
#######################################################
#                                                     #
#                        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   15 (   75),  selected   15 , name T0320TS239_2_1
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS239_2_1.T0320.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
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    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
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    M       1      N     201          0.496
LGA    Q       2      I     202          0.656
LGA    S       4      W     203          0.317
LGA    K       5      S     204          0.290
LGA    A       6      F     205          0.345
LGA    A       7      L     206          0.522
LGA    E       8      L     207          0.930
LGA    M       9      Y     208          0.777
LGA    C      10      S     209          0.512
LGA    Y      11      N     210          0.525
LGA    E      12      E     211          2.119
LGA    I      13      P     212          2.630
LGA    T      14      I     213          2.123
LGA    N      15      C     214          2.513
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           -
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    S      16      S     270          2.157
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  287    5.0     15    1.42    13.33      4.939     0.988

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.659233 * X  +  -0.010476 * Y  +   0.751865 * Z  + -40.318768
  Y_new =  -0.748523 * X  +  -0.104336 * Y  +   0.654849 * Z  +  25.984989
  Z_new =   0.071587 * X  +  -0.994487 * Y  +  -0.076624 * Z  +  93.105835 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.647693    1.493900  [ DEG:   -94.4058     85.5942 ]
  Theta =  -0.071648   -3.069945  [ DEG:    -4.1051   -175.8949 ]
  Phi   =  -0.848740    2.292852  [ DEG:   -48.6292    131.3708 ]
 
# 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_2_1                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_2_1.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  287   5.0   15   1.42   13.33   4.939
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_2_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       6.619  14.559  18.708  1.00  9.99
ATOM      2  CA  MET     1       5.744  15.534  19.397  1.00  9.99
ATOM      3  C   MET     1       6.347  16.927  19.196  1.00  9.99
ATOM      4  O   MET     1       5.516  17.857  19.100  1.00  9.99
ATOM      5  CB  MET     1       5.578  15.216  20.865  1.00  9.99
ATOM      6  N   GLN     2       7.639  17.050  19.020  1.00  9.99
ATOM      7  CA  GLN     2       8.226  18.357  18.734  1.00  9.99
ATOM      8  C   GLN     2       7.647  18.958  17.481  1.00  9.99
ATOM      9  O   GLN     2       7.257  20.156  17.398  1.00  9.99
ATOM     10  CB  GLN     2       9.758  18.270  18.755  1.00  9.99
ATOM     11  N   SER     4       7.631  18.188  16.404  1.00  9.99
ATOM     12  CA  SER     4       7.087  18.611  15.130  1.00  9.99
ATOM     13  C   SER     4       5.625  18.932  15.228  1.00  9.99
ATOM     14  O   SER     4       5.115  19.922  14.659  1.00  9.99
ATOM     15  CB  SER     4       7.271  17.505  14.065  1.00  9.99
ATOM     16  N   LYS     5       4.850  18.194  15.987  1.00  9.99
ATOM     17  CA  LYS     5       3.452  18.395  16.192  1.00  9.99
ATOM     18  C   LYS     5       3.267  19.754  16.895  1.00  9.99
ATOM     19  O   LYS     5       2.415  20.565  16.521  1.00  9.99
ATOM     20  CB  LYS     5       2.772  17.311  16.973  1.00  9.99
ATOM     21  N   ALA     6       3.969  20.005  17.996  1.00  9.99
