
#######################################################
#                                                     #
#                        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   17 (   85),  selected   17 , name T0320TS239_3_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_3_1-D1.T0320_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    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    M       1      A      33          1.323
LGA    Q       2      I      34          1.658
LGA    S       4      R      35          1.780
LGA    K       5      L      36          1.198
LGA    A       6      T      37          0.434
LGA    A       7      R      38          0.715
LGA    E       8      K      39          0.354
LGA    M       9      Y      40          1.008
LGA    C      10      L      41          1.572
LGA    Y      11      L      42          1.657
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    E      12      C      76          3.963
LGA    I      13      L      77          5.886
LGA    T      14      W      78          4.145
LGA    N      15      E      79          2.425
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    S      16      F      82          1.580
LGA    -       -      I      83           -
LGA    T      30      K      84          4.310
LGA    Q      31      A      85          4.477
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  214    5.0     17    2.77     0.00      6.233     0.592

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.622379 * X  +  -0.764540 * Y  +  -0.167699 * Z  +  88.218712
  Y_new =  -0.140473 * X  +  -0.101670 * Y  +   0.984850 * Z  +  -4.348282
  Z_new =  -0.770008 * X  +   0.636507 * Y  +  -0.044120 * Z  +   6.076890 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.640001   -1.501592  [ DEG:    93.9651    -86.0349 ]
  Theta =   0.878853    2.262739  [ DEG:    50.3546    129.6454 ]
  Phi   =  -2.919609    0.221984  [ DEG:  -167.2812     12.7187 ]
 
# 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: T0320TS239_3_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_3_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  214   5.0   17   2.77    0.00   6.233
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_3_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       4.231  16.260  25.827  1.00  9.99
ATOM      2  CA  MET     1       5.620  16.444  26.303  1.00  9.99
ATOM      3  C   MET     1       5.762  17.892  26.781  1.00  9.99
ATOM      4  O   MET     1       6.536  18.059  27.749  1.00  9.99
ATOM      5  CB  MET     1       6.639  16.117  25.236  1.00  9.99
ATOM      6  N   GLN     2       5.005  18.821  26.253  1.00  9.99
ATOM      7  CA  GLN     2       5.056  20.193  26.757  1.00  9.99
ATOM      8  C   GLN     2       4.710  20.254  28.221  1.00  9.99
ATOM      9  O   GLN     2       5.378  20.911  29.067  1.00  9.99
ATOM     10  CB  GLN     2       4.224  21.121  25.861  1.00  9.99
ATOM     11  N   SER     4       3.599  19.641  28.597  1.00  9.99
ATOM     12  CA  SER     4       3.142  19.590  29.970  1.00  9.99
ATOM     13  C   SER     4       4.126  18.887  30.858  1.00  9.99
ATOM     14  O   SER     4       4.413  19.300  32.003  1.00  9.99
ATOM     15  CB  SER     4       1.787  18.852  30.066  1.00  9.99
ATOM     16  N   LYS     5       4.767  17.834  30.407  1.00  9.99
ATOM     17  CA  LYS     5       5.743  17.084  31.129  1.00  9.99
ATOM     18  C   LYS     5       6.945  18.008  31.402  1.00  9.99
ATOM     19  O   LYS     5       7.476  18.066  32.515  1.00  9.99
ATOM     20  CB  LYS     5       6.198  15.830  30.445  1.00  9.99
ATOM     21  N   ALA     6       7.485  18.672  30.386  1.00  9.99
ATOM     22  CA  ALA     6       8.664  19.521  30.552  1.00  9.99
ATOM     23  C   ALA     6       8.339  20.690  31.466  1.00  9.99
ATOM     24  O   ALA     6       9.148  20.990  32.373  1.00  9.99
ATOM     25  CB  ALA     6       9.107  20.052  29.189  1.00  9.99
ATOM     26  N   ALA     7       7.142  21.252  31.382  1.00  9.99
