
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0382AL381_1
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382AL381_1.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    V      87      Q      12          1.080
LGA    K      88      D      13          1.842
LGA    A      89      L      14          2.406
LGA    R      90      V      15          2.548
LGA    E      91      A      16          1.177
LGA    Q      92      L      17          1.009
LGA    L      93      F      18          1.068
LGA    E      94      A      19          1.097
LGA    A      95      K      20          1.570
LGA    I      96      V      21          1.596
LGA    V      97      T      22          2.026
LGA    W     101      V      23          1.075
LGA    F     102      E      24          0.330
LGA    P     103      Q      25          1.537
LGA    Q     104      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    -       -      N      38           -
LGA    -       -      R      39           -
LGA    A     105      L      40          3.043
LGA    G     106      F      41          1.586
LGA    D     107      G      42          1.855
LGA    A     108      V      43          1.817
LGA    G     109      M      44          1.244
LGA    M     110      A      45          0.643
LGA    C     111      E      46          0.228
LGA    L     112      I      47          1.027
LGA    D     113      A      48          1.353
LGA    L     114      D      49          0.948
LGA    L     115      E      50          0.716
LGA    D     116      L      51          0.314
LGA    D     117      K      52          1.990
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    G     118      D      55          3.340
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29  121    5.0     28    1.63     0.00     21.335     1.619

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.021761 * X  +   0.999315 * Y  +   0.029937 * Z  + -11.391836
  Y_new =   0.330078 * X  +   0.035446 * Y  +  -0.943288 * Z  +  44.332863
  Z_new =  -0.943703 * X  +  -0.010646 * Y  +  -0.330623 * Z  + -25.806837 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.109404    0.032188  [ DEG:  -178.1557      1.8443 ]
  Theta =   1.233651    1.907941  [ DEG:    70.6830    109.3170 ]
  Phi   =   1.636629   -1.504963  [ DEG:    93.7720    -86.2280 ]
 
# 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: T0382AL381_1                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382AL381_1.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29  121   5.0   28   1.63    0.00  21.335
REMARK  ---------------------------------------------------------- 
MOLECULE T0382AL381_1
REMARK Aligment from pdb entry: 1zl8B
ATOM      1  N   VAL    87     -19.186  39.369 -10.954  1.00  0.00              
ATOM      2  CA  VAL    87     -19.363  39.485  -9.516  1.00  0.00              
ATOM      3  C   VAL    87     -18.845  38.230  -8.815  1.00  0.00              
ATOM      4  O   VAL    87     -18.338  38.302  -7.697  1.00  0.00              
ATOM      5  N   LYS    88     -18.992  37.105  -9.499  1.00  0.00              
ATOM      6  CA  LYS    88     -18.546  35.834  -8.955  1.00  0.00              
ATOM      7  C   LYS    88     -17.054  35.892  -8.622  1.00  0.00              
ATOM      8  O   LYS    88     -16.576  35.156  -7.761  1.00  0.00              
ATOM      9  N   ALA    89     -16.360  36.774  -9.326  1.00  0.00              
ATOM     10  CA  ALA    89     -14.931  36.939  -9.117  1.00  0.00              
ATOM     11  C   ALA    89     -14.681  37.425  -7.687  1.00  0.00              
ATOM     12  O   ALA    89     -14.017  36.745  -6.904  1.00  0.00              
ATOM     13  N   ARG    90     -15.224  38.596  -7.389  1.00  0.00              
ATOM     14  CA  ARG    90     -15.070  39.178  -6.068  1.00  0.00              
ATOM     15  C   ARG    90     -16.009  38.470  -5.089  1.00  0.00              
ATOM     16  O   ARG    90     -15.804  38.524  -3.879  1.00  0.00              
