A      76           -
LGA    -       -      L      77           -
LGA    -       -      G      78           -
LGA    -       -      K      79           -
LGA    -       -      M      80           -
LGA    E      47      D      81          3.329
LGA    E      48      K      82          1.170
LGA    I      49      W      83          0.875
LGA    -       -      L      84           -
LGA    -       -      Y      85           -
LGA    -       -      A      86           -
LGA    V      50      D      87           #
LGA    E      51      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    Y      52      R     124          1.334
LGA    A      53      N     125           -
LGA    V      54      A     126           -
LGA    K      55      T     127           -
LGA    P      56      L     128           -
LGA    L      57      Y     129           -
LGA    L      58      D     130           -
LGA    A      59      A     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    -       -      A     134           -
LGA    -       -      M     135           -
LGA    -       -      K     136           -
LGA    -       -      F     137           -
LGA    -       -      A     138           -
LGA    -       -      D     139           -
LGA    -       -      F     140           -
LGA    -       -      A     141           -
LGA    -       -      V     142           -
LGA    -       -      W     143           -
LGA    P      63      S     144          5.269
LGA    L      64      E     145          0.757
LGA    D      65      A     146          2.108
LGA    D      66      R     147          1.651
LGA    -       -      F     148           -
LGA    -       -      S     149           -
LGA    I      67      G     150          2.332
LGA    D      68      M     151          1.017
LGA    V      69      V     152          3.467
LGA    -       -      K     153           -
LGA    -       -      T     154           -
LGA    A      70      A     155          2.852
LGA    -       -      L     156           -
LGA    L      71      T     157          1.417
LGA    -       -      L     158           -
LGA    -       -      A     159           -
LGA    R      72      V     160          1.373
LGA    L      73      T     161          2.260
LGA    -       -      T     162           -
LGA    -       -      T     163           -
LGA    I      74      L     164          1.519
LGA    Y      75      K     165          3.105
LGA    -       -      E     166           -
LGA    -       -      L     167           -
LGA    -       -      T     168           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  166    5.0     22    2.56     9.09      9.101     0.826

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.530182 * X  +  -0.545314 * Y  +  -0.649261 * Z  +  36.038624
  Y_new =   0.401123 * X  +   0.513316 * Y  +  -0.758688 * Z  +  -2.248910
  Z_new =   0.746999 * X  +  -0.662677 * Y  +  -0.053413 * Z  +  46.745323 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.651224    1.490368  [ DEG:   -94.6082     85.3918 ]
  Theta =  -0.843536   -2.298057  [ DEG:   -48.3311   -131.6689 ]
  Phi   =   2.493896   -0.647697  [ DEG:   142.8897    -37.1103 ]
 
# 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: T0361AL381_5                                  
REMARK     2: T0361.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0361AL381_5.T0361.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  166   5.0   22   2.56    9.09   9.101
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL381_5
REMARK Aligment from pdb entry: 4dcg
ATOM      1  N   PRO    39      13.194  -5.707  16.482  1.00  0.00              
