
#######################################################
#                                                     #
#                        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
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS239_3_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          0.731
LGA    Q       2      I     202          0.635
LGA    S       4      W     203          0.364
LGA    K       5      S     204          0.571
LGA    A       6      F     205          0.623
LGA    A       7      L     206          0.634
LGA    E       8      L     207          1.026
LGA    M       9      Y     208          0.916
LGA    C      10      S     209          0.447
LGA    Y      11      N     210          0.719
LGA    E      12      E     211          2.639
LGA    I      13      P     212          3.458
LGA    T      14      I     213          2.683
LGA    -       -      C     214           -
LGA    N      15      G     215          2.079
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          0.852
LGA    T      30      P     271          2.787
LGA    Q      31      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)   17  287    5.0     16    1.65    12.50      5.242     0.913

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.620403 * X  +  -0.088845 * Y  +   0.779235 * Z  + -34.257008
  Y_new =  -0.780212 * X  +  -0.171019 * Y  +   0.601682 * Z  +  33.946182
  Z_new =   0.079807 * X  +  -0.981254 * Y  +  -0.175419 * Z  +  95.501381 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.747698    1.393895  [ DEG:  -100.1357     79.8643 ]
  Theta =  -0.079892   -3.061700  [ DEG:    -4.5775   -175.4225 ]
  Phi   =  -0.899007    2.242586  [ DEG:   -51.5093    128.4907 ]
 
# 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                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_3_1.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  287   5.0   16   1.65   12.50   5.242
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_3_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       6.418  14.675  19.062  1.00  9.99
ATOM      2  CA  MET     1       5.651  15.745  19.738  1.00  9.99
ATOM      3  C   MET     1       6.313  17.083  19.395  1.00  9.99
ATOM      4  O   MET     1       5.530  18.053  19.290  1.00  9.99
ATOM      5  CB  MET     1       5.575  15.539  21.233  1.00  9.99
ATOM      6  N   GLN     2       7.594  17.116  19.123  1.00  9.99
ATOM      7  CA  GLN     2       8.230  18.363  18.703  1.00  9.99
ATOM      8  C   GLN     2       7.595  18.911  17.452  1.00  9.99
ATOM      9  O   GLN     2       7.267  20.122  17.311  1.00  9.99
ATOM     10  CB  GLN     2       9.752  18.185  18.625  1.00  9.99
ATOM     11  N   SER     4       7.457  18.072  16.438  1.00  9.99
ATOM     12  CA  SER     4       6.846  18.439  15.177  1.00  9.99
ATOM     13  C   SER     4       5.415  18.853  15.352  1.00  9.99
ATOM     14  O   SER     4       4.920  19.830  14.750  1.00  9.99
ATOM     15  CB  SER     4       6.891  17.254  14.185  1.00  9.99
ATOM     16  N   LYS     5       4.658  18.216  16.215  1.00  9.99
ATOM     17  CA  LYS     5       3.292  18.515  16.500  1.00  9.99
ATOM     18  C   LYS     5       3.234  19.927  17.115  1.00  9.99
ATOM     19  O   LYS     5       2.403  20.761  16.743  1.00  9.99
ATOM     20  CB  LYS     5       2.612  17.529  17.402  1.00  9.99
ATOM     21  N   ALA     6       4.027  20.210  18.143  1.00  9.99
ATOM     22  CA  ALA     6       3.989  21.506  18.818  1.00  9.99
ATOM     23  C   ALA     6       4.420  22.605  17.863  1.00  9.99
ATOM     24  O   ALA     6       3.748  23.660  17.814  1.00  9.99
ATOM     25  CB  ALA     6       4.931  21.482  20.022  1.00  9.99
ATOM     26  N   ALA     7       5.394  22.354  16.999  1.00  9.99
ATOM     27  CA  ALA     7       5.781  23.320  15.981  1.00  9.99