ATOM     17  N   GLU    91     -17.019  37.823  -5.651  1.00  0.00              
ATOM     18  CA  GLU    91     -17.990  37.105  -4.845  1.00  0.00              
ATOM     19  C   GLU    91     -17.279  36.261  -3.783  1.00  0.00              
ATOM     20  O   GLU    91     -17.769  36.126  -2.663  1.00  0.00              
ATOM     21  N   GLN    92     -16.137  35.716  -4.175  1.00  0.00              
ATOM     22  CA  GLN    92     -15.355  34.889  -3.272  1.00  0.00              
ATOM     23  C   GLN    92     -14.975  35.710  -2.038  1.00  0.00              
ATOM     24  O   GLN    92     -14.879  35.171  -0.936  1.00  0.00              
ATOM     25  N   LEU    93     -14.770  36.999  -2.264  1.00  0.00              
ATOM     26  CA  LEU    93     -14.402  37.900  -1.183  1.00  0.00              
ATOM     27  C   LEU    93     -15.568  38.010  -0.199  1.00  0.00              
ATOM     28  O   LEU    93     -15.360  38.212   0.996  1.00  0.00              
ATOM     29  N   GLU    94     -16.772  37.875  -0.739  1.00  0.00              
ATOM     30  CA  GLU    94     -17.971  37.958   0.077  1.00  0.00              
ATOM     31  C   GLU    94     -17.948  36.882   1.166  1.00  0.00              
ATOM     32  O   GLU    94     -18.416  37.113   2.280  1.00  0.00              
ATOM     33  N   ALA    95     -17.400  35.732   0.805  1.00  0.00              
ATOM     34  CA  ALA    95     -17.309  34.620   1.738  1.00  0.00              
ATOM     35  C   ALA    95     -16.095  34.791   2.650  1.00  0.00              
ATOM     36  O   ALA    95     -16.102  34.333   3.792  1.00  0.00              
ATOM     37  N   ILE    96     -15.078  35.450   2.113  1.00  0.00              
ATOM     38  CA  ILE    96     -13.858  35.686   2.865  1.00  0.00              
ATOM     39  C   ILE    96     -14.140  36.688   3.986  1.00  0.00              
ATOM     40  O   ILE    96     -13.322  36.863   4.888  1.00  0.00              
ATOM     41  N   VAL    97     -15.301  37.320   3.891  1.00  0.00              
ATOM     42  CA  VAL    97     -15.701  38.300   4.888  1.00  0.00              
ATOM     43  C   VAL    97     -15.752  37.651   6.271  1.00  0.00              
ATOM     44  O   VAL    97     -15.579  38.326   7.285  1.00  0.00              
ATOM     45  N   TRP   101     -15.990  36.347   6.269  1.00  0.00              
ATOM     46  CA  TRP   101     -16.067  35.598   7.511  1.00  0.00              
ATOM     47  C   TRP   101     -14.683  35.019   7.809  1.00  0.00              
ATOM     48  O   TRP   101     -14.261  34.970   8.964  1.00  0.00              
ATOM     49  N   PHE   102     -14.014  34.592   6.748  1.00  0.00              
ATOM     50  CA  PHE   102     -12.687  34.017   6.880  1.00  0.00              
ATOM     51  C   PHE   102     -11.622  35.112   6.974  1.00  0.00              
ATOM     52  O   PHE   102     -11.445  35.891   6.040  1.00  0.00              
ATOM     53  N   PRO   103     -10.923  35.136   8.139  1.00  0.00              
ATOM     54  CA  PRO   103      -9.880  36.122   8.368  1.00  0.00              
ATOM     55  C   PRO   103      -8.617  35.776   7.577  1.00  0.00              
ATOM     56  O   PRO   103      -7.796  34.978   8.028  1.00  0.00              
ATOM     57  N   GLN   104      -8.500  36.395   6.412  1.00  0.00              
ATOM     58  CA  GLN   104      -7.351  36.164   5.552  1.00  0.00              
ATOM     59  C   GLN   104      -6.467  37.412   5.500  1.00  0.00              
ATOM     60  O   GLN   104      -6.770  38.418   6.139  1.00  0.00              
ATOM     61  N   ALA   105      -5.393  37.306   4.732  1.00  0.00              
ATOM     62  CA  ALA   105      -4.465  38.413   4.588  1.00  0.00              
ATOM     63  C   ALA   105      -5.193  39.606   3.965  1.00  0.00              
ATOM     64  O   ALA   105      -5.637  39.537   2.819  1.00  0.00              
ATOM     65  N   GLY   106      -5.292  40.672   4.744  1.00  0.00              
ATOM     66  CA  GLY   106      -5.958  41.878   4.285  1.00  0.00              
