
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0342AL333_4-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342AL333_4-D1.T0342_D1.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    G      81      E      14           -
LGA    V      82      E      15           -
LGA    V      83      S      16           -
LGA    Q      97      F      17           -
LGA    E      98      L      18           -
LGA    G      99      Y      19           -
LGA    V     100      F      20           -
LGA    K     101      A      21           -
LGA    -       -      Y      22           -
LGA    -       -      G      23           -
LGA    -       -      S      24           -
LGA    -       -      N      25           -
LGA    S     102      L      26           #
LGA    -       -      L      27           -
LGA    -       -      T      28           -
LGA    -       -      E      29           -
LGA    -       -      R      30           -
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    -       -      A      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      C      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      Q      47           -
LGA    -       -      D      48           -
LGA    -       -      F      49           -
LGA    -       -      K      50           -
LGA    -       -      L      51           -
LGA    -       -      D      52           -
LGA    -       -      F      53           -
LGA    -       -      G      54           -
LGA    -       -      N      55           -
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    -       -      T      70           -
LGA    -       -      I      71           -
LGA    -       -      F      72           -
LGA    -       -      Q      73           -
LGA    -       -      S      74           -
LGA    -       -      P      75           -
LGA    -       -      G      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    G     103      V      79          2.866
LGA    M     104      W      80          1.827
LGA    Y     105      G      81          2.075
LGA    -       -      V      82           -
LGA    V     106      V      83          1.180
LGA    V     107      W      84          3.315
LGA    -       -      K      85           -
LGA    I     108      M      86          2.130
LGA    E     109      N      87          4.204
LGA    -       -      K      88           -
LGA    -       -      S      89           -
LGA    V     110      N      90          3.188
LGA    -       -      L      91           -
LGA    -       -      N      92           -
LGA    K     111      S      93          1.911
LGA    V     112      L      94          2.906
LGA    -       -      D      95           -
LGA    -       -      E      96           -
LGA    -       -      Q      97           -
LGA    -       -      E      98           -
LGA    A     113      G      99          3.958
LGA    T     114      V     100          1.327
LGA    -       -      K     101           -
LGA    -       -      S     102           -
LGA    -       -      G     103           -
LGA    Q     115      M     104           #
LGA    E     116      Y     105          3.719
LGA    G     117      V     106          3.865
LGA    K     118      V     107          3.065
LGA    E     119      -       -           -
LGA    I     120      I     108          1.794
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      K     111           -
LGA    -       -      V     112           -
LGA    -       -      A     113           -
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      C     122           -
LGA    -       -      R     123           -
LGA    -       -      S     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      M     127           -
LGA    -       -      T     128           -
LGA    -       -      N     129           -
LGA    -       -      Y     130           -
LGA    -       -      E     131           -
LGA    -       -      S     132           -
LGA    -       -      A     133           -
LGA    -       -      P     134           -
LGA    -       -      P     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27  122    5.0     16    2.87    12.50      8.481     0.539

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.904042 * X  +   0.354481 * Y  +   0.238855 * Z  +   5.328267
  Y_new =   0.393109 * X  +   0.470073 * Y  +   0.790251 * Z  +  26.847078
  Z_new =   0.167850 * X  +   0.808315 * Y  +  -0.564316 * Z  + -23.502087 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.180272   -0.961321  [ DEG:   124.9204    -55.0796 ]
  Theta =  -0.168648   -2.972944  [ DEG:    -9.6628   -170.3372 ]
