
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0304AL381_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL381_4-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      96      R      17           -
LGA    L      97      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    T      98      P      23          4.415
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    C      99      G      31          4.634
LGA    K     100      A      32          2.141
LGA    A     101      R      33          0.887
LGA    D     102      L      34          3.314
LGA    T     103      V      35          2.659
LGA    L     104      Q      36          3.062
LGA    S     105      E      37          3.968
LGA    S     106      G      38          2.678
LGA    C     107      N      39          1.249
LGA    D     108      R      40          3.280
LGA    Y     109      L      41          3.432
LGA    V     110      H      42          4.282
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    -       -      M      70           -
LGA    -       -      K      71           -
LGA    -       -      Q      72           -
LGA    -       -      L      73           -
LGA    -       -      E      74           -
LGA    -       -      L      75           -
LGA    -       -      M      76           -
LGA    -       -      L      77           -
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    -       -      N      83           -
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    Y     111      Y     111          4.643
LGA    L     112      L     112          3.680
LGA    A     113      A     113          2.080
LGA    V     114      V     114          2.188
LGA    Y     115      Y     115          1.631
LGA    P     116      P     116          2.318
LGA    T     117      T     117          0.762

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  101    5.0     20    3.10    35.00     12.827     0.625

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.166885 * X  +   0.735934 * Y  +  -0.656164 * Z  + 166.090134
  Y_new =   0.935194 * X  +  -0.328971 * Y  +  -0.131112 * Z  + 107.596901
  Z_new =  -0.312349 * X  +  -0.591760 * Y  +  -0.743141 * Z  + 216.314926 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.469115    0.672478  [ DEG:  -141.4699     38.5301 ]
  Theta =   0.317665    2.823928  [ DEG:    18.2008    161.7991 ]
  Phi   =   1.394205   -1.747388  [ DEG:    79.8821   -100.1179 ]
 
