
#######################################################
#                                                     #
#                        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 (  134),  selected   27 , name T0295TS239_2_1
# Molecule2: number of CA atoms  275 ( 2193),  selected  275 , name T0295
# PARAMETERS: T0295TS239_2_1.T0295  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     249      H       1           -
LGA    -       -      L       2           -
LGA    -       -      L       3           -
LGA    -       -      K       4           -
LGA    -       -      N       5           -
LGA    -       -      P       6           -
LGA    -       -      G       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      D      10           -
LGA    -       -      K      11           -
LGA    -       -      I      12           -
LGA    -       -      I      13           -
LGA    -       -      Y      14           -
LGA    -       -      A      15           -
LGA    -       -      A      16           -
LGA    -       -      K      17           -
LGA    -       -      I      18           -
LGA    -       -      K      19           -
LGA    -       -      S      20           -
LGA    -       -      S      21           -
LGA    -       -      D      22           -
LGA    -       -      I      23           -
LGA    -       -      V      24           -
LGA    -       -      L      25           -
LGA    -       -      E      26           -
LGA    -       -      I      27           -
LGA    -       -      G      28           -
LGA    -       -      C      29           -
LGA    -       -      G      30           -
LGA    -       -      T      31           -
LGA    -       -      G      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      T      35           -
LGA    -       -      V      36           -
LGA    -       -      K      37           -
LGA    -       -      L      38           -
LGA    -       -      L      39           -
LGA    -       -      P      40           -
LGA    -       -      L      41           -
LGA    -       -      A      42           -
LGA    -       -      K      43           -
LGA    -       -      K      44           -
LGA    -       -      V      45           -
LGA    -       -      I      46           -
LGA    -       -      T      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    -       -      R      53           -
LGA    -       -      M      54           -
LGA    -       -      I      55           -
LGA    -       -      S      56           -
LGA    -       -      E      57           -
LGA    -       -      V      58           -
LGA    -       -      K      59           -
LGA    -       -      K      60           -
LGA    -       -      R      61           -
LGA    -       -      C      62           -
LGA    -       -      L      63           -
LGA    -       -      Y      64           -
LGA    -       -      E      65           -
LGA    -       -      G      66           -
LGA    -       -      Y      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      V      72           -
LGA    -       -      Y      73           -
LGA    -       -      E      74           -
LGA    -       -      G      75           -
LGA    -       -      D      76           -
LGA    -       -      A      77           -
LGA    -       -      I      78           -
LGA    -       -      K      79           -
LGA    -       -      T      80           -
LGA    -       -      V      81           -
LGA    -       -      F      82           -
LGA    -       -      P      83           -
LGA    -       -      K      84           -
LGA    -       -      F      85           -
LGA    -       -      D      86           -
LGA    -       -      V      87           -
LGA    -       -      C      88           -
LGA    -       -      T      89           -
LGA    -       -      A      90           -
LGA    -       -      N      91           -
LGA    -       -      I      92           -
LGA    -       -      P      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      I      96           -
LGA    -       -      S      97           -
LGA    -       -      S      98           -
LGA    -       -      P      99           -
LGA    -       -      L     100           -
LGA    -       -      I     101           -
LGA    -       -      F     102           -
LGA    -       -      K     103           -
LGA    -       -      L     104           -
LGA    -       -      I     105           -
LGA    -       -      S     106           -
LGA    -       -      H     107           -
LGA    -       -      R     108           -
LGA    -       -      P     109           -
LGA    -       -      L     110           -
LGA    -       -      F     111           -
LGA    -       -      K     112           -
LGA    -       -      C     113           -
LGA    -       -      A     114           -
LGA    -       -      V     115           -
LGA    -       -      L     116           -
LGA    -       -      M     117           -
LGA    -       -      F     118           -
LGA    -       -      Q     119           -
LGA    -       -      K     120           -
LGA    -       -      E     121           -
LGA    -       -      F     122           -
LGA    -       -      A     123           -
LGA    -       -      E     124           -
LGA    -       -      R     125           -