ATOM     27  CA  ALA     7       6.723  22.301  32.302  1.00  9.99
ATOM     28  C   ALA     7       6.793  21.814  33.697  1.00  9.99
ATOM     29  O   ALA     7       7.235  22.506  34.647  1.00  9.99
ATOM     30  CB  ALA     7       5.278  22.679  32.022  1.00  9.99
ATOM     31  N   GLU     8       6.280  20.608  34.008  1.00  9.99
ATOM     32  CA  GLU     8       6.280  20.059  35.356  1.00  9.99
ATOM     33  C   GLU     8       7.673  19.809  35.828  1.00  9.99
ATOM     34  O   GLU     8       8.117  20.097  36.972  1.00  9.99
ATOM     35  CB  GLU     8       5.415  18.774  35.452  1.00  9.99
ATOM     36  N   MET     9       8.522  19.232  34.975  1.00  9.99
ATOM     37  CA  MET     9       9.875  18.867  35.326  1.00  9.99
ATOM     38  C   MET     9      10.704  20.126  35.642  1.00  9.99
ATOM     39  O   MET     9      11.608  20.017  36.489  1.00  9.99
ATOM     40  CB  MET     9      10.533  18.004  34.236  1.00  9.99
ATOM     41  N   CYS    10      10.471  21.189  34.933  1.00  9.99
ATOM     42  CA  CYS    10      11.261  22.427  35.127  1.00  9.99
ATOM     43  C   CYS    10      10.598  23.342  36.133  1.00  9.99
ATOM     44  O   CYS    10      11.102  24.478  36.338  1.00  9.99
ATOM     45  CB  CYS    10      11.494  23.084  33.773  1.00  9.99
ATOM     46  N   TYR    11       9.459  22.942  36.705  1.00  9.99
ATOM     47  CA  TYR    11       8.799  23.719  37.784  1.00  9.99
ATOM     48  C   TYR    11       8.199  24.967  37.274  1.00  9.99
ATOM     49  O   TYR    11       8.143  26.030  38.019  1.00  9.99
ATOM     50  CB  TYR    11       9.706  23.804  39.012  1.00  9.99
ATOM     51  N   GLU    12       7.688  25.186  36.081  1.00  9.99
ATOM     52  CA  GLU    12       7.216  26.369  35.498  1.00  9.99
ATOM     53  C   GLU    12       5.706  26.700  35.663  1.00  9.99
ATOM     54  O   GLU    12       4.866  25.809  35.384  1.00  9.99
ATOM     55  CB  GLU    12       7.442  26.454  33.979  1.00  9.99
ATOM     56  N   ILE    13       5.300  27.902  36.005  1.00  9.99
ATOM     57  CA  ILE    13       3.896  28.364  35.993  1.00  9.99
ATOM     58  C   ILE    13       3.524  29.147  34.792  1.00  9.99
ATOM     59  O   ILE    13       4.257  29.947  34.290  1.00  9.99
ATOM     60  CB  ILE    13       3.687  29.430  37.114  1.00  9.99
ATOM     61  N   THR    14       2.266  29.013  34.299  1.00  9.99
ATOM     62  CA  THR    14       1.752  29.724  33.166  1.00  9.99
ATOM     63  C   THR    14       1.567  31.196  33.571  1.00  9.99
ATOM     64  O   THR    14       1.714  32.076  32.815  1.00  9.99
ATOM     65  CB  THR    14       0.326  29.204  32.852  1.00  9.99
ATOM     66  N   ASN    15       1.275  31.175  34.914  1.00  9.99
ATOM     67  CA  ASN    15       0.873  32.216  35.797  1.00  9.99
ATOM     68  C   ASN    15       1.544  32.283  37.231  1.00  9.99
ATOM     69  O   ASN    15       1.411  31.362  38.024  1.00  9.99
ATOM     70  CB  ASN    15      -0.661  32.093  36.087  1.00  9.99
ATOM     71  N   SER    16       2.109  33.478  37.342  1.00  9.99
ATOM     72  CA  SER    16       2.756  33.880  38.609  1.00  9.99
ATOM     73  C   SER    16       2.266  35.315  39.010  1.00  9.99
ATOM     74  O   SER    16       1.808  36.261  38.389  1.00  9.99
ATOM     75  CB  SER    16       4.302  33.868  38.521  1.00  9.99
ATOM     76  N   THR    30       2.571  35.413  40.326  1.00  9.99
ATOM     77  CA  THR    30       2.382  36.674  41.111  1.00  9.99
ATOM     78  C   THR    30       3.819  37.118  41.404  1.00  9.99
ATOM     79  O   THR    30       4.524  36.473  42.221  1.00  9.99
ATOM     80  CB  THR    30       1.648  36.282  42.372  1.00  9.99
ATOM     81  N   GLN    31       4.260  38.227  40.903  1.00  9.99
ATOM     82  CA  GLN    31       5.666  38.642  41.002  1.00  9.99
ATOM     83  C   GLN    31       6.086  38.887  42.426  1.00  9.99
ATOM     84  O   GLN    31       7.185  38.452  42.807  1.00  9.99
ATOM     85  CB  GLN    31       5.818  39.923  40.173  1.00  9.99
TER
END