# 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: T0304AL381_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_4-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  101   5.0   20   3.10   35.00  12.827
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_4-D1
REMARK Aligment from pdb entry: 2alaA
ATOM      1  N   GLY    96      37.677  29.847  32.820  1.00  0.00              
ATOM      2  CA  GLY    96      37.328  28.825  33.816  1.00  0.00              
ATOM      3  C   GLY    96      38.441  28.660  34.863  1.00  0.00              
ATOM      4  O   GLY    96      38.848  27.542  35.185  1.00  0.00              
ATOM      5  N   LEU    97      38.924  29.782  35.392  1.00  0.00              
ATOM      6  CA  LEU    97      39.984  29.764  36.398  1.00  0.00              
ATOM      7  C   LEU    97      39.434  29.363  37.766  1.00  0.00              
ATOM      8  O   LEU    97      38.572  30.047  38.324  1.00  0.00              
ATOM      9  N   THR    98      39.936  28.251  38.295  1.00  0.00              
ATOM     10  CA  THR    98      39.564  27.772  39.625  1.00  0.00              
ATOM     11  C   THR    98      40.812  27.351  40.397  1.00  0.00              
ATOM     12  O   THR    98      41.837  27.022  39.797  1.00  0.00              
ATOM     13  N   CYS    99      40.711  27.350  41.724  1.00  0.00              
ATOM     14  CA  CYS    99      41.874  27.205  42.600  1.00  0.00              
ATOM     15  C   CYS    99      41.653  26.185  43.716  1.00  0.00              
ATOM     16  O   CYS    99      40.932  26.456  44.678  1.00  0.00              
ATOM     17  N   LYS   100      42.290  25.021  43.585  1.00  0.00              
ATOM     18  CA  LYS   100      42.265  23.986  44.622  1.00  0.00              
ATOM     19  C   LYS   100      43.561  24.026  45.437  1.00  0.00              
ATOM     20  O   LYS   100      44.627  24.336  44.902  1.00  0.00              
ATOM     21  N   ALA   101      43.455  23.715  46.729  1.00  0.00              
ATOM     22  CA  ALA   101      44.609  23.654  47.626  1.00  0.00              
ATOM     23  C   ALA   101      44.828  22.208  48.062  1.00  0.00              
ATOM     24  O   ALA   101      43.964  21.613  48.707  1.00  0.00              
ATOM     25  N   ASP   102      45.984  21.650  47.707  1.00  0.00              
ATOM     26  CA  ASP   102      46.296  20.250  47.998  1.00  0.00              
ATOM     27  C   ASP   102      46.654  20.053  49.469  1.00  0.00              
ATOM     28  O   ASP   102      45.997  19.287  50.178  1.00  0.00              
ATOM     29  N   THR   103      47.704  20.739  49.915  1.00  0.00              
ATOM     30  CA  THR   103      48.140  20.696  51.311  1.00  0.00              
ATOM     31  C   THR   103      48.632  22.071  51.747  1.00  0.00              
ATOM     32  O   THR   103      48.928  22.928  50.911  1.00  0.00              
ATOM     33  N   LEU   104      48.719  22.271  53.059  1.00  0.00              
ATOM     34  CA  LEU   104      49.061  23.577  53.616  1.00  0.00              
ATOM     35  C   LEU   104      49.465  23.496  55.092  1.00  0.00              
ATOM     36  O   LEU   104      48.943  22.669  55.842  1.00  0.00              
ATOM     37  N   SER   105      54.609  28.360  58.212  1.00  0.00              
ATOM     38  CA  SER   105      55.905  27.911  57.704  1.00  0.00              
ATOM     39  C   SER   105      56.469  28.931  56.715  1.00  0.00              
ATOM     40  O   SER   105      55.847  29.967  56.459  1.00  0.00              
ATOM     41  N   SER   106      57.649  28.640  56.169  1.00  0.00              
ATOM     42  CA  SER   106      58.256  29.499  55.154  1.00  0.00              
ATOM     43  C   SER   106      57.401  29.469  53.884  1.00  0.00              
ATOM     44  O   SER   106      57.009  30.519  53.380  1.00  0.00              
ATOM     45  N   CYS   107      57.120  28.265  53.383  1.00  0.00              
ATOM     46  CA  CYS   107      56.218  28.065  52.237  1.00  0.00              
ATOM     47  C   CYS   107      55.482  26.726  52.353  1.00  0.00              
ATOM     48  O   CYS   107      55.743  25.792  51.590  1.00  0.00              
ATOM     49  N   ASP   108      54.563  26.640  53.311  1.00  0.00              
ATOM     50  CA  ASP   108      53.825  25.404  53.567  1.00  0.00              
ATOM     51  C   ASP   108      52.749  25.089  52.540  1.00  0.00              
ATOM     52  O   ASP   108      52.410  23.923  52.329  1.00  0.00              
ATOM     53  N   TYR   109      52.218  26.126  51.896  1.00  0.00              
ATOM     54  CA  TYR   109      51.081  25.980  50.991  1.00  0.00              
ATOM     55  C   TYR   109      51.389  25.289  49.672  1.00  0.00              
ATOM     56  O   TYR   109      52.467  25.474  49.101  1.00  0.00              
ATOM     57  N   VAL   110      50.432  24.490  49.197  1.00  0.00              
ATOM     58  CA  VAL   110      50.524  23.822  47.895  1.00  0.00              
ATOM     59  C   VAL   110      49.160  23.857  47.193  1.00  0.00              
ATOM     60  O   VAL   110      48.296  23.016  47.460  1.00  0.00              
ATOM     61  N   TYR   111      48.976  24.832  46.301  1.00  0.00              
ATOM     62  CA  TYR   111      47.726  24.983  45.547  1.00  0.00              
ATOM     63  C   TYR   111      47.944  24.740  44.057  1.00  0.00              
ATOM     64  O   TYR   111      49.060  24.878  43.554  1.00  0.00              
ATOM     65  N   LEU   112      46.863  24.385  43.361  1.00  0.00              
ATOM     66  CA  LEU   112      46.882  24.175  41.910  1.00  0.00              
ATOM     67  C   LEU   112      45.698  24.893  41.255  1.00  0.00              
ATOM     68  O   LEU   112      44.620  24.994  41.847  1.00  0.00              
ATOM     69  N   ALA   113      45.910  25.386  40.036  1.00  0.00              
ATOM     70  CA  ALA   113      44.882  26.117  39.301  1.00  0.00              
ATOM     71  C   ALA   113      44.487  25.390  38.021  1.00  0.00              
ATOM     72  O   ALA   113      45.333  25.129  37.165  1.00  0.00              
ATOM     73  N   VAL   114      43.201  25.062  37.899  1.00  0.00              
ATOM     74  CA  VAL   114      42.652  24.533  36.651  1.00  0.00              
ATOM     75  C   VAL   114      42.073  25.684  35.833  1.00  0.00              
ATOM     76  O   VAL   114      41.559  26.657  36.389  1.00  0.00              
ATOM     77  N   TYR   115      42.166  25.560  34.511  1.00  0.00              
ATOM     78  CA  TYR   115      41.800  26.638  33.593  1.00  0.00              
ATOM     79  C   TYR   115      41.751  26.137  32.145  1.00  0.00              
ATOM     80  O   TYR   115      41.983  24.956  31.876  1.00  0.00              
ATOM     81  N   PRO   116      41.437  27.047  31.227  1.00  0.00              
ATOM     82  CA  PRO   116      41.585  26.812  29.793  1.00  0.00              
ATOM     83  C   PRO   116      42.235  28.039  29.163  1.00  0.00              
ATOM     84  O   PRO   116      41.901  29.166  29.519  1.00  0.00              
ATOM     85  N   THR   117      43.161  27.819  28.235  1.00  0.00              
ATOM     86  CA  THR   117      43.816  28.917  27.524  1.00  0.00              
ATOM     87  C   THR   117      43.968  28.602  26.037  1.00  0.00              
ATOM     88  O   THR   117      44.149  27.445  25.653  1.00  0.00              
END