LGA    -       -      M     126           -
LGA    -       -      L     127           -
LGA    -       -      A     128           -
LGA    -       -      N     129           -
LGA    -       -      V     130           -
LGA    -       -      G     131           -
LGA    -       -      D     132           -
LGA    -       -      S     133           -
LGA    -       -      N     134           -
LGA    -       -      Y     135           -
LGA    -       -      S     136           -
LGA    -       -      R     137           -
LGA    -       -      L     138           -
LGA    -       -      T     139           -
LGA    -       -      I     140           -
LGA    -       -      N     141           -
LGA    -       -      V     142           -
LGA    -       -      K     143           -
LGA    -       -      L     144           -
LGA    -       -      F     145           -
LGA    -       -      C     146           -
LGA    -       -      K     147           -
LGA    -       -      V     148           -
LGA    -       -      T     149           -
LGA    -       -      K     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      N     153           -
LGA    -       -      V     154           -
LGA    -       -      N     155           -
LGA    -       -      R     156           -
LGA    -       -      S     157           -
LGA    -       -      S     158           -
LGA    -       -      F     159           -
LGA    -       -      N     160           -
LGA    -       -      P     161           -
LGA    -       -      P     162           -
LGA    -       -      P     163           -
LGA    -       -      K     164           -
LGA    -       -      V     165           -
LGA    -       -      D     166           -
LGA    -       -      S     167           -
LGA    -       -      V     168           -
LGA    -       -      I     169           -
LGA    -       -      V     170           -
LGA    -       -      K     171           -
LGA    -       -      L     172           -
LGA    -       -      I     173           -
LGA    -       -      P     174           -
LGA    -       -      K     175           -
LGA    -       -      E     176           -
LGA    -       -      S     177           -
LGA    -       -      S     178           -
LGA    -       -      F     179           -
LGA    -       -      L     180           -
LGA    -       -      T     181           -
LGA    -       -      N     182           -
LGA    -       -      F     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    K     250      L     190          5.739
LGA    R     251      R     191           -
LGA    -       -      I     192           -
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    -       -      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    -       -      T     200           -
LGA    S     252      L     201          4.301
LGA    I     253      H     202          1.127
LGA    N     254      A     203          3.205
LGA    L     255      I     204          2.301
LGA    -       -      F     205           -
LGA    -       -      K     206           -
LGA    D     256      R     207          1.053
LGA    E     257      N     208          0.617
LGA    N     258      A     209          0.237
LGA    D     259      V     210          0.307
LGA    F     260      L     211          0.617
LGA    L     261      N     212          0.614
LGA    K     262      M     213          0.295
LGA    L     263      L     214          0.269
LGA    L     264      E     215          0.551
LGA    L     265      H     216          0.485
LGA    E     266      N     217          0.397
LGA    F     267      Y     218          0.660
LGA    N     268      K     219          0.383
LGA    K     269      N     220          0.579
LGA    K     270      W     221          1.050
LGA    G     271      C     222          0.648
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      N     225           -
LGA    -       -      K     226           -
LGA    -       -      Q     227           -
LGA    I     272      V     228           #
LGA    H     273      P     229          1.727
LGA    F     274      V     230          2.245
LGA    F     275      N     231          2.494
LGA    -       -      F     232           -
LGA    -       -      P     233           -
LGA    -       -      F     234           -
LGA    -       -      K     235           -
LGA    -       -      K     236           -
LGA    -       -      Y     237           -
LGA    -       -      C     238           -
LGA    -       -      L     239           -
LGA    -       -      D     240           -
LGA    -       -      V     241           -
LGA    -       -      L     242           -
LGA    -       -      E     243           -
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    -       -      D     246           -
LGA    -       -      M     247           -
LGA    -       -      C     248           -
LGA    -       -      E     249           -
LGA    -       -      K     250           -
LGA    -       -      R     251           -
LGA    -       -      S     252           -
LGA    -       -      I     253           -
LGA    -       -      N     254           -
LGA    -       -      L     255           -
LGA    -       -      D     256           -
LGA    -       -      E     257           -
LGA    -       -      N     258           -
LGA    -       -      D     259           -
