
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0363AL242_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_3-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          1.693
LGA    Q      12      Q      12          1.491
LGA    I      13      I      13          1.437
LGA    N      14      N      14          0.697
LGA    I      15      I      15          1.231
LGA    E      16      E      16          1.311
LGA    I      17      I      17          1.151
LGA    A      18      A      18          1.427
LGA    Y      19      Y      19          1.859
LGA    D      33      A      20          3.056
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    E      34      Y      25          2.741
LGA    G      35      Y      26          4.013
LGA    I      36      L      27          2.597
LGA    T      37      K      28          1.228
LGA    V      38      S      29          1.230
LGA    Q      39      F      30          1.194
LGA    T      40      Q      31          1.492
LGA    A      41      V      32          0.746
LGA    I      42      D      33          2.984
LGA    T      43      E      34          3.449
LGA    Q      44      G      35          2.611
LGA    S      45      I      36          0.230
LGA    G      46      T      37          0.780
LGA    I      47      V      38          1.292
LGA    L      48      Q      39          1.538
LGA    S      49      T      40          1.168
LGA    Q      50      A      41          1.789
LGA    F      51      I      42          1.812
LGA    P      52      T      43          2.005
LGA    E      53      Q      44          1.981
LGA    I      54      S      45          3.560
LGA    D      55      G      46          5.521
LGA    -       -      I      47           -
LGA    L      56      L      48          2.202
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   46    5.0     33    2.21    30.30     61.236     1.430

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.594165 * X  +  -0.217619 * Y  +  -0.774345 * Z  +  26.852156
  Y_new =  -0.482183 * X  +  -0.674174 * Y  +   0.559453 * Z  +  15.318841
  Z_new =  -0.643791 * X  +   0.705784 * Y  +   0.295639 * Z  +   8.418121 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.174121   -1.967472  [ DEG:    67.2722   -112.7278 ]
  Theta =   0.699442    2.442150  [ DEG:    40.0751    139.9249 ]
  Phi   =  -2.459860    0.681732  [ DEG:  -140.9396     39.0604 ]
 
# 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: T0363AL242_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   46   5.0   33   2.21   30.30  61.236
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_3-D1
REMARK Aligment from pdb entry: 1ryj_A
ATOM      9  N   ASN    11      14.739   0.225  12.455  1.00  0.00              
ATOM     10  CA  ASN    11      15.958   1.007  12.314  1.00  0.00              
ATOM     11  C   ASN    11      16.193   1.386  10.859  1.00  0.00              
ATOM     12  O   ASN    11      16.085   0.550   9.958  1.00  0.00              
ATOM     13  N   GLN    12      16.499   2.656  10.646  1.00  0.00              
ATOM     14  CA  GLN    12      16.701   3.173   9.309  1.00  0.00              
ATOM     15  C   GLN    12      16.560   4.680   9.286  1.00  0.00              
ATOM     16  O   GLN    12      15.451   5.206   9.389  1.00  0.00              
ATOM     17  N   ILE    13      17.680   5.372   9.167  1.00  0.00              
ATOM     18  CA  ILE    13      17.683   6.825   9.246  1.00  0.00              
ATOM     19  C   ILE    13      17.992   7.446   7.890  1.00  0.00              
ATOM     20  O   ILE    13      18.949   7.060   7.224  1.00  0.00              
ATOM     21  N   ASN    14      17.176   8.400   7.482  1.00  0.00              
ATOM     22  CA  ASN    14      17.431   9.144   6.262  1.00  0.00              
ATOM     23  C   ASN    14      17.699  10.601   6.594  1.00  0.00              
ATOM     24  O   ASN    14      16.913  11.249   7.285  1.00  0.00              
ATOM     25  N   ILE    15      18.819  11.107   6.112  1.00  0.00              
ATOM     26  CA  ILE    15      19.247  12.455   6.431  1.00  0.00              
ATOM     27  C   ILE    15      19.808  13.136   5.195  1.00  0.00              
ATOM     28  O   ILE    15      20.049  12.485   4.175  1.00  0.00              
ATOM     29  N   GLU    16      20.006  14.438   5.276  1.00  0.00              
ATOM     30  CA  GLU    16      20.557  15.173   4.160  1.00  0.00              
