
#######################################################
#                                                     #
#                        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
# Molecule2: number of CA atoms  166 ( 1335),  selected  166 , name T0361.pdb
# PARAMETERS: T0361AL242_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    -       -      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    -       -      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    -       -      A      76           -
LGA    -       -      L      77           -
LGA    -       -      G      78           -
LGA    -       -      K      79           -
LGA    -       -      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    -       -      F     137           -
LGA    -       -      A     138           -
LGA    -       -      D     139           -
LGA    -       -      F     140           -
LGA    L      41      A     141          4.060
LGA    F      42      V     142          1.044
LGA    V      43      W     143          1.407
LGA    D      44      S     144          2.732
LGA    N      45      E     145          1.230
LGA    D      46      A     146          1.418
LGA    E      47      R     147          0.882
LGA    E      48      F     148          1.466
LGA    I      49      S     149          1.374
LGA    V      50      G     150          0.636
LGA    E      51      M     151          2.008
LGA    Y      52      V     152          2.169
LGA    A      53      K     153          1.652
LGA    V      54      T     154          1.395
LGA    K      55      A     155          2.820
LGA    P      56      L     156          2.845
LGA    L      57      T     157          0.685
LGA    -       -      L     158           -
LGA    L      58      A     159          3.317
LGA    A      59      V     160          4.316
LGA    Q      60      T     161          2.101
LGA    S      61      T     162          3.896
LGA    G      62      T     163          3.060
LGA    P      63      L     164           #
LGA    L      64      K     165          3.543
LGA    D      65      E     166          4.129
LGA    -       -      L     167           -
LGA    -       -      T     168           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25  166    5.0     24    2.53     0.00     11.679     0.912

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.663483 * X  +  -0.569823 * Y  +   0.484863 * Z  +   9.270231
  Y_new =   0.745008 * X  +  -0.443446 * Y  +   0.498316 * Z  +  -4.450675
  Z_new =  -0.068942 * X  +   0.691851 * Y  +   0.718742 * Z  +  36.026432 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.766337   -2.375256  [ DEG:    43.9079   -136.0921 ]
  Theta =   0.068996    3.072596  [ DEG:     3.9532    176.0468 ]
  Phi   =   2.298378   -0.843214  [ DEG:   131.6874    -48.3126 ]
 
# 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                                  
REMARK     2: T0361.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0361AL242_5.T0361.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  166   5.0   24   2.53    0.00  11.679
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL242_5
REMARK Aligment from pdb entry: 2mlp
ATOM      1  N   LEU    41       3.714 -17.343  53.949  1.00  0.00              
ATOM      2  CA  LEU    41       2.844 -16.163  53.634  1.00  0.00              
ATOM      3  C   LEU    41       3.649 -15.048  52.866  1.00  0.00              
ATOM      4  O   LEU    41       4.425 -14.300  53.469  1.00  0.00              
ATOM      5  N   PHE    42       3.514 -14.973  51.525  1.00  0.00              
ATOM      6  CA  PHE    42       4.530 -14.339  50.617  1.00  0.00              
ATOM      7  C   PHE    42       3.945 -14.017  49.188  1.00  0.00              