ATOM      2  CA  PRO    39      13.068  -6.255  15.127  1.00  0.00              
ATOM      3  C   PRO    39      12.493  -5.137  14.256  1.00  0.00              
ATOM      4  O   PRO    39      12.987  -4.858  13.160  1.00  0.00              
ATOM      5  N   SER    40      11.478  -4.472  14.796  1.00  0.00              
ATOM      6  CA  SER    40      10.798  -3.361  14.141  1.00  0.00              
ATOM      7  C   SER    40      11.785  -2.242  13.801  1.00  0.00              
ATOM      8  O   SER    40      11.721  -1.655  12.723  1.00  0.00              
ATOM      9  N   LEU    41      12.711  -1.965  14.713  1.00  0.00              
ATOM     10  CA  LEU    41      13.707  -0.919  14.501  1.00  0.00              
ATOM     11  C   LEU    41      14.923  -1.415  13.736  1.00  0.00              
ATOM     12  O   LEU    41      15.894  -0.677  13.556  1.00  0.00              
ATOM     13  N   PHE    42      14.888  -2.683  13.338  1.00  0.00              
ATOM     14  CA  PHE    42      15.989  -3.266  12.593  1.00  0.00              
ATOM     15  C   PHE    42      17.262  -3.514  13.377  1.00  0.00              
ATOM     16  O   PHE    42      18.325  -3.712  12.794  1.00  0.00              
ATOM     17  N   VAL    43      17.164  -3.593  14.693  1.00  0.00              
ATOM     18  CA  VAL    43      18.367  -3.804  15.477  1.00  0.00              
ATOM     19  C   VAL    43      18.576  -5.208  16.031  1.00  0.00              
ATOM     20  O   VAL    43      19.582  -5.483  16.683  1.00  0.00              
ATOM     21  N   ASP    44      17.660  -6.114  15.711  1.00  0.00              
ATOM     22  CA  ASP    44      17.761  -7.489  16.194  1.00  0.00              
ATOM     23  C   ASP    44      18.652  -8.401  15.326  1.00  0.00              
ATOM     24  O   ASP    44      19.545  -9.085  15.833  1.00  0.00              
ATOM     25  N   ASN    45      18.411  -8.388  14.016  1.00  0.00              
ATOM     26  CA  ASN    45      19.158  -9.241  13.089  1.00  0.00              
ATOM     27  C   ASN    45      20.658  -9.031  13.190  1.00  0.00              
ATOM     28  O   ASN    45      21.143  -7.903  13.128  1.00  0.00              
ATOM     29  N   ASP    46      21.379 -10.130  13.371  1.00  0.00              
ATOM     30  CA  ASP    46      22.821 -10.077  13.470  1.00  0.00              
ATOM     31  C   ASP    46      23.355  -9.805  14.864  1.00  0.00              
ATOM     32  O   ASP    46      24.564  -9.759  15.054  1.00  0.00              
ATOM     33  N   GLU    47      22.479  -9.626  15.841  1.00  0.00              
ATOM     34  CA  GLU    47      22.937  -9.354  17.202  1.00  0.00              
ATOM     35  C   GLU    47      23.206 -10.608  18.012  1.00  0.00              
ATOM     36  O   GLU    47      22.831 -11.717  17.606  1.00  0.00              
ATOM     37  N   GLU    48      23.925 -10.436  19.120  1.00  0.00              
ATOM     38  CA  GLU    48      24.181 -11.522  20.063  1.00  0.00              
ATOM     39  C   GLU    48      23.422 -11.114  21.323  1.00  0.00              
ATOM     40  O   GLU    48      23.624 -10.005  21.838  1.00  0.00              
ATOM     41  N   ILE    49      22.467 -11.934  21.755  1.00  0.00              
ATOM     42  CA  ILE    49      21.718 -11.629  22.963  1.00  0.00              
ATOM     43  C   ILE    49      22.469 -12.239  24.152  1.00  0.00              
ATOM     44  O   ILE    49      22.655 -13.456  24.225  1.00  0.00              
ATOM     45  N   VAL    50      22.971 -11.385  25.042  1.00  0.00              
ATOM     46  CA  VAL    50      23.660 -11.848  26.240  1.00  0.00              