  Phi   =   2.731421   -0.410172  [ DEG:   156.4989    -23.5011 ]
 
# 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: T0342AL333_4-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342AL333_4-D1.T0342_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  122   5.0   16   2.87   12.50   8.481
REMARK  ---------------------------------------------------------- 
MOLECULE T0342AL333_4-D1
REMARK Aligment from pdb entry: 1xgs_A
ATOM      1  N   GLY    81      24.311  73.939  18.277  1.00  0.00              
ATOM      2  CA  GLY    81      24.159  73.394  16.946  1.00  0.00              
ATOM      3  C   GLY    81      22.732  73.439  16.443  1.00  0.00              
ATOM      4  O   GLY    81      22.322  72.615  15.640  1.00  0.00              
ATOM      5  N   VAL    82      21.961  74.411  16.902  1.00  0.00              
ATOM      6  CA  VAL    82      20.594  74.517  16.434  1.00  0.00              
ATOM      7  C   VAL    82      20.135  75.977  16.418  1.00  0.00              
ATOM      8  O   VAL    82      20.514  76.743  17.288  1.00  0.00              
ATOM      9  N   VAL    83      19.380  76.368  15.399  1.00  0.00              
ATOM     10  CA  VAL    83      18.870  77.736  15.309  1.00  0.00              
ATOM     11  C   VAL    83      17.366  77.794  15.588  1.00  0.00              
ATOM     12  O   VAL    83      16.615  76.848  15.315  1.00  0.00              
ATOM     13  N   GLN    97      16.945  78.897  16.189  1.00  0.00              
ATOM     14  CA  GLN    97      15.553  79.108  16.507  1.00  0.00              
ATOM     15  C   GLN    97      15.154  80.404  15.832  1.00  0.00              
ATOM     16  O   GLN    97      16.007  81.248  15.540  1.00  0.00              
ATOM     17  N   GLU    98      13.865  80.527  15.555  1.00  0.00              
ATOM     18  CA  GLU    98      13.304  81.710  14.944  1.00  0.00              
ATOM     19  C   GLU    98      13.032  82.764  16.011  1.00  0.00              
ATOM     20  O   GLU    98      12.510  82.459  17.079  1.00  0.00              
ATOM     21  N   GLY    99      13.432  84.000  15.728  1.00  0.00              
ATOM     22  CA  GLY    99      13.239  85.120  16.642  1.00  0.00              
ATOM     23  C   GLY    99      12.795  86.336  15.815  1.00  0.00              
ATOM     24  O   GLY    99      13.006  86.387  14.608  1.00  0.00              
ATOM     25  N   VAL   100      12.047  87.259  16.426  1.00  0.00              
ATOM     26  CA  VAL   100      11.604  88.448  15.686  1.00  0.00              
ATOM     27  C   VAL   100      12.835  89.347  15.474  1.00  0.00              
ATOM     28  O   VAL   100      13.784  89.304  16.275  1.00  0.00              
ATOM     29  N   LYS   101      12.807  90.243  14.468  1.00  0.00              
ATOM     30  CA  LYS   101      11.759  90.536  13.488  1.00  0.00              
ATOM     31  C   LYS   101      11.760  89.653  12.254  1.00  0.00              
ATOM     32  O   LYS   101      12.683  88.886  12.031  1.00  0.00              
ATOM     33  N   SER   102      10.707  89.782  11.462  1.00  0.00              
ATOM     34  CA  SER   102      10.588  89.072  10.199  1.00  0.00              
ATOM     35  C   SER   102      10.968  90.171   9.218  1.00  0.00              
ATOM     36  O   SER   102      10.281  91.185   9.143  1.00  0.00              
ATOM     37  N   GLY   103      12.105  90.035   8.548  1.00  0.00              
ATOM     38  CA  GLY   103      12.553  91.060   7.612  1.00  0.00              
ATOM     39  C   GLY   103      12.562  90.605   6.170  1.00  0.00              
ATOM     40  O   GLY   103      12.953  91.367   5.295  1.00  0.00              
ATOM     41  N   MET   104      12.189  89.345   5.950  1.00  0.00              
ATOM     42  CA  MET   104      12.168  88.705   4.639  1.00  0.00              
ATOM     43  C   MET   104      10.873  87.925   4.491  1.00  0.00              
ATOM     44  O   MET   104      10.441  87.264   5.423  1.00  0.00              
ATOM     45  N   TYR   105      10.283  87.971   3.301  1.00  0.00              
ATOM     46  CA  TYR   105       9.034  87.272   3.020  1.00  0.00              
ATOM     47  C   TYR   105       9.144  86.639   1.659  1.00  0.00              
ATOM     48  O   TYR   105      10.056  86.923   0.888  1.00  0.00              
ATOM     49  N   VAL   106       8.159  85.826   1.331  1.00  0.00              
ATOM     50  CA  VAL   106       8.161  85.185   0.049  1.00  0.00              
ATOM     51  C   VAL   106       6.755  84.862  -0.364  1.00  0.00              