ATOM      8  O   PHE    42       3.167 -13.071  49.030  1.00  0.00              
ATOM      9  N   VAL    43       4.262 -14.833  48.163  1.00  0.00              
ATOM     10  CA  VAL    43       3.604 -14.829  46.811  1.00  0.00              
ATOM     11  C   VAL    43       3.184 -13.399  46.294  1.00  0.00              
ATOM     12  O   VAL    43       2.125 -13.244  45.676  1.00  0.00              
ATOM     13  N   ASP    44       4.030 -12.366  46.484  1.00  0.00              
ATOM     14  CA  ASP    44       4.053 -11.107  45.662  1.00  0.00              
ATOM     15  C   ASP    44       3.395 -11.267  44.240  1.00  0.00              
ATOM     16  O   ASP    44       4.092 -11.530  43.251  1.00  0.00              
ATOM     17  N   ASN    45       2.070 -11.053  44.111  1.00  0.00              
ATOM     18  CA  ASN    45       1.361 -10.843  42.796  1.00  0.00              
ATOM     19  C   ASN    45       0.605  -9.469  42.678  1.00  0.00              
ATOM     20  O   ASN    45       0.493  -8.905  41.583  1.00  0.00              
ATOM     21  N   ASP    46       0.165  -8.879  43.807  1.00  0.00              
ATOM     22  CA  ASP    46      -0.035  -7.393  43.922  1.00  0.00              
ATOM     23  C   ASP    46       1.327  -6.588  43.860  1.00  0.00              
ATOM     24  O   ASP    46       1.367  -5.365  44.014  1.00  0.00              
ATOM     25  N   GLU    47       2.444  -7.283  43.566  1.00  0.00              
ATOM     26  CA  GLU    47       3.796  -6.710  43.256  1.00  0.00              
ATOM     27  C   GLU    47       4.536  -7.491  42.104  1.00  0.00              
ATOM     28  O   GLU    47       5.616  -7.090  41.663  1.00  0.00              
ATOM     29  N   GLU    48       3.920  -8.573  41.573  1.00  0.00              
ATOM     30  CA  GLU    48       4.384  -9.287  40.333  1.00  0.00              
ATOM     31  C   GLU    48       4.104  -8.487  39.004  1.00  0.00              
ATOM     32  O   GLU    48       4.763  -8.701  37.984  1.00  0.00              
ATOM     33  N   ILE    49       3.073  -7.617  38.998  1.00  0.00              
ATOM     34  CA  ILE    49       2.821  -6.644  37.876  1.00  0.00              
ATOM     35  C   ILE    49       3.766  -5.379  37.947  1.00  0.00              
ATOM     36  O   ILE    49       4.263  -4.871  36.940  1.00  0.00              
ATOM     37  N   VAL    50       4.063  -4.908  39.177  1.00  0.00              
ATOM     38  CA  VAL    50       5.271  -4.080  39.514  1.00  0.00              
ATOM     39  C   VAL    50       6.586  -4.708  38.900  1.00  0.00              
ATOM     40  O   VAL    50       7.508  -3.989  38.506  1.00  0.00              
ATOM     41  N   GLU    51       6.661  -6.052  38.816  1.00  0.00              
ATOM     42  CA  GLU    51       7.867  -6.819  38.370  1.00  0.00              
ATOM     43  C   GLU    51       8.032  -6.747  36.808  1.00  0.00              
ATOM     44  O   GLU    51       9.054  -6.313  36.273  1.00  0.00              
ATOM     45  N   TYR    52       7.035  -7.279  36.061  1.00  0.00              
ATOM     46  CA  TYR    52       7.068  -7.383  34.565  1.00  0.00              
ATOM     47  C   TYR    52       6.941  -6.000  33.835  1.00  0.00              
ATOM     48  O   TYR    52       7.354  -5.808  32.692  1.00  0.00              
ATOM     49  N   ALA    53       6.253  -5.026  34.490  1.00  0.00              
ATOM     50  CA  ALA    53       6.342  -3.569  34.147  1.00  0.00              
ATOM     51  C   ALA    53       7.699  -2.879  34.570  1.00  0.00              
ATOM     52  O   ALA    53       8.151  -1.923  33.934  1.00  0.00              
ATOM     53  N   VAL    54       8.364  -3.417  35.610  1.00  0.00              
ATOM     54  CA  VAL    54       9.818  -3.153  35.869  1.00  0.00              
