
#######################################################
#                                                     #
#                        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-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_2_1-D1.T0320_D1.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    M       1      A      33          0.869
LGA    Q       2      I      34          0.815
LGA    S       4      R      35          1.704
LGA    K       5      L      36          1.102
LGA    A       6      T      37          0.171
LGA    A       7      R      38          0.917
LGA    E       8      K      39          1.031
LGA    M       9      Y      40          0.596
LGA    C      10      L      41          1.676
LGA    Y      11      L      42          1.884
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          3.234
LGA    I      13      L      77          4.080
LGA    T      14      W      78          3.121
LGA    N      15      E      79          2.963
LGA    -       -      Y      80           -
LGA    S      16      F      81          1.373
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    -       -      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)   15  214    5.0     15    2.03     0.00      5.969     0.705

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.673718 * X  +  -0.735641 * Y  +  -0.070268 * Z  +  83.716827
  Y_new =  -0.209817 * X  +   0.099245 * Y  +   0.972691 * Z  + -17.204004
  Z_new =  -0.708577 * X  +   0.670062 * Y  +  -0.221213 * Z  +   8.578413 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.889669   -1.251924  [ DEG:   108.2701    -71.7299 ]
  Theta =   0.787479    2.354113  [ DEG:    45.1192    134.8808 ]
  Phi   =  -2.839681    0.301912  [ DEG:  -162.7017     17.2983 ]
 
# 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-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_2_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  214   5.0   15   2.03    0.00   5.969
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_2_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       3.398  15.633  26.999  1.00  9.99
ATOM      2  CA  MET     1       4.822  15.749  27.385  1.00  9.99
ATOM      3  C   MET     1       5.134  17.236  27.580  1.00  9.99
ATOM      4  O   MET     1       5.972  17.491  28.472  1.00  9.99
ATOM      5  CB  MET     1       5.745  15.125  26.363  1.00  9.99
ATOM      6  N   GLN     2       4.447  18.130  26.914  1.00  9.99
ATOM      7  CA  GLN     2       4.662  19.556  27.151  1.00  9.99
ATOM      8  C   GLN     2       4.403  19.920  28.589  1.00  9.99
ATOM      9  O   GLN     2       5.178  20.644  29.274  1.00  9.99
ATOM     10  CB  GLN     2       3.880  20.391  26.127  1.00  9.99
ATOM     11  N   SER     4       3.258  19.510  29.110  1.00  9.99
ATOM     12  CA  SER     4       2.872  19.759  30.484  1.00  9.99
ATOM     13  C   SER     4       3.827  19.127  31.453  1.00  9.99
ATOM     14  O   SER     4       4.214  19.707  32.490  1.00  9.99
ATOM     15  CB  SER     4       1.457  19.202  30.762  1.00  9.99
ATOM     16  N   LYS     5       4.334  17.947  31.185  1.00  9.99
ATOM     17  CA  LYS     5       5.267  17.238  32.000  1.00  9.99
ATOM     18  C   LYS     5       6.569  18.061  32.055  1.00  9.99
ATOM     19  O   LYS     5       7.162  18.263  33.119  1.00  9.99
ATOM     20  CB  LYS     5       5.557  15.839  31.547  1.00  9.99
ATOM     21  N   ALA     6       7.118  18.467  30.914  1.00  9.99
ATOM     22  CA  ALA     6       8.382  19.199  30.880  1.00  9.99
