
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0369AL044_2
# Molecule2: number of CA atoms  147 ( 1193),  selected  147 , name T0369.pdb
# PARAMETERS: T0369AL044_2.T0369.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      D       3           -
LGA    -       -      W       4           -
LGA    -       -      Q       5           -
LGA    -       -      Q       6           -
LGA    -       -      A       7           -
LGA    -       -      L       8           -
LGA    -       -      D       9           -
LGA    -       -      R      10           -
LGA    -       -      H      11           -
LGA    -       -      V      12           -
LGA    -       -      G      13           -
LGA    -       -      V      14           -
LGA    -       -      G      15           -
LGA    -       -      V      16           -
LGA    -       -      R      17           -
LGA    -       -      T      18           -
LGA    -       -      T      19           -
LGA    -       -      R      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      I      23           -
LGA    -       -      R      24           -
LGA    -       -      L      25           -
LGA    -       -      I      26           -
LGA    -       -      Q      27           -
LGA    Q      70      P      28          1.826
LGA    -       -      E      29           -
LGA    -       -      D      30           -
LGA    -       -      W      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      R      34           -
LGA    -       -      P      35           -
LGA    -       -      I      36           -
LGA    -       -      S      37           -
LGA    -       -      G      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      S      41           -
LGA    -       -      V      42           -
LGA    -       -      Y      43           -
LGA    -       -      E      44           -
LGA    -       -      V      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      H      48           -
LGA    -       -      L      49           -
LGA    -       -      A      50           -
LGA    -       -      V      51           -
LGA    -       -      L      52           -
LGA    -       -      L      53           -
LGA    -       -      E      54           -
LGA    -       -      A      55           -
LGA    -       -      D      56           -
LGA    -       -      L      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      A      60           -
LGA    -       -      T      61           -
LGA    -       -      G      62           -
LGA    -       -      A      63           -
LGA    -       -      T      64           -
LGA    -       -      A      65           -
LGA    -       -      D      66           -
LGA    -       -      E      67           -
LGA    -       -      M      68           -
LGA    -       -      A      69           -
LGA    -       -      Q      70           -
LGA    -       -      F      71           -
LGA    -       -      Y      72           -
LGA    -       -      A      73           -
LGA    -       -      V      74           -
LGA    -       -      P      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      P      78           -
LGA    -       -      E      79           -
LGA    -       -      Q      80           -
LGA    -       -      L      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      R      84           -
LGA    -       -      L      85           -
LGA    F      71      D      86          3.583
LGA    Y      72      Q      87           -
LGA    -       -      S      88           -
LGA    -       -      W      89           -
LGA    -       -      Q      90           -
LGA    -       -      Y      91           -
LGA    -       -      Y      92           -
LGA    -       -      Q      93           -
LGA    -       -      D      94           -
LGA    -       -      R      95           -
LGA    -       -      L      96           -