ATOM     47  C   VAL    50      22.611 -11.775  27.370  1.00  0.00              
ATOM     48  O   VAL    50      22.132 -10.686  27.715  1.00  0.00              
ATOM     49  N   GLU    51      22.194 -12.938  27.872  1.00  0.00              
ATOM     50  CA  GLU    51      21.179 -13.033  28.914  1.00  0.00              
ATOM     51  C   GLU    51      21.888 -13.503  30.170  1.00  0.00              
ATOM     52  O   GLU    51      22.409 -14.632  30.215  1.00  0.00              
ATOM     53  N   TYR    52      21.948 -12.620  31.169  1.00  0.00              
ATOM     54  CA  TYR    52      22.588 -12.907  32.455  1.00  0.00              
ATOM     55  C   TYR    52      21.492 -13.169  33.488  1.00  0.00              
ATOM     56  O   TYR    52      20.572 -12.351  33.678  1.00  0.00              
ATOM     57  N   ALA    53      27.046  -3.854  33.647  1.00  0.00              
ATOM     58  CA  ALA    53      26.789  -4.733  32.504  1.00  0.00              
ATOM     59  C   ALA    53      26.687  -3.853  31.260  1.00  0.00              
ATOM     60  O   ALA    53      27.254  -4.161  30.212  1.00  0.00              
ATOM     61  N   VAL    54      25.945  -2.756  31.385  1.00  0.00              
ATOM     62  CA  VAL    54      25.760  -1.812  30.285  1.00  0.00              
ATOM     63  C   VAL    54      27.053  -1.054  29.947  1.00  0.00              
ATOM     64  O   VAL    54      27.450  -0.972  28.779  1.00  0.00              
ATOM     65  N   LYS    55      27.743  -0.563  30.976  1.00  0.00              
ATOM     66  CA  LYS    55      28.984   0.178  30.759  1.00  0.00              
ATOM     67  C   LYS    55      30.086  -0.646  30.124  1.00  0.00              
ATOM     68  O   LYS    55      30.804  -0.152  29.261  1.00  0.00              
ATOM     69  N   PRO    56      30.232  -1.893  30.561  1.00  0.00              
ATOM     70  CA  PRO    56      31.270  -2.768  30.005  1.00  0.00              
ATOM     71  C   PRO    56      30.877  -3.422  28.669  1.00  0.00              
ATOM     72  O   PRO    56      31.664  -3.442  27.729  1.00  0.00              
ATOM     73  N   LEU    57      29.654  -3.930  28.573  1.00  0.00              
ATOM     74  CA  LEU    57      29.222  -4.586  27.343  1.00  0.00              
ATOM     75  C   LEU    57      28.876  -3.601  26.240  1.00  0.00              
ATOM     76  O   LEU    57      29.013  -3.915  25.058  1.00  0.00              
ATOM     77  N   LEU    58      28.420  -2.410  26.617  1.00  0.00              
ATOM     78  CA  LEU    58      28.043  -1.391  25.642  1.00  0.00              
ATOM     79  C   LEU    58      27.049  -1.946  24.591  1.00  0.00              
ATOM     80  O   LEU    58      27.309  -1.935  23.381  1.00  0.00              
ATOM     81  N   ALA    59      25.872  -2.391  25.050  1.00  0.00              
ATOM     82  CA  ALA    59      24.828  -2.956  24.195  1.00  0.00              
ATOM     83  C   ALA    59      24.053  -1.946  23.374  1.00  0.00              
ATOM     84  O   ALA    59      23.994  -0.769  23.734  1.00  0.00              
ATOM     85  N   PRO    63       3.636 -11.639  39.893  1.00  0.00              
ATOM     86  CA  PRO    63       2.895 -12.102  41.075  1.00  0.00              
ATOM     87  C   PRO    63       1.825 -11.056  41.419  1.00  0.00              
ATOM     88  O   PRO    63       1.972  -9.885  41.087  1.00  0.00              
ATOM     89  N   LEU    64       0.750 -11.498  42.061  1.00  0.00              
ATOM     90  CA  LEU    64      -0.380 -10.648  42.416  1.00  0.00              
ATOM     91  C   LEU    64      -0.065  -9.244  42.938  1.00  0.00              