ATOM     22  CA  ALA     6       3.806  21.245  18.753  1.00  9.99
ATOM     23  C   ALA     6       4.235  22.432  17.909  1.00  9.99
ATOM     24  O   ALA     6       3.506  23.449  17.883  1.00  9.99
ATOM     25  CB  ALA     6       4.663  21.187  20.018  1.00  9.99
ATOM     26  N   ALA     7       5.280  22.298  17.103  1.00  9.99
ATOM     27  CA  ALA     7       5.677  23.355  16.184  1.00  9.99
ATOM     28  C   ALA     7       4.561  23.686  15.272  1.00  9.99
ATOM     29  O   ALA     7       4.257  24.863  14.955  1.00  9.99
ATOM     30  CB  ALA     7       6.840  22.878  15.329  1.00  9.99
ATOM     31  N   GLU     8       3.879  22.695  14.668  1.00  9.99
ATOM     32  CA  GLU     8       2.785  22.926  13.736  1.00  9.99
ATOM     33  C   GLU     8       1.628  23.570  14.424  1.00  9.99
ATOM     34  O   GLU     8       0.954  24.533  13.968  1.00  9.99
ATOM     35  CB  GLU     8       2.355  21.618  13.020  1.00  9.99
ATOM     36  N   MET     9       1.272  23.091  15.617  1.00  9.99
ATOM     37  CA  MET     9       0.128  23.572  16.357  1.00  9.99
ATOM     38  C   MET     9       0.334  25.043  16.764  1.00  9.99
ATOM     39  O   MET     9      -0.677  25.761  16.841  1.00  9.99
ATOM     40  CB  MET     9      -0.183  22.678  17.569  1.00  9.99
ATOM     41  N   CYS    10       1.536  25.409  17.096  1.00  9.99
ATOM     42  CA  CYS    10       1.816  26.788  17.558  1.00  9.99
ATOM     43  C   CYS    10       2.209  27.680  16.401  1.00  9.99
ATOM     44  O   CYS    10       2.567  28.862  16.645  1.00  9.99
ATOM     45  CB  CYS    10       2.859  26.738  18.666  1.00  9.99
ATOM     46  N   TYR    11       2.237  27.153  15.173  1.00  9.99
ATOM     47  CA  TYR    11       2.500  27.976  13.965  1.00  9.99
ATOM     48  C   TYR    11       3.906  28.419  13.897  1.00  9.99
ATOM     49  O   TYR    11       4.218  29.560  13.363  1.00  9.99
ATOM     50  CB  TYR    11       1.404  29.026  13.787  1.00  9.99
ATOM     51  N   GLU    12       4.972  27.788  14.345  1.00  9.99
ATOM     52  CA  GLU    12       6.308  28.202  14.418  1.00  9.99
ATOM     53  C   GLU    12       7.230  27.876  13.211  1.00  9.99
ATOM     54  O   GLU    12       7.249  26.698  12.776  1.00  9.99
ATOM     55  CB  GLU    12       7.075  27.635  15.625  1.00  9.99
ATOM     56  N   ILE    13       8.038  28.777  12.700  1.00  9.99
ATOM     57  CA  ILE    13       9.086  28.511  11.692  1.00  9.99
ATOM     58  C   ILE    13      10.447  28.367  12.255  1.00  9.99
ATOM     59  O   ILE    13      10.854  29.053  13.146  1.00  9.99
ATOM     60  CB  ILE    13       9.274  29.770  10.789  1.00  9.99
ATOM     61  N   THR    14      11.295  27.480  11.674  1.00  9.99
ATOM     62  CA  THR    14      12.648  27.251  12.087  1.00  9.99
ATOM     63  C   THR    14      13.479  28.485  11.698  1.00  9.99
ATOM     64  O   THR    14      14.386  28.855  12.336  1.00  9.99
ATOM     65  CB  THR    14      13.236  26.083  11.254  1.00  9.99
ATOM     66  N   ASN    15      12.885  28.988  10.565  1.00  9.99
ATOM     67  CA  ASN    15      13.290  30.030   9.683  1.00  9.99
ATOM     68  C   ASN    15      12.193  31.063   9.191  1.00  9.99
ATOM     69  O   ASN    15      11.232  30.685   8.537  1.00  9.99
ATOM     70  CB  ASN    15      13.861  29.407   8.365  1.00  9.99
ATOM     71  N   SER    16      12.609  32.271   9.546  1.00  9.99
ATOM     72  CA  SER    16      11.835  33.469   9.156  1.00  9.99
ATOM     73  C   SER    16      12.806  34.540   8.547  1.00  9.99
ATOM     74  O   SER    16      14.002  34.761   8.652  1.00  9.99
ATOM     75  CB  SER    16      11.059  34.091  10.343  1.00  9.99
TER
END