LGA    -       -      M      97           -
LGA    A      73      A      98          3.406
LGA    -       -      D      99           -
LGA    V      74      F     100           #
LGA    P      75      S     101           -
LGA    V      76      T     102           -
LGA    -       -      E     103           -
LGA    -       -      T     104           -
LGA    -       -      T     105           -
LGA    -       -      Y     106           -
LGA    -       -      W     107           -
LGA    -       -      G     108           -
LGA    -       -      V     109           -
LGA    -       -      T     110           -
LGA    -       -      D     111           -
LGA    -       -      S     112           -
LGA    -       -      T     113           -
LGA    L      77      T     114          4.765
LGA    P      78      G     115          1.827
LGA    -       -      W     116           -
LGA    -       -      L     117           -
LGA    E      79      L     118          0.807
LGA    Q      80      E     119          2.758
LGA    L      81      A     120          2.068
LGA    -       -      A     121           -
LGA    V      82      V     122          1.214
LGA    D      83      H     123          3.211
LGA    Q      87      L     124          3.667
LGA    W      89      Y     125          1.894
LGA    Q      90      H     126          2.610
LGA    Y      92      H     127          0.607
LGA    Q      93      R     128          2.576
LGA    -       -      S     129           -
LGA    L      96      Q     130          2.066
LGA    -       -      L     131           -
LGA    -       -      L     132           -
LGA    -       -      D     133           -
LGA    M      97      Y     134          1.961
LGA    A      98      L     135          1.580
LGA    D      99      N     136          1.606
LGA    -       -      L     137           -
LGA    S     101      L     138          1.203
LGA    T     102      G     139          3.569
LGA    E     103      Y     140          5.344
LGA    -       -      D     141           -
LGA    -       -      I     142           -
LGA    -       -      K     143           -
LGA    -       -      L     144           -
LGA    -       -      D     145           -
LGA    -       -      L     146           -
LGA    -       -      F     147           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26  147    5.0     22    2.74     9.09     11.015     0.775

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.372933 * X  +   0.927006 * Y  +  -0.039775 * Z  +   8.997660
  Y_new =  -0.852099 * X  +   0.359133 * Y  +   0.380724 * Z  +  15.732758
  Z_new =   0.367218 * X  +  -0.108093 * Y  +   0.923833 * Z  +   4.307187 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.116475    3.025118  [ DEG:    -6.6735    173.3265 ]
  Theta =  -0.376016   -2.765576  [ DEG:   -21.5441   -158.4559 ]
  Phi   =  -1.158249    1.983344  [ DEG:   -66.3628    113.6372 ]
 
# 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: T0369AL044_2                                  
REMARK     2: T0369.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0369AL044_2.T0369.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26  147   5.0   22   2.74    9.09  11.015
REMARK  ---------------------------------------------------------- 
MOLECULE T0369AL044_2
REMARK Aligment from pdb entry: 1rxq_A
ATOM      1  N   GLN    70       8.783 -19.586  -8.240  1.00  0.00              
ATOM      2  CA  GLN    70       8.664 -20.232  -9.554  1.00  0.00              
ATOM      3  C   GLN    70       9.959 -20.851 -10.092  1.00  0.00              
ATOM      4  O   GLN    70       9.937 -21.433 -11.162  1.00  0.00              
ATOM      5  N   PHE    71      20.306  -4.238  -8.276  1.00  0.00              
ATOM      6  CA  PHE    71      20.246  -2.935  -8.940  1.00  0.00              
ATOM      7  C   PHE    71      21.115  -1.950  -8.145  1.00  0.00              