ATOM     23  C   ALA     6       8.226  20.542  31.570  1.00  9.99
ATOM     24  O   ALA     6       9.109  20.913  32.377  1.00  9.99
ATOM     25  CB  ALA     6       8.803  19.422  29.427  1.00  9.99
ATOM     26  N   ALA     7       7.088  21.207  31.424  1.00  9.99
ATOM     27  CA  ALA     7       6.827  22.444  32.146  1.00  9.99
ATOM     28  C   ALA     7       6.922  22.214  33.604  1.00  9.99
ATOM     29  O   ALA     7       7.482  23.016  34.392  1.00  9.99
ATOM     30  CB  ALA     7       5.414  22.919  31.850  1.00  9.99
ATOM     31  N   GLU     8       6.309  21.148  34.151  1.00  9.99
ATOM     32  CA  GLU     8       6.326  20.857  35.577  1.00  9.99
ATOM     33  C   GLU     8       7.710  20.547  36.040  1.00  9.99
ATOM     34  O   GLU     8       8.241  20.989  37.095  1.00  9.99
ATOM     35  CB  GLU     8       5.343  19.712  35.941  1.00  9.99
ATOM     36  N   MET     9       8.450  19.736  35.281  1.00  9.99
ATOM     37  CA  MET     9       9.776  19.296  35.648  1.00  9.99
ATOM     38  C   MET     9      10.743  20.494  35.694  1.00  9.99
ATOM     39  O   MET     9      11.676  20.444  36.515  1.00  9.99
ATOM     40  CB  MET     9      10.285  18.183  34.716  1.00  9.99
ATOM     41  N   CYS    10      10.580  21.430  34.808  1.00  9.99
ATOM     42  CA  CYS    10      11.499  22.590  34.741  1.00  9.99
ATOM     43  C   CYS    10      10.986  23.739  35.581  1.00  9.99
ATOM     44  O   CYS    10      11.612  24.831  35.553  1.00  9.99
ATOM     45  CB  CYS    10      11.724  22.960  33.281  1.00  9.99
ATOM     46  N   TYR    11       9.846  23.574  36.255  1.00  9.99
ATOM     47  CA  TYR    11       9.325  24.602  37.193  1.00  9.99
ATOM     48  C   TYR    11       8.827  25.794  36.480  1.00  9.99
ATOM     49  O   TYR    11       8.917  26.974  37.015  1.00  9.99
ATOM     50  CB  TYR    11      10.301  24.810  38.351  1.00  9.99
ATOM     51  N   GLU    12       8.277  25.846  35.285  1.00  9.99
ATOM     52  CA  GLU    12       7.895  26.948  34.508  1.00  9.99
ATOM     53  C   GLU    12       6.438  27.465  34.660  1.00  9.99
ATOM     54  O   GLU    12       5.499  26.635  34.581  1.00  9.99
ATOM     55  CB  GLU    12       8.047  26.731  32.993  1.00  9.99
ATOM     56  N   ILE    13       6.173  28.746  34.785  1.00  9.99
ATOM     57  CA  ILE    13       4.824  29.348  34.736  1.00  9.99
ATOM     58  C   ILE    13       4.468  29.935  33.424  1.00  9.99
ATOM     59  O   ILE    13       5.250  30.546  32.756  1.00  9.99
ATOM     60  CB  ILE    13       4.783  30.616  35.645  1.00  9.99
ATOM     61  N   THR    14       3.179  29.851  33.008  1.00  9.99
ATOM     62  CA  THR    14       2.679  30.395  31.779  1.00  9.99
ATOM     63  C   THR    14       2.664  31.928  31.910  1.00  9.99
ATOM     64  O   THR    14       2.858  32.634  30.998  1.00  9.99
ATOM     65  CB  THR    14       1.193  29.984  31.618  1.00  9.99
ATOM     66  N   ASN    15       2.444  32.183  33.242  1.00  9.99
ATOM     67  CA  ASN    15       2.196  33.405  33.929  1.00  9.99
ATOM     68  C   ASN    15       2.946  33.658  35.301  1.00  9.99
ATOM     69  O   ASN    15       2.764  32.916  36.256  1.00  9.99
ATOM     70  CB  ASN    15       0.675  33.503  34.289  1.00  9.99
ATOM     71  N   SER    16       3.633  34.784  35.168  1.00  9.99
ATOM     72  CA  SER    16       4.384  35.338  36.315  1.00  9.99
ATOM     73  C   SER    16       4.063  36.867  36.458  1.00  9.99
ATOM     74  O   SER    16       3.669  37.728  35.688  1.00  9.99
ATOM     75  CB  SER    16       5.915  35.143  36.178  1.00  9.99
TER
END