ATOM     52  O   VAL   106       5.954  84.383   0.436  1.00  0.00              
ATOM     53  N   VAL   107       6.459  85.175  -1.612  1.00  0.00              
ATOM     54  CA  VAL   107       5.157  84.910  -2.200  1.00  0.00              
ATOM     55  C   VAL   107       5.033  83.398  -2.372  1.00  0.00              
ATOM     56  O   VAL   107       5.892  82.764  -2.996  1.00  0.00              
ATOM     57  N   ILE   108       1.459  81.657  -2.715  1.00  0.00              
ATOM     58  CA  ILE   108       0.268  81.156  -3.377  1.00  0.00              
ATOM     59  C   ILE   108      -0.653  82.255  -3.865  1.00  0.00              
ATOM     60  O   ILE   108      -0.790  83.295  -3.219  1.00  0.00              
ATOM     61  N   GLU   109      -1.322  81.995  -4.987  1.00  0.00              
ATOM     62  CA  GLU   109      -2.257  82.957  -5.560  1.00  0.00              
ATOM     63  C   GLU   109      -3.616  82.840  -4.850  1.00  0.00              
ATOM     64  O   GLU   109      -4.397  81.926  -5.128  1.00  0.00              
ATOM     65  N   VAL   110      -3.864  83.749  -3.908  1.00  0.00              
ATOM     66  CA  VAL   110      -5.104  83.784  -3.122  1.00  0.00              
ATOM     67  C   VAL   110      -5.854  85.115  -3.285  1.00  0.00              
ATOM     68  O   VAL   110      -5.239  86.163  -3.504  1.00  0.00              
ATOM     69  N   LYS   111      -7.193  85.087  -3.219  1.00  0.00              
ATOM     70  CA  LYS   111      -7.974  86.320  -3.353  1.00  0.00              
ATOM     71  C   LYS   111      -7.795  87.165  -2.098  1.00  0.00              
ATOM     72  O   LYS   111      -7.958  86.665  -0.973  1.00  0.00              
ATOM     73  N   VAL   112      -7.384  88.417  -2.281  1.00  0.00              
ATOM     74  CA  VAL   112      -7.179  89.318  -1.152  1.00  0.00              
ATOM     75  C   VAL   112      -8.354  90.254  -1.196  1.00  0.00              
ATOM     76  O   VAL   112      -8.650  90.824  -2.243  1.00  0.00              
ATOM     77  N   ALA   113      -9.040  90.378  -0.067  1.00  0.00              
ATOM     78  CA  ALA   113     -10.221  91.226   0.035  1.00  0.00              
ATOM     79  C   ALA   113      -9.871  92.722   0.080  1.00  0.00              
ATOM     80  O   ALA   113     -10.586  93.541  -0.476  1.00  0.00              
ATOM     81  N   THR   114      -8.782  93.064   0.765  1.00  0.00              
ATOM     82  CA  THR   114      -8.325  94.450   0.918  1.00  0.00              
ATOM     83  C   THR   114      -7.591  94.980  -0.336  1.00  0.00              
ATOM     84  O   THR   114      -6.742  94.301  -0.910  1.00  0.00              
ATOM     85  N   GLN   115      -7.840  96.233  -0.696  1.00  0.00              
ATOM     86  CA  GLN   115      -7.227  96.832  -1.889  1.00  0.00              
ATOM     87  C   GLN   115      -5.738  97.164  -1.868  1.00  0.00              
ATOM     88  O   GLN   115      -5.058  96.932  -2.863  1.00  0.00              
ATOM     89  N   GLU   116      -5.232  97.762  -0.792  1.00  0.00              
ATOM     90  CA  GLU   116      -3.803  98.066  -0.756  1.00  0.00              
ATOM     91  C   GLU   116      -2.990  96.771  -0.648  1.00  0.00              
ATOM     92  O   GLU   116      -1.881  96.682  -1.173  1.00  0.00              
ATOM     93  N   GLY   117      -3.549  95.776   0.043  1.00  0.00              
ATOM     94  CA  GLY   117      -2.908  94.474   0.187  1.00  0.00              
ATOM     95  C   GLY   117      -2.890  93.834  -1.201  1.00  0.00              
ATOM     96  O   GLY   117      -1.876  93.302  -1.645  1.00  0.00              
ATOM     97  N   LYS   118      -4.006  93.932  -1.907  1.00  0.00              
ATOM     98  CA  LYS   118      -4.111  93.386  -3.249  1.00  0.00              
ATOM     99  C   LYS   118      -3.145  94.051  -4.259  1.00  0.00              
ATOM    100  O   LYS   118      -2.603  93.372  -5.135  1.00  0.00              
ATOM    101  N   GLU   119      -2.962  95.371  -4.163  1.00  0.00              
ATOM    102  CA  GLU   119      -2.039  96.086  -5.050  1.00  0.00              
ATOM    103  C   GLU   119      -0.630  95.726  -4.636  1.00  0.00              
ATOM    104  O   GLU   119       0.280  95.677  -5.459  1.00  0.00              
ATOM    105  N   ILE   120      -0.440  95.537  -3.335  1.00  0.00              
ATOM    106  CA  ILE   120       0.864  95.168  -2.800  1.00  0.00              
ATOM    107  C   ILE   120       1.274  93.791  -3.333  1.00  0.00              
ATOM    108  O   ILE   120       2.377  93.614  -3.837  1.00  0.00              
END