ATOM      8  O   PHE    71      21.368  -2.158  -6.964  1.00  0.00              
ATOM      9  N   TYR    72      21.585  -0.895  -8.796  1.00  0.00              
ATOM     10  CA  TYR    72      22.441   0.106  -8.160  1.00  0.00              
ATOM     11  C   TYR    72      21.530   1.160  -7.539  1.00  0.00              
ATOM     12  O   TYR    72      21.190   2.135  -8.189  1.00  0.00              
ATOM     13  N   ALA    73      17.060  12.001 -12.703  1.00  0.00              
ATOM     14  CA  ALA    73      16.299  13.248 -12.582  1.00  0.00              
ATOM     15  C   ALA    73      14.897  13.031 -12.011  1.00  0.00              
ATOM     16  O   ALA    73      14.445  13.761 -11.131  1.00  0.00              
ATOM     17  N   VAL    74      14.209  12.007 -12.497  1.00  0.00              
ATOM     18  CA  VAL    74      12.885  11.698 -11.991  1.00  0.00              
ATOM     19  C   VAL    74      12.867  11.441 -10.474  1.00  0.00              
ATOM     20  O   VAL    74      11.967  11.907  -9.772  1.00  0.00              
ATOM     21  N   PRO    75      13.838  10.692  -9.972  1.00  0.00              
ATOM     22  CA  PRO    75      13.911  10.386  -8.540  1.00  0.00              
ATOM     23  C   PRO    75      14.137  11.658  -7.701  1.00  0.00              
ATOM     24  O   PRO    75      13.717  11.764  -6.538  1.00  0.00              
ATOM     25  N   VAL    76      14.821  12.632  -8.282  1.00  0.00              
ATOM     26  CA  VAL    76      15.111  13.870  -7.573  1.00  0.00              
ATOM     27  C   VAL    76      14.011  14.937  -7.671  1.00  0.00              
ATOM     28  O   VAL    76      14.035  15.906  -6.886  1.00  0.00              
ATOM     29  N   LEU    77      13.074  14.787  -8.615  1.00  0.00              
ATOM     30  CA  LEU    77      12.077  15.834  -8.889  1.00  0.00              
ATOM     31  C   LEU    77      10.585  15.442  -8.901  1.00  0.00              
ATOM     32  O   LEU    77       9.740  16.305  -8.706  1.00  0.00              
ATOM     33  N   PRO    78       6.908  14.370  -7.898  1.00  0.00              
ATOM     34  CA  PRO    78       6.075  14.509  -6.713  1.00  0.00              
ATOM     35  C   PRO    78       5.930  13.157  -6.024  1.00  0.00              
ATOM     36  O   PRO    78       5.801  12.136  -6.707  1.00  0.00              
ATOM     37  N   GLU    79       5.970  13.112  -4.692  1.00  0.00              
ATOM     38  CA  GLU    79       5.826  11.818  -4.026  1.00  0.00              
ATOM     39  C   GLU    79       4.487  11.134  -4.276  1.00  0.00              
ATOM     40  O   GLU    79       4.440   9.918  -4.159  1.00  0.00              
ATOM     41  N   GLN    80       3.435  11.877  -4.608  1.00  0.00              
ATOM     42  CA  GLN    80       2.094  11.286  -4.692  1.00  0.00              
ATOM     43  C   GLN    80       2.019  10.022  -5.561  1.00  0.00              
ATOM     44  O   GLN    80       1.374   9.061  -5.169  1.00  0.00              
ATOM     45  N   LEU    81       4.373   7.782  -6.290  1.00  0.00              
ATOM     46  CA  LEU    81       5.052   6.684  -5.615  1.00  0.00              
ATOM     47  C   LEU    81       4.293   6.247  -4.392  1.00  0.00              
ATOM     48  O   LEU    81       4.266   5.072  -4.089  1.00  0.00              
ATOM     49  N   VAL    82       3.687   7.192  -3.680  1.00  0.00              
ATOM     50  CA  VAL    82       2.876   6.798  -2.532  1.00  0.00              
ATOM     51  C   VAL    82       1.677   5.937  -2.963  1.00  0.00              
ATOM     52  O   VAL    82       1.365   4.940  -2.331  1.00  0.00              
ATOM     53  N   ASP    83       1.037   6.305  -4.065  1.00  0.00              
ATOM     54  CA  ASP    83      -0.095   5.558  -4.587  1.00  0.00              
ATOM     55  C   ASP    83       0.349   4.200  -5.121  1.00  0.00              
ATOM     56  O   ASP    83      -0.334   3.194  -4.941  1.00  0.00              
