
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0319AL381_1
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL381_1.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    -       -      L       9           -
LGA    -       -      K      10           -
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      P      24           -
LGA    -       -      L      25           -
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    S     104      S      30          3.366
LGA    I     105      K      31          1.703
LGA    A     106      C      32          0.911
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      P      72           -
LGA    -       -      P      73           -
LGA    -       -      T      74           -
LGA    -       -      K      75           -
LGA    -       -      P      76           -
LGA    -       -      S      77           -
LGA    -       -      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    -       -      M      90           -
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    -       -      L      93           -
LGA    -       -      N      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      H      97           -
LGA    -       -      T      98           -
LGA    -       -      L      99           -
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    E     107      E     107          2.515
LGA    G     108      G     108          3.398
LGA    E     109      E     109          1.499
LGA    M     110      M     110          1.481
LGA    K     111      K     111          1.016
LGA    C     112      C     112          0.560
LGA    R     113      R     113          0.387
LGA    N     114      N     114          0.694
LGA    C     115      C     115          1.069
LGA    G     116      G     116          1.083
LGA    H     117      H     117          1.518
LGA    I     118      I     118          1.344
LGA    Y     119      Y     119          0.598
LGA    Y     120      Y     120          0.873
LGA    I     121      I     121          1.914
LGA    K     122      K     122          0.887
LGA    N     123      N     123           #
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    G     124      N     127          2.794
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  135    5.0     20    1.72    85.00     13.707     1.099

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.672826 * X  +   0.149358 * Y  +   0.724567 * Z  +   1.196875
  Y_new =  -0.737097 * X  +  -0.219008 * Y  +  -0.639315 * Z  +   3.363001
  Z_new =   0.063199 * X  +  -0.964224 * Y  +   0.257445 * Z  +  -4.772945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.309885    1.831707  [ DEG:   -75.0509    104.9491 ]
  Theta =  -0.063241   -3.078351  [ DEG:    -3.6235   -176.3765 ]
  Phi   =  -2.310642    0.830951  [ DEG:  -132.3900     47.6100 ]
 
# 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: T0319AL381_1                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_1.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  135   5.0   20   1.72   85.00  13.707
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_1
REMARK Aligment from pdb entry: 1dx8A
ATOM      1  N   SER   104      14.369  15.869   1.226  1.00  0.00              
ATOM      2  CA  SER   104      15.619  16.068   2.012  1.00  0.00              
ATOM      3  C   SER   104      15.390  15.673   3.474  1.00  0.00              
ATOM      4  O   SER   104      14.785  16.402   4.235  1.00  0.00              
ATOM      5  N   ILE   105      15.864  14.524   3.873  1.00  0.00              
ATOM      6  CA  ILE   105      15.665  14.088   5.286  1.00  0.00              
ATOM      7  C   ILE   105      16.947  13.456   5.833  1.00  0.00              
ATOM      8  O   ILE   105      17.859  13.138   5.096  1.00  0.00              
ATOM      9  N   ALA   106      17.024  13.271   7.129  1.00  0.00              
ATOM     10  CA  ALA   106      18.251  12.658   7.745  1.00  0.00              
ATOM     11  C   ALA   106      18.168  12.681   9.279  1.00  0.00              
ATOM     12  O   ALA   106      18.795  11.887   9.949  1.00  0.00              
ATOM     13  N   GLU   107      17.413  13.588   9.839  1.00  0.00              
ATOM     14  CA  GLU   107      17.310  13.660  11.328  1.00  0.00              
ATOM     15  C   GLU   107      16.542  12.452  11.877  1.00  0.00              
ATOM     16  O   GLU   107      15.503  12.592  12.491  1.00  0.00              
ATOM     17  N   GLY   108      17.050  11.267  11.664  1.00  0.00              
ATOM     18  CA  GLY   108      16.358  10.045  12.174  1.00  0.00              
ATOM     19  C   GLY   108      14.873  10.084  11.804  1.00  0.00              
ATOM     20  O   GLY   108      14.048   9.482  12.461  1.00  0.00              
ATOM     21  N   GLU   109      14.523  10.782  10.757  1.00  0.00              
ATOM     22  CA  GLU   109      13.088  10.838  10.356  1.00  0.00              