ATOM     31  C   GLU    16      21.790  15.956   4.582  1.00  0.00              
ATOM     32  O   GLU    16      21.800  16.623   5.619  1.00  0.00              
ATOM     33  N   ILE    17      22.839  15.832   3.791  1.00  0.00              
ATOM     34  CA  ILE    17      24.043  16.610   3.988  1.00  0.00              
ATOM     35  C   ILE    17      24.157  17.634   2.871  1.00  0.00              
ATOM     36  O   ILE    17      24.213  17.271   1.701  1.00  0.00              
ATOM     37  N   ALA    18      24.166  18.908   3.220  1.00  0.00              
ATOM     38  CA  ALA    18      24.227  19.955   2.214  1.00  0.00              
ATOM     39  C   ALA    18      25.655  20.483   2.099  1.00  0.00              
ATOM     40  O   ALA    18      26.307  20.786   3.098  1.00  0.00              
ATOM     41  N   TYR    19      26.149  20.526   0.871  1.00  0.00              
ATOM     42  CA  TYR    19      27.484  21.032   0.580  1.00  0.00              
ATOM     43  C   TYR    19      27.439  21.830  -0.728  1.00  0.00              
ATOM     44  O   TYR    19      26.360  22.223  -1.169  1.00  0.00              
ATOM     45  N   ASP    33      28.595  22.076  -1.346  1.00  0.00              
ATOM     46  CA  ASP    33      28.654  22.767  -2.638  1.00  0.00              
ATOM     47  C   ASP    33      27.903  21.976  -3.703  1.00  0.00              
ATOM     48  O   ASP    33      27.389  22.534  -4.671  1.00  0.00              
ATOM     49  N   GLU    34      27.847  20.664  -3.498  1.00  0.00              
ATOM     50  CA  GLU    34      27.141  19.752  -4.395  1.00  0.00              
ATOM     51  C   GLU    34      25.627  19.879  -4.207  1.00  0.00              
ATOM     52  O   GLU    34      24.838  19.355  -4.994  1.00  0.00              
ATOM     53  N   GLY    35      25.232  20.608  -3.173  1.00  0.00              
ATOM     54  CA  GLY    35      23.830  20.767  -2.858  1.00  0.00              
ATOM     55  C   GLY    35      23.410  19.853  -1.730  1.00  0.00              
ATOM     56  O   GLY    35      24.258  19.334  -1.001  1.00  0.00              
ATOM     57  N   ILE    36      22.110  19.663  -1.574  1.00  0.00              
ATOM     58  CA  ILE    36      21.592  18.734  -0.585  1.00  0.00              
ATOM     59  C   ILE    36      21.744  17.304  -1.073  1.00  0.00              
ATOM     60  O   ILE    36      21.191  16.922  -2.107  1.00  0.00              
ATOM     61  N   THR    37      22.503  16.524  -0.328  1.00  0.00              
ATOM     62  CA  THR    37      22.748  15.133  -0.664  1.00  0.00              
ATOM     63  C   THR    37      21.886  14.245   0.223  1.00  0.00              
ATOM     64  O   THR    37      21.963  14.321   1.449  1.00  0.00              
ATOM     65  N   VAL    38      21.048  13.428  -0.396  1.00  0.00              
ATOM     66  CA  VAL    38      20.141  12.562   0.343  1.00  0.00              
ATOM     67  C   VAL    38      20.683  11.141   0.413  1.00  0.00              
ATOM     68  O   VAL    38      20.932  10.505  -0.614  1.00  0.00              
ATOM     69  N   GLN    39      20.887  10.661   1.628  1.00  0.00              
ATOM     70  CA  GLN    39      21.335   9.297   1.845  1.00  0.00              
ATOM     71  C   GLN    39      20.692   8.730   3.104  1.00  0.00              
ATOM     72  O   GLN    39      20.510   9.442   4.097  1.00  0.00              
ATOM     73  N   THR    40      20.321   7.461   3.057  1.00  0.00              
ATOM     74  CA  THR    40      19.725   6.809   4.209  1.00  0.00              
ATOM     75  C   THR    40      20.547   5.596   4.630  1.00  0.00              
ATOM     76  O   THR    40      21.045   4.842   3.796  1.00  0.00              
ATOM     77  N   ALA    41      20.699   5.436   5.933  1.00  0.00              
ATOM     78  CA  ALA    41      21.507   4.369   6.497  1.00  0.00              
ATOM     79  C   ALA    41      20.634   3.483   7.380  1.00  0.00              
ATOM     80  O   ALA    41      19.886   3.982   8.224  1.00  0.00              
ATOM     81  N   ILE    42      20.723   2.174   7.173  1.00  0.00              
ATOM     82  CA  ILE    42      19.905   1.236   7.922  1.00  0.00              
ATOM     83  C   ILE    42      20.201   1.254   9.410  1.00  0.00              
ATOM     84  O   ILE    42      19.313   1.010  10.228  1.00  0.00              
ATOM     85  N   THR    43      21.446   1.525   9.764  1.00  0.00              