ATOM     57  N   GLN    87       1.491   4.175  -5.798  1.00  0.00              
ATOM     58  CA  GLN    87       2.032   2.918  -6.302  1.00  0.00              
ATOM     59  C   GLN    87       2.316   1.963  -5.142  1.00  0.00              
ATOM     60  O   GLN    87       1.955   0.797  -5.194  1.00  0.00              
ATOM     61  N   TRP    89       2.934   2.471  -4.083  1.00  0.00              
ATOM     62  CA  TRP    89       3.272   1.662  -2.932  1.00  0.00              
ATOM     63  C   TRP    89       2.043   1.059  -2.261  1.00  0.00              
ATOM     64  O   TRP    89       2.062  -0.089  -1.853  1.00  0.00              
ATOM     65  N   GLN    90      -0.849   0.330  -3.702  1.00  0.00              
ATOM     66  CA  GLN    90      -1.351  -0.748  -4.519  1.00  0.00              
ATOM     67  C   GLN    90      -0.378  -1.935  -4.565  1.00  0.00              
ATOM     68  O   GLN    90      -0.802  -3.095  -4.574  1.00  0.00              
ATOM     69  N   TYR    92       0.921  -1.646  -4.523  1.00  0.00              
ATOM     70  CA  TYR    92       1.924  -2.698  -4.613  1.00  0.00              
ATOM     71  C   TYR    92       1.896  -3.534  -3.344  1.00  0.00              
ATOM     72  O   TYR    92       1.884  -4.742  -3.396  1.00  0.00              
ATOM     73  N   GLN    93       1.865  -2.887  -2.194  1.00  0.00              
ATOM     74  CA  GLN    93       1.789  -3.631  -0.951  1.00  0.00              
ATOM     75  C   GLN    93       0.466  -4.384  -0.833  1.00  0.00              
ATOM     76  O   GLN    93       0.409  -5.433  -0.190  1.00  0.00              
ATOM     77  N   LEU    96      -0.596  -3.868  -1.450  1.00  0.00              
ATOM     78  CA  LEU    96      -1.842  -4.616  -1.563  1.00  0.00              
ATOM     79  C   LEU    96      -1.659  -5.958  -2.265  1.00  0.00              
ATOM     80  O   LEU    96      -2.050  -6.996  -1.745  1.00  0.00              
ATOM     81  N   MET    97      -0.411 -11.871  -2.261  1.00  0.00              
ATOM     82  CA  MET    97       0.409 -13.000  -2.640  1.00  0.00              
ATOM     83  C   MET    97       0.840 -13.744  -1.357  1.00  0.00              
ATOM     84  O   MET    97       0.734 -14.970  -1.249  1.00  0.00              
ATOM     85  N   ALA    98       1.282 -12.982  -0.378  1.00  0.00              
ATOM     86  CA  ALA    98       1.830 -13.571   0.843  1.00  0.00              
ATOM     87  C   ALA    98       0.796 -14.409   1.579  1.00  0.00              
ATOM     88  O   ALA    98       1.116 -15.448   2.174  1.00  0.00              
ATOM     89  N   ASP    99      -0.449 -13.953   1.557  1.00  0.00              
ATOM     90  CA  ASP    99      -1.518 -14.677   2.231  1.00  0.00              
ATOM     91  C   ASP    99      -1.876 -15.998   1.542  1.00  0.00              
ATOM     92  O   ASP    99      -2.501 -16.855   2.162  1.00  0.00              
ATOM     93  N   SER   101      -1.473 -16.186   0.281  1.00  0.00              
ATOM     94  CA  SER   101      -1.725 -17.458  -0.399  1.00  0.00              
ATOM     95  C   SER   101      -0.662 -18.514  -0.128  1.00  0.00              
ATOM     96  O   SER   101      -0.876 -19.689  -0.447  1.00  0.00              
ATOM     97  N   THR   102       1.879 -21.293   1.317  1.00  0.00              
ATOM     98  CA  THR   102       1.980 -22.352   2.319  1.00  0.00              
ATOM     99  C   THR   102       3.240 -22.162   3.157  1.00  0.00              
ATOM    100  O   THR   102       4.118 -21.396   2.801  1.00  0.00              
ATOM    101  N   GLU   103       3.356 -22.904   4.256  1.00  0.00              
ATOM    102  CA  GLU   103       4.568 -22.857   5.065  1.00  0.00              
ATOM    103  C   GLU   103       5.805 -23.252   4.259  1.00  0.00              
ATOM    104  O   GLU   103       6.873 -22.647   4.425  1.00  0.00              
END