ATOM     23  C   GLU   109      12.691   9.528   9.672  1.00  0.00              
ATOM     24  O   GLU   109      13.218   9.176   8.636  1.00  0.00              
ATOM     25  N   MET   110      11.772   8.800  10.243  1.00  0.00              
ATOM     26  CA  MET   110      11.353   7.512   9.619  1.00  0.00              
ATOM     27  C   MET   110      10.041   7.704   8.857  1.00  0.00              
ATOM     28  O   MET   110       9.202   8.493   9.239  1.00  0.00              
ATOM     29  N   LYS   111       9.858   6.991   7.780  1.00  0.00              
ATOM     30  CA  LYS   111       8.599   7.137   6.995  1.00  0.00              
ATOM     31  C   LYS   111       7.827   5.814   6.981  1.00  0.00              
ATOM     32  O   LYS   111       8.365   4.775   6.654  1.00  0.00              
ATOM     33  N   CYS   112       6.571   5.846   7.332  1.00  0.00              
ATOM     34  CA  CYS   112       5.766   4.591   7.337  1.00  0.00              
ATOM     35  C   CYS   112       5.524   4.115   5.907  1.00  0.00              
ATOM     36  O   CYS   112       4.797   4.734   5.156  1.00  0.00              
ATOM     37  N   ARG   113       6.101   3.013   5.528  1.00  0.00              
ATOM     38  CA  ARG   113       5.866   2.503   4.149  1.00  0.00              
ATOM     39  C   ARG   113       4.410   2.040   4.013  1.00  0.00              
ATOM     40  O   ARG   113       3.933   1.766   2.930  1.00  0.00              
ATOM     41  N   ASN   114       3.707   1.937   5.113  1.00  0.00              
ATOM     42  CA  ASN   114       2.292   1.475   5.059  1.00  0.00              
ATOM     43  C   ASN   114       1.326   2.632   4.768  1.00  0.00              
ATOM     44  O   ASN   114       0.366   2.464   4.042  1.00  0.00              
ATOM     45  N   CYS   115       1.542   3.796   5.333  1.00  0.00              
ATOM     46  CA  CYS   115       0.585   4.913   5.071  1.00  0.00              
ATOM     47  C   CYS   115       1.304   6.167   4.545  1.00  0.00              
ATOM     48  O   CYS   115       0.763   6.911   3.752  1.00  0.00              
ATOM     49  N   GLY   116       2.511   6.408   4.972  1.00  0.00              
ATOM     50  CA  GLY   116       3.243   7.613   4.482  1.00  0.00              
ATOM     51  C   GLY   116       3.440   8.605   5.632  1.00  0.00              
ATOM     52  O   GLY   116       3.653   9.783   5.423  1.00  0.00              
ATOM     53  N   HIS   117       3.378   8.136   6.846  1.00  0.00              
ATOM     54  CA  HIS   117       3.568   9.040   8.013  1.00  0.00              
ATOM     55  C   HIS   117       5.062   9.225   8.279  1.00  0.00              
ATOM     56  O   HIS   117       5.873   8.398   7.914  1.00  0.00              
ATOM     57  N   ILE   118       5.435  10.303   8.909  1.00  0.00              
ATOM     58  CA  ILE   118       6.881  10.532   9.187  1.00  0.00              
ATOM     59  C   ILE   118       7.117  10.654  10.697  1.00  0.00              
ATOM     60  O   ILE   118       6.738  11.627  11.317  1.00  0.00              
ATOM     61  N   TYR   119       7.753   9.679  11.287  1.00  0.00              
ATOM     62  CA  TYR   119       8.027   9.747  12.749  1.00  0.00              
ATOM     63  C   TYR   119       9.176  10.725  13.013  1.00  0.00              
ATOM     64  O   TYR   119      10.246  10.610  12.446  1.00  0.00              
ATOM     65  N   TYR   120       8.965  11.678  13.875  1.00  0.00              
ATOM     66  CA  TYR   120      10.044  12.655  14.184  1.00  0.00              
ATOM     67  C   TYR   120      10.690  12.303  15.530  1.00  0.00              
ATOM     68  O   TYR   120      10.063  12.435  16.563  1.00  0.00              
ATOM     69  N   ILE   121      11.925  11.862  15.485  1.00  0.00              
ATOM     70  CA  ILE   121      12.637  11.491  16.733  1.00  0.00              
ATOM     71  C   ILE   121      12.930  12.727  17.581  1.00  0.00              
ATOM     72  O   ILE   121      12.351  12.925  18.631  1.00  0.00              
ATOM     73  N   LYS   122      13.823  13.557  17.133  1.00  0.00              
ATOM     74  CA  LYS   122      14.167  14.791  17.902  1.00  0.00              
ATOM     75  C   LYS   122      12.892  15.522  18.346  1.00  0.00              
ATOM     76  O   LYS   122      12.884  16.232  19.330  1.00  0.00              
ATOM     77  N   ASN   123      11.816  15.346  17.628  1.00  0.00              
ATOM     78  CA  ASN   123      10.545  16.027  18.011  1.00  0.00              
ATOM     79  C   ASN   123       9.696  15.104  18.888  1.00  0.00              
ATOM     80  O   ASN   123       8.999  15.547  19.780  1.00  0.00              
ATOM     81  N   GLY   124       9.753  13.824  18.647  1.00  0.00              
ATOM     82  CA  GLY   124       8.958  12.875  19.472  1.00  0.00              
ATOM     83  C   GLY   124       7.571  12.685  18.861  1.00  0.00              
ATOM     84  O   GLY   124       7.078  13.522  18.131  1.00  0.00              
END