ATOM     92  O   LEU    64      -0.684  -8.265  42.509  1.00  0.00              
ATOM     93  N   ASP    65       0.905  -9.134  43.836  1.00  0.00              
ATOM     94  CA  ASP    65       1.257  -7.841  44.398  1.00  0.00              
ATOM     95  C   ASP    65       2.669  -7.365  44.128  1.00  0.00              
ATOM     96  O   ASP    65       3.168  -6.452  44.794  1.00  0.00              
ATOM     97  N   ASP    66       3.295  -7.922  43.098  1.00  0.00              
ATOM     98  CA  ASP    66       4.642  -7.531  42.732  1.00  0.00              
ATOM     99  C   ASP    66       4.717  -6.088  42.186  1.00  0.00              
ATOM    100  O   ASP    66       3.855  -5.638  41.412  1.00  0.00              
ATOM    101  N   ILE    67       5.769  -5.372  42.576  1.00  0.00              
ATOM    102  CA  ILE    67       5.977  -4.001  42.112  1.00  0.00              
ATOM    103  C   ILE    67       7.075  -3.997  41.052  1.00  0.00              
ATOM    104  O   ILE    67       7.573  -2.947  40.656  1.00  0.00              
ATOM    105  N   ASP    68       7.436  -5.186  40.567  1.00  0.00              
ATOM    106  CA  ASP    68       8.491  -5.351  39.553  1.00  0.00              
ATOM    107  C   ASP    68       8.047  -5.016  38.129  1.00  0.00              
ATOM    108  O   ASP    68       6.921  -5.317  37.733  1.00  0.00              
ATOM    109  N   VAL    69       8.942  -4.410  37.355  1.00  0.00              
ATOM    110  CA  VAL    69       8.672  -4.079  35.955  1.00  0.00              
ATOM    111  C   VAL    69       9.971  -4.313  35.181  1.00  0.00              
ATOM    112  O   VAL    69      10.953  -4.800  35.756  1.00  0.00              
ATOM    113  N   ALA    70       9.974  -4.053  33.876  1.00  0.00              
ATOM    114  CA  ALA    70      11.193  -4.239  33.092  1.00  0.00              
ATOM    115  C   ALA    70      11.586  -2.923  32.425  1.00  0.00              
ATOM    116  O   ALA    70      10.789  -2.299  31.724  1.00  0.00              
ATOM    117  N   LEU    71      12.836  -2.526  32.625  1.00  0.00              
ATOM    118  CA  LEU    71      13.374  -1.283  32.071  1.00  0.00              
ATOM    119  C   LEU    71      13.933  -1.604  30.678  1.00  0.00              
ATOM    120  O   LEU    71      14.886  -2.367  30.555  1.00  0.00              
ATOM    121  N   ARG    72      13.305  -1.036  29.646  1.00  0.00              
ATOM    122  CA  ARG    72      13.686  -1.252  28.251  1.00  0.00              
ATOM    123  C   ARG    72      14.379  -0.018  27.682  1.00  0.00              
ATOM    124  O   ARG    72      13.751   1.026  27.558  1.00  0.00              
ATOM    125  N   LEU    73      15.635  -0.160  27.264  1.00  0.00              
ATOM    126  CA  LEU    73      16.411   0.961  26.719  1.00  0.00              
ATOM    127  C   LEU    73      17.082   0.643  25.379  1.00  0.00              
ATOM    128  O   LEU    73      17.516  -0.485  25.136  1.00  0.00              
ATOM    129  N   ILE    74      17.171   1.651  24.518  1.00  0.00              
ATOM    130  CA  ILE    74      17.824   1.528  23.216  1.00  0.00              
ATOM    131  C   ILE    74      18.903   2.604  23.217  1.00  0.00              
ATOM    132  O   ILE    74      18.622   3.781  23.458  1.00  0.00              
ATOM    133  N   TYR    75      20.135   2.198  22.959  1.00  0.00              
ATOM    134  CA  TYR    75      21.244   3.123  22.995  1.00  0.00              
ATOM    135  C   TYR    75      21.656   3.728  21.672  1.00  0.00              
ATOM    136  O   TYR    75      21.889   3.021  20.698  1.00  0.00              
END