ATOM     86  CA  THR    43      21.840   1.596  11.161  1.00  0.00              
ATOM     87  C   THR    43      22.079   3.043  11.578  1.00  0.00              
ATOM     88  O   THR    43      22.865   3.753  10.951  1.00  0.00              
ATOM     89  N   GLN    44      21.377   3.507  12.624  1.00  0.00              
ATOM     90  CA  GLN    44      21.575   4.849  13.183  1.00  0.00              
ATOM     91  C   GLN    44      22.978   5.013  13.764  1.00  0.00              
ATOM     92  O   GLN    44      23.317   4.409  14.784  1.00  0.00              
ATOM     93  N   SER    45      23.787   5.833  13.109  1.00  0.00              
ATOM     94  CA  SER    45      25.202   5.943  13.436  1.00  0.00              
ATOM     95  C   SER    45      25.571   7.351  13.886  1.00  0.00              
ATOM     96  O   SER    45      24.736   8.258  13.896  1.00  0.00              
ATOM     97  N   GLY    46      26.827   7.514  14.258  1.00  0.00              
ATOM     98  CA  GLY    46      27.354   8.780  14.727  1.00  0.00              
ATOM     99  C   GLY    46      27.893   9.591  13.548  1.00  0.00              
ATOM    100  O   GLY    46      28.204   9.023  12.498  1.00  0.00              
ATOM    101  N   ILE    47      27.983  10.914  13.714  1.00  0.00              
ATOM    102  CA  ILE    47      28.530  11.793  12.678  1.00  0.00              
ATOM    103  C   ILE    47      29.875  11.264  12.191  1.00  0.00              
ATOM    104  O   ILE    47      30.107  11.142  10.987  1.00  0.00              
ATOM    105  N   LEU    48      30.735  10.917  13.141  1.00  0.00              
ATOM    106  CA  LEU    48      32.088  10.463  12.847  1.00  0.00              
ATOM    107  C   LEU    48      32.101   9.214  11.973  1.00  0.00              
ATOM    108  O   LEU    48      33.037   9.009  11.206  1.00  0.00              
ATOM    109  N   SER    49      31.073   8.384  12.084  1.00  0.00              
ATOM    110  CA  SER    49      31.011   7.151  11.302  1.00  0.00              
ATOM    111  C   SER    49      30.909   7.469   9.818  1.00  0.00              
ATOM    112  O   SER    49      31.792   7.129   9.035  1.00  0.00              
ATOM    113  N   GLN    50      29.833   8.148   9.443  1.00  0.00              
ATOM    114  CA  GLN    50      29.600   8.505   8.050  1.00  0.00              
ATOM    115  C   GLN    50      30.671   9.472   7.559  1.00  0.00              
ATOM    116  O   GLN    50      31.155   9.363   6.427  1.00  0.00              
ATOM    117  N   PHE    51      31.060  10.400   8.426  1.00  0.00              
ATOM    118  CA  PHE    51      32.092  11.373   8.099  1.00  0.00              
ATOM    119  C   PHE    51      33.422  10.671   7.845  1.00  0.00              
ATOM    120  O   PHE    51      34.153  11.032   6.930  1.00  0.00              
ATOM    121  N   PRO    52      33.722   9.670   8.671  1.00  0.00              
ATOM    122  CA  PRO    52      34.950   8.911   8.533  1.00  0.00              
ATOM    123  C   PRO    52      34.961   7.997   7.317  1.00  0.00              
ATOM    124  O   PRO    52      36.007   7.798   6.698  1.00  0.00              
ATOM    125  N   GLU    53      33.807   7.431   6.974  1.00  0.00              
ATOM    126  CA  GLU    53      33.708   6.533   5.821  1.00  0.00              
ATOM    127  C   GLU    53      33.987   7.273   4.517  1.00  0.00              
ATOM    128  O   GLU    53      34.680   6.765   3.638  1.00  0.00              
ATOM    129  N   ILE    54      33.447   8.477   4.395  1.00  0.00              
ATOM    130  CA  ILE    54      33.730   9.325   3.240  1.00  0.00              
ATOM    131  C   ILE    54      35.002  10.124   3.490  1.00  0.00              
ATOM    132  O   ILE    54      35.531  10.774   2.588  1.00  0.00              
ATOM    133  N   ASP    55      35.480  10.031   4.728  1.00  0.00              
ATOM    134  CA  ASP    55      36.605  10.812   5.237  1.00  0.00              
ATOM    135  C   ASP    55      36.558  12.252   4.746  1.00  0.00              
ATOM    136  O   ASP    55      37.351  12.668   3.896  1.00  0.00              
ATOM    137  N   LEU    56      35.596  13.000   5.254  1.00  0.00              
ATOM    138  CA  LEU    56      35.508  14.416   4.957  1.00  0.00              
ATOM    139  C   LEU    56      36.253  15.187   6.034  1.00  0.00              
ATOM    140  O   LEU    56      35.843  15.195   7.197  1.00  0.00              
END
