
#######################################################
#                                                     #
#                        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 T0382AL381_2
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382AL381_2.T0382.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    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    A      83      T      11          3.114
LGA    V      84      Q      12          2.058
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    A      85      V      15          0.690
LGA    P      86      A      16          4.015
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      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    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    V      87      L      63           #
LGA    K      88      S      64          4.310
LGA    A      89      L      65          2.629
LGA    R      90      -       -           -
LGA    E      91      -       -           -
LGA    Q      92      F      66          3.740
LGA    L      93      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    E      94      T      81           #
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    A      95      K      88          3.150
LGA    I      96      A      89          1.564
LGA    V      97      -       -           -
LGA    S      98      R      90          4.459
LGA    S      99      E      91          4.293
LGA    K     100      Q      92          3.532
LGA    W     101      L      93          5.064
LGA    F     102      E      94          3.819
LGA    P     103      A      95          3.639
LGA    Q     104      I      96          2.550
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      A     105          1.573
LGA    G     106      G     106          3.112
LGA    -       -      D     107           -
LGA    D     107      A     108          2.214
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)   25  121    5.0     19    3.33    10.53      9.173     0.555

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.658066 * X  +   0.343852 * Y  +   0.669862 * Z  + -57.014050
  Y_new =   0.731903 * X  +   0.501035 * Y  +   0.461824 * Z  +   4.887251
  Z_new =  -0.176825 * X  +   0.794185 * Y  +  -0.581381 * Z  +  25.584177 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.202708   -0.938884  [ DEG:   126.2059    -53.7941 ]
  Theta =   0.177760    2.963833  [ DEG:    10.1849    169.8151 ]
  Phi   =   2.303123   -0.838470  [ DEG:   131.9592    -48.0408 ]
 
# 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_2                                  
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382AL381_2.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  121   5.0   19   3.33   10.53   9.173
REMARK  ---------------------------------------------------------- 
MOLECULE T0382AL381_2
REMARK Aligment from pdb entry: 1mgrA
ATOM      1  N   ALA    83     -17.751  42.704 -10.037  1.00  0.00              
ATOM      2  CA  ALA    83     -18.911  41.909 -10.347  1.00  0.00              
ATOM      3  C   ALA    83     -18.943  40.548  -9.660  1.00  0.00              
ATOM      4  O   ALA    83     -20.014  39.946  -9.501  1.00  0.00              
ATOM      5  N   VAL    84     -17.777  40.090  -9.210  1.00  0.00              
ATOM      6  CA  VAL    84     -17.584  38.799  -8.615  1.00  0.00              
ATOM      7  C   VAL    84     -17.646  38.875  -7.065  1.00  0.00              
ATOM      8  O   VAL    84     -17.479  37.881  -6.376  1.00  0.00              
ATOM      9  N   ALA    85     -17.868  40.052  -6.527  1.00  0.00              
ATOM     10  CA  ALA    85     -17.959  40.153  -5.059  1.00  0.00              
ATOM     11  C   ALA    85     -19.377  39.784  -4.615  1.00  0.00              
ATOM     12  O   ALA    85     -20.353  39.977  -5.360  1.00  0.00              
ATOM     13  N   PRO    86     -19.535  39.317  -3.385  1.00  0.00              
ATOM     14  CA  PRO    86     -20.891  39.057  -2.850  1.00  0.00              
ATOM     15  C   PRO    86     -21.704  40.377  -2.678  1.00  0.00              
ATOM     16  O   PRO    86     -21.110  41.455  -2.549  1.00  0.00              
ATOM     17  N   VAL    87     -23.040  40.290  -2.728  1.00  0.00              
ATOM     18  CA  VAL    87     -23.917  41.467  -2.747  1.00  0.00              
ATOM     19  C   VAL    87     -23.743  42.337  -1.487  1.00  0.00              
ATOM     20  O   VAL    87     -23.816  43.542  -1.569  1.00  0.00              
ATOM     21  N   LYS    88     -23.493  41.698  -0.352  1.00  0.00              
ATOM     22  CA  LYS    88     -23.128  42.414   0.895  1.00  0.00              
ATOM     23  C   LYS    88     -21.868  43.279   0.734  1.00  0.00              
ATOM     24  O   LYS    88     -21.777  44.359   1.329  1.00  0.00              
ATOM     25  N   ALA    89     -20.876  42.838  -0.056  1.00  0.00              
ATOM     26  CA  ALA    89     -19.739  43.688  -0.282  1.00  0.00              
ATOM     27  C   ALA    89     -20.148  44.894  -1.124  1.00  0.00              
ATOM     28  O   ALA    89     -19.587  45.942  -0.993  1.00  0.00              
ATOM     29  N   ARG    90     -21.082  44.709  -2.070  1.00  0.00              
ATOM     30  CA  ARG    90     -21.583  45.808  -2.831  1.00  0.00              
ATOM     31  C   ARG    90     -22.249  46.810  -1.863  1.00  0.00              
ATOM     32  O   ARG    90     -21.986  48.000  -1.952  1.00  0.00              