ATOM     28  C   ALA     7       4.621  23.655  15.127  1.00  9.99
ATOM     29  O   ALA     7       4.360  24.823  14.747  1.00  9.99
ATOM     30  CB  ALA     7       6.850  22.717  15.084  1.00  9.99
ATOM     31  N   GLU     8       3.843  22.668  14.643  1.00  9.99
ATOM     32  CA  GLU     8       2.698  22.900  13.775  1.00  9.99
ATOM     33  C   GLU     8       1.632  23.657  14.493  1.00  9.99
ATOM     34  O   GLU     8       0.981  24.626  14.016  1.00  9.99
ATOM     35  CB  GLU     8       2.146  21.574  13.187  1.00  9.99
ATOM     36  N   MET     9       1.338  23.283  15.739  1.00  9.99
ATOM     37  CA  MET     9       0.279  23.881  16.520  1.00  9.99
ATOM     38  C   MET     9       0.596  25.361  16.805  1.00  9.99
ATOM     39  O   MET     9      -0.366  26.143  16.899  1.00  9.99
ATOM     40  CB  MET     9       0.009  23.092  17.812  1.00  9.99
ATOM     41  N   CYS    10       1.837  25.676  17.026  1.00  9.99
ATOM     42  CA  CYS    10       2.225  27.065  17.366  1.00  9.99
ATOM     43  C   CYS    10       2.581  27.850  16.123  1.00  9.99
ATOM     44  O   CYS    10       3.021  29.022  16.256  1.00  9.99
ATOM     45  CB  CYS    10       3.343  27.027  18.400  1.00  9.99
ATOM     46  N   TYR    11       2.491  27.240  14.938  1.00  9.99
ATOM     47  CA  TYR    11       2.710  27.962  13.658  1.00  9.99
ATOM     48  C   TYR    11       4.129  28.314  13.461  1.00  9.99
ATOM     49  O   TYR    11       4.464  29.395  12.826  1.00  9.99
ATOM     50  CB  TYR    11       1.663  29.062  13.481  1.00  9.99
ATOM     51  N   GLU    12       5.188  27.652  13.879  1.00  9.99
ATOM     52  CA  GLU    12       6.547  27.989  13.830  1.00  9.99
ATOM     53  C   GLU    12       7.359  27.526  12.589  1.00  9.99
ATOM     54  O   GLU    12       7.281  26.322  12.240  1.00  9.99
ATOM     55  CB  GLU    12       7.368  27.460  15.019  1.00  9.99
ATOM     56  N   ILE    13       8.176  28.340  11.959  1.00  9.99
ATOM     57  CA  ILE    13       9.131  27.943  10.903  1.00  9.99
ATOM     58  C   ILE    13      10.520  27.756  11.380  1.00  9.99
ATOM     59  O   ILE    13      11.028  28.476  12.189  1.00  9.99
ATOM     60  CB  ILE    13       9.322  29.124   9.901  1.00  9.99
ATOM     61  N   THR    14      11.273  26.782  10.808  1.00  9.99
ATOM     62  CA  THR    14      12.638  26.501  11.142  1.00  9.99
ATOM     63  C   THR    14      13.505  27.654  10.608  1.00  9.99
ATOM     64  O   THR    14      14.475  28.011  11.154  1.00  9.99
ATOM     65  CB  THR    14      13.098  25.246  10.357  1.00  9.99
ATOM     66  N   ASN    15      12.858  28.113   9.486  1.00  9.99
ATOM     67  CA  ASN    15      13.254  29.066   8.505  1.00  9.99
ATOM     68  C   ASN    15      12.184  30.127   8.016  1.00  9.99
ATOM     69  O   ASN    15      11.158  29.764   7.459  1.00  9.99
ATOM     70  CB  ASN    15      13.693  28.321   7.199  1.00  9.99
ATOM     71  N   SER    16      12.691  31.330   8.253  1.00  9.99
ATOM     72  CA  SER    16      11.957  32.542   7.832  1.00  9.99
ATOM     73  C   SER    16      12.939  33.509   7.082  1.00  9.99
ATOM     74  O   SER    16      14.149  33.665   7.088  1.00  9.99
ATOM     75  CB  SER    16      11.305  33.290   9.021  1.00  9.99
ATOM     76  N   THR    30      12.121  34.349   6.404  1.00  9.99
ATOM     77  CA  THR    30      12.629  35.524   5.627  1.00  9.99
ATOM     78  C   THR    30      12.123  36.720   6.440  1.00  9.99
ATOM     79  O   THR    30      10.897  37.001   6.454  1.00  9.99
ATOM     80  CB  THR    30      11.970  35.450   4.269  1.00  9.99
ATOM     81  N   GLN    31      12.974  37.513   7.008  1.00  9.99
ATOM     82  CA  GLN    31      12.573  38.582   7.932  1.00  9.99
ATOM     83  C   GLN    31      11.743  39.638   7.253  1.00  9.99
ATOM     84  O   GLN    31      10.734  40.069   7.833  1.00  9.99
ATOM     85  CB  GLN    31      13.859  39.197   8.498  1.00  9.99
TER
END