ATOM     67  C   GLY   106      -5.378  42.290   2.930  1.00  0.00              
ATOM     68  O   GLY   106      -6.053  42.943   2.134  1.00  0.00              
ATOM     69  N   ASP   107      -4.135  41.890   2.707  1.00  0.00              
ATOM     70  CA  ASP   107      -3.457  42.209   1.463  1.00  0.00              
ATOM     71  C   ASP   107      -3.976  41.290   0.354  1.00  0.00              
ATOM     72  O   ASP   107      -4.324  41.755  -0.731  1.00  0.00              
ATOM     73  N   ALA   108      -4.009  40.003   0.665  1.00  0.00              
ATOM     74  CA  ALA   108      -4.480  39.014  -0.290  1.00  0.00              
ATOM     75  C   ALA   108      -5.923  39.338  -0.684  1.00  0.00              
ATOM     76  O   ALA   108      -6.231  39.470  -1.868  1.00  0.00              
ATOM     77  N   GLY   109      -6.768  39.456   0.329  1.00  0.00              
ATOM     78  CA  GLY   109      -8.169  39.761   0.104  1.00  0.00              
ATOM     79  C   GLY   109      -8.283  41.092  -0.644  1.00  0.00              
ATOM     80  O   GLY   109      -9.232  41.305  -1.397  1.00  0.00              
ATOM     81  N   MET   110      -7.302  41.952  -0.409  1.00  0.00              
ATOM     82  CA  MET   110      -7.281  43.254  -1.052  1.00  0.00              
ATOM     83  C   MET   110      -6.924  43.111  -2.532  1.00  0.00              
ATOM     84  O   MET   110      -7.304  43.948  -3.350  1.00  0.00              
ATOM     85  N   CYS   111      -6.198  42.045  -2.833  1.00  0.00              
ATOM     86  CA  CYS   111      -5.785  41.782  -4.201  1.00  0.00              
ATOM     87  C   CYS   111      -7.025  41.548  -5.065  1.00  0.00              
ATOM     88  O   CYS   111      -7.100  42.035  -6.193  1.00  0.00              
ATOM     89  N   LEU   112      -7.967  40.802  -4.508  1.00  0.00              
ATOM     90  CA  LEU   112      -9.199  40.498  -5.214  1.00  0.00              
ATOM     91  C   LEU   112     -10.039  41.771  -5.335  1.00  0.00              
ATOM     92  O   LEU   112     -10.748  41.959  -6.324  1.00  0.00              
ATOM     93  N   ASP   113      -9.931  42.612  -4.317  1.00  0.00              
ATOM     94  CA  ASP   113     -10.673  43.861  -4.298  1.00  0.00              
ATOM     95  C   ASP   113     -10.069  44.852  -5.297  1.00  0.00              
ATOM     96  O   ASP   113     -10.786  45.439  -6.104  1.00  0.00              
ATOM     97  N   LEU   114      -8.756  45.007  -5.207  1.00  0.00              
ATOM     98  CA  LEU   114      -8.048  45.917  -6.091  1.00  0.00              
ATOM     99  C   LEU   114      -8.184  45.426  -7.534  1.00  0.00              
ATOM    100  O   LEU   114      -7.975  46.190  -8.475  1.00  0.00              
ATOM    101  N   LEU   115      -8.531  44.154  -7.663  1.00  0.00              
ATOM    102  CA  LEU   115      -8.697  43.553  -8.975  1.00  0.00              
ATOM    103  C   LEU   115      -9.927  44.160  -9.658  1.00  0.00              
ATOM    104  O   LEU   115     -10.168  43.914 -10.839  1.00  0.00              
ATOM    105  N   ASP   116     -10.668  44.938  -8.885  1.00  0.00              
ATOM    106  CA  ASP   116     -11.865  45.580  -9.400  1.00  0.00              
ATOM    107  C   ASP   116     -11.633  47.084  -9.571  1.00  0.00              
ATOM    108  O   ASP   116     -11.964  47.871  -8.686  1.00  0.00              
ATOM    109  N   ASP   117     -11.064  47.436 -10.714  1.00  0.00              
ATOM    110  CA  ASP   117     -10.784  48.830 -11.012  1.00  0.00              
ATOM    111  C   ASP   117     -11.619  49.297 -12.206  1.00  0.00              
ATOM    112  O   ASP   117     -12.384  48.518 -12.775  1.00  0.00              
ATOM    113  N   GLY   118     -11.441  50.597 -12.559  1.00  0.00              
ATOM    114  CA  GLY   118     -12.168  51.178 -13.675  1.00  0.00              
ATOM    115  C   GLY   118     -11.595  50.701 -15.011  1.00  0.00              
ATOM    116  O   GLY   118     -12.085  51.082 -16.072  1.00  0.00              
END