ATOM     33  N   GLU    91     -23.067  46.296  -0.957  1.00  0.00              
ATOM     34  CA  GLU    91     -23.681  47.135   0.079  1.00  0.00              
ATOM     35  C   GLU    91     -22.636  47.939   0.858  1.00  0.00              
ATOM     36  O   GLU    91     -22.763  49.131   1.022  1.00  0.00              
ATOM     37  N   GLN    92     -21.593  47.267   1.363  1.00  0.00              
ATOM     38  CA  GLN    92     -20.515  47.985   2.033  1.00  0.00              
ATOM     39  C   GLN    92     -19.897  49.071   1.232  1.00  0.00              
ATOM     40  O   GLN    92     -19.610  50.123   1.743  1.00  0.00              
ATOM     41  N   LEU    93     -19.582  48.798  -0.038  1.00  0.00              
ATOM     42  CA  LEU    93     -18.957  49.807  -0.861  1.00  0.00              
ATOM     43  C   LEU    93     -19.856  51.029  -1.052  1.00  0.00              
ATOM     44  O   LEU    93     -19.369  52.143  -0.984  1.00  0.00              
ATOM     45  N   GLU    94     -21.132  50.786  -1.216  1.00  0.00              
ATOM     46  CA  GLU    94     -22.153  51.841  -1.329  1.00  0.00              
ATOM     47  C   GLU    94     -22.168  52.688  -0.023  1.00  0.00              
ATOM     48  O   GLU    94     -22.142  53.929  -0.041  1.00  0.00              
ATOM     49  N   ALA    95     -22.128  51.996   1.114  1.00  0.00              
ATOM     50  CA  ALA    95     -22.140  52.709   2.362  1.00  0.00              
ATOM     51  C   ALA    95     -20.890  53.545   2.537  1.00  0.00              
ATOM     52  O   ALA    95     -20.939  54.582   3.082  1.00  0.00              
ATOM     53  N   ILE    96     -19.714  53.057   2.147  1.00  0.00              
ATOM     54  CA  ILE    96     -18.522  53.828   2.255  1.00  0.00              
ATOM     55  C   ILE    96     -18.660  55.100   1.372  1.00  0.00              
ATOM     56  O   ILE    96     -18.224  56.126   1.762  1.00  0.00              
ATOM     57  N   VAL    97     -19.242  54.956   0.193  1.00  0.00              
ATOM     58  CA  VAL    97     -19.397  56.097  -0.730  1.00  0.00              
ATOM     59  C   VAL    97     -20.283  57.159  -0.082  1.00  0.00              
ATOM     60  O   VAL    97     -20.061  58.349  -0.224  1.00  0.00              
ATOM     61  N   SER    98     -21.257  56.687   0.661  1.00  0.00              
ATOM     62  CA  SER    98     -22.248  57.590   1.323  1.00  0.00              
ATOM     63  C   SER    98     -21.804  58.145   2.670  1.00  0.00              
ATOM     64  O   SER    98     -22.327  59.156   3.141  1.00  0.00              
ATOM     65  N   SER    99     -20.839  57.489   3.317  1.00  0.00              
ATOM     66  CA  SER    99     -20.352  57.928   4.578  1.00  0.00              
ATOM     67  C   SER    99     -21.141  57.296   5.747  1.00  0.00              
ATOM     68  O   SER    99     -21.008  57.796   6.853  1.00  0.00              
ATOM     69  N   LYS   100     -21.879  56.228   5.501  1.00  0.00              
ATOM     70  CA  LYS   100     -22.649  55.543   6.528  1.00  0.00              
ATOM     71  C   LYS   100     -24.093  55.422   6.092  1.00  0.00              
ATOM     72  O   LYS   100     -24.420  55.867   5.002  1.00  0.00              
ATOM     73  N   TRP   101     -24.978  54.858   6.911  1.00  0.00              
ATOM     74  CA  TRP   101     -24.668  54.357   8.267  1.00  0.00              
ATOM     75  C   TRP   101     -24.054  52.993   8.276  1.00  0.00              
ATOM     76  O   TRP   101     -24.409  52.206   7.406  1.00  0.00              
ATOM     77  N   PHE   102     -23.191  52.723   9.264  1.00  0.00              
ATOM     78  CA  PHE   102     -22.511  51.441   9.352  1.00  0.00              
ATOM     79  C   PHE   102     -23.042  50.678  10.530  1.00  0.00              
ATOM     80  O   PHE   102     -23.379  51.270  11.547  1.00  0.00              
ATOM     81  N   PRO   103     -23.118  49.374  10.361  1.00  0.00              
ATOM     82  CA  PRO   103     -23.711  48.515  11.395  1.00  0.00              
ATOM     83  C   PRO   103     -22.863  48.254  12.640  1.00  0.00              
ATOM     84  O   PRO   103     -23.464  48.013  13.728  1.00  0.00              
ATOM     85  N   GLN   104     -21.543  48.388  12.552  1.00  0.00              
ATOM     86  CA  GLN   104     -20.657  48.047  13.651  1.00  0.00              
ATOM     87  C   GLN   104     -19.806  49.194  14.058  1.00  0.00              
ATOM     88  O   GLN   104     -19.412  50.031  13.232  1.00  0.00              
ATOM     89  N   ALA   105     -19.420  49.215  15.321  1.00  0.00              
ATOM     90  CA  ALA   105     -18.663  50.301  15.844  1.00  0.00              
ATOM     91  C   ALA   105     -17.284  50.389  15.194  1.00  0.00              
ATOM     92  O   ALA   105     -16.746  51.454  15.117  1.00  0.00              
ATOM     93  N   GLY   106     -16.720  49.253  14.785  1.00  0.00              
ATOM     94  CA  GLY   106     -15.390  49.269  14.212  1.00  0.00              
ATOM     95  C   GLY   106     -15.384  49.722  12.765  1.00  0.00              
ATOM     96  O   GLY   106     -14.318  49.912  12.173  1.00  0.00              
ATOM     97  N   ASP   107     -16.537  49.902  12.182  1.00  0.00              
ATOM     98  CA  ASP   107     -16.570  50.313  10.738  1.00  0.00              
ATOM     99  C   ASP   107     -16.079  51.717  10.621  1.00  0.00              
ATOM    100  O   ASP   107     -16.615  52.648  11.230  1.00  0.00              
END