ATOM     55  C   VAL    54      10.696  -3.754  34.696  1.00  0.00              
ATOM     56  O   VAL    54      11.712  -3.158  34.335  1.00  0.00              
ATOM     57  N   LYS    55      10.227  -4.861  34.093  1.00  0.00              
ATOM     58  CA  LYS    55      10.893  -5.549  32.938  1.00  0.00              
ATOM     59  C   LYS    55      10.795  -4.696  31.610  1.00  0.00              
ATOM     60  O   LYS    55      11.720  -4.643  30.804  1.00  0.00              
ATOM     61  N   PRO    56       9.644  -4.007  31.406  1.00  0.00              
ATOM     62  CA  PRO    56       9.512  -2.788  30.545  1.00  0.00              
ATOM     63  C   PRO    56      10.578  -1.653  30.853  1.00  0.00              
ATOM     64  O   PRO    56      10.864  -0.818  29.996  1.00  0.00              
ATOM     65  N   LEU    57      11.049  -1.618  32.114  1.00  0.00              
ATOM     66  CA  LEU    57      12.288  -0.870  32.522  1.00  0.00              
ATOM     67  C   LEU    57      13.643  -1.650  32.390  1.00  0.00              
ATOM     68  O   LEU    57      14.729  -1.057  32.404  1.00  0.00              
ATOM     69  N   LEU    58      13.789  -2.751  29.445  1.00  0.00              
ATOM     70  CA  LEU    58      13.712  -1.856  28.252  1.00  0.00              
ATOM     71  C   LEU    58      14.067  -0.358  28.573  1.00  0.00              
ATOM     72  O   LEU    58      14.697   0.377  27.809  1.00  0.00              
ATOM     73  N   ALA    59      13.650   0.122  29.775  1.00  0.00              
ATOM     74  CA  ALA    59      14.295   1.329  30.423  1.00  0.00              
ATOM     75  C   ALA    59      15.867   1.266  30.154  1.00  0.00              
ATOM     76  O   ALA    59      16.590   2.222  29.872  1.00  0.00              
ATOM     77  N   GLN    60      16.403   0.024  30.185  1.00  0.00              
ATOM     78  CA  GLN    60      17.771  -0.500  29.864  1.00  0.00              
ATOM     79  C   GLN    60      17.874  -1.011  28.371  1.00  0.00              
ATOM     80  O   GLN    60      18.646  -0.598  27.506  1.00  0.00              
ATOM     81  N   SER    61      16.938  -1.936  28.015  1.00  0.00              
ATOM     82  CA  SER    61      16.878  -2.957  26.905  1.00  0.00              
ATOM     83  C   SER    61      18.097  -3.958  26.775  1.00  0.00              
ATOM     84  O   SER    61      17.976  -5.067  26.249  1.00  0.00              
ATOM     85  N   GLY    62      19.285  -3.510  27.212  1.00  0.00              
ATOM     86  CA  GLY    62      20.614  -4.084  26.811  1.00  0.00              
ATOM     87  C   GLY    62      21.902  -3.355  27.374  1.00  0.00              
ATOM     88  O   GLY    62      22.333  -2.376  26.757  1.00  0.00              
ATOM     89  N   PRO    63      22.597  -3.793  28.462  1.00  0.00              
ATOM     90  CA  PRO    63      23.907  -3.286  28.994  1.00  0.00              
ATOM     91  C   PRO    63      24.663  -2.190  28.164  1.00  0.00              
ATOM     92  O   PRO    63      25.785  -2.389  27.692  1.00  0.00              
ATOM     93  N   LEU    64      24.072  -0.982  28.066  1.00  0.00              
ATOM     94  CA  LEU    64      24.598   0.227  27.341  1.00  0.00              
ATOM     95  C   LEU    64      25.552  -0.069  26.118  1.00  0.00              
ATOM     96  O   LEU    64      25.493  -1.105  25.452  1.00  0.00              
ATOM     97  N   ASP    65      26.394   0.932  25.755  1.00  0.00              
ATOM     98  CA  ASP    65      27.579   0.758  24.856  1.00  0.00              
ATOM     99  C   ASP    65      28.260  -0.659  24.902  1.00  0.00              
ATOM    100  O   ASP    65      27.832  -1.594  24.218  1.00  0.00              
END