LGA    -       -      F     260           -
LGA    -       -      L     261           -
LGA    -       -      K     262           -
LGA    -       -      L     263           -
LGA    -       -      L     264           -
LGA    -       -      L     265           -
LGA    -       -      E     266           -
LGA    -       -      F     267           -
LGA    -       -      N     268           -
LGA    -       -      K     269           -
LGA    -       -      K     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27  275    5.0     24    1.92     4.17      8.246     1.190

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.032544 * X  +   0.268959 * Y  +  -0.962602 * Z  +  24.917107
  Y_new =   0.940280 * X  +   0.334756 * Y  +   0.061745 * Z  +  21.448235
  Z_new =   0.338844 * X  +  -0.903105 * Y  +  -0.263791 * Z  +  -5.296016 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.854983    1.286609  [ DEG:  -106.2827     73.7173 ]
  Theta =  -0.345688   -2.795905  [ DEG:   -19.8065   -160.1935 ]
  Phi   =   1.605393   -1.536199  [ DEG:    91.9823    -88.0177 ]
 
# 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: T0295TS239_2_1                                
REMARK     2: T0295                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS239_2_1.T0295 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  275   5.0   24   1.92    4.17   8.246
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS239_2_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0295
PARENT 1zq9_A
ATOM   1234  N   GLU   249      18.953  16.409  -1.172  1.00  9.99
ATOM   1235  CA  GLU   249      18.619  15.204  -1.925  1.00  9.99
ATOM   1236  C   GLU   249      18.273  15.528  -3.384  1.00  9.99
ATOM   1237  O   GLU   249      17.798  14.662  -4.126  1.00  9.99
ATOM   1238  CB  GLU   249      17.441  14.464  -1.242  1.00  9.99
ATOM   1239  N   LYS   250      18.502  16.778  -3.784  1.00  9.99
ATOM   1240  CA  LYS   250      18.313  17.175  -5.186  1.00  9.99
ATOM   1241  C   LYS   250      19.583  17.078  -5.992  1.00  9.99
ATOM   1242  O   LYS   250      20.658  17.005  -5.435  1.00  9.99
ATOM   1243  CB  LYS   250      17.776  18.587  -5.290  1.00  9.99
ATOM   1244  N   ARG   251      19.430  17.105  -7.317  1.00  9.99
ATOM   1245  CA  ARG   251      20.532  16.993  -8.246  1.00  9.99
ATOM   1246  C   ARG   251      20.445  18.234  -9.137  1.00  9.99
ATOM   1247  O   ARG   251      19.336  18.651  -9.536  1.00  9.99
ATOM   1248  CB  ARG   251      20.370  15.734  -9.087  1.00  9.99
ATOM   1249  N   SER   252      21.600  18.824  -9.439  1.00  9.99
ATOM   1250  CA  SER   252      21.642  20.038 -10.254  1.00  9.99
ATOM   1251  C   SER   252      20.861  19.909 -11.572  1.00  9.99
ATOM   1252  O   SER   252      20.226  20.843 -12.000  1.00  9.99
ATOM   1253  CB  SER   252      23.073  20.424 -10.527  1.00  9.99
ATOM   1254  N   ILE   253      20.880  18.744 -12.195  1.00  9.99
ATOM   1255  CA  ILE   253      20.200  18.542 -13.476  1.00  9.99
ATOM   1256  C   ILE   253      18.682  18.783 -13.433  1.00  9.99
ATOM   1257  O   ILE   253      18.063  18.941 -14.472  1.00  9.99
ATOM   1258  CB  ILE   253      20.447  17.120 -14.005  1.00  9.99
ATOM   1259  N   ASN   254      18.095  18.723 -12.236  1.00  9.99
ATOM   1260  CA  ASN   254      16.662  18.946 -12.068  1.00  9.99
ATOM   1261  C   ASN   254      16.335  20.275 -11.361  1.00  9.99
ATOM   1262  O   ASN   254      15.188  20.535 -11.009  1.00  9.99
ATOM   1263  CB  ASN   254      16.047  17.766 -11.310  1.00  9.99
ATOM   1264  N   LEU   255      17.342  21.124 -11.169  1.00  9.99
ATOM   1265  CA  LEU   255      17.138  22.327 -10.390  1.00  9.99
ATOM   1266  C   LEU   255      17.080  23.503 -11.370  1.00  9.99
ATOM   1267  O   LEU   255      17.897  23.579 -12.308  1.00  9.99
ATOM   1268  CB  LEU   255      18.276  22.511  -9.367  1.00  9.99
ATOM   1269  N   ASP   256      16.130  24.408 -11.139  1.00  9.99
ATOM   1270  CA  ASP   256      15.935  25.588 -11.972  1.00  9.99
ATOM   1271  C   ASP   256      16.591  26.823 -11.358  1.00  9.99
ATOM   1272  O   ASP   256      17.273  26.715 -10.333  1.00  9.99
ATOM   1273  CB  ASP   256      14.435  25.810 -12.252  1.00  9.99
ATOM   1274  N   GLU   257      16.420  27.988 -11.986  1.00  9.99
ATOM   1275  CA  GLU   257      17.069  29.205 -11.495  1.00  9.99
ATOM   1276  C   GLU   257      16.569  29.619 -10.095  1.00  9.99
ATOM   1277  O   GLU   257      17.372  29.984  -9.253  1.00  9.99
ATOM   1278  CB  GLU   257      16.926  30.384 -12.494  1.00  9.99
ATOM   1279  N   ASN   258      15.262  29.572  -9.872  1.00  9.99
ATOM   1280  CA  ASN   258      14.683  29.851  -8.547  1.00  9.99
ATOM   1281  C   ASN   258      15.427  29.028  -7.473  1.00  9.99
ATOM   1282  O   ASN   258      15.843  29.565  -6.442  1.00  9.99
ATOM   1283  CB  ASN   258      13.192  29.495  -8.521  1.00  9.99
ATOM   1284  N   ASP   259      15.591  27.726  -7.738  1.00  9.99
ATOM   1285  CA  ASP   259      16.278  26.794  -6.833  1.00  9.99
ATOM   1286  C   ASP   259      17.710  27.194  -6.521  1.00  9.99
ATOM   1287  O   ASP   259      18.112  27.169  -5.373  1.00  9.99
ATOM   1288  CB  ASP   259      16.300  25.369  -7.413  1.00  9.99
ATOM   1289  N   PHE   260      18.495  27.512  -7.552  1.00  9.99
ATOM   1290  CA  PHE   260      19.875  27.868  -7.315  1.00  9.99
ATOM   1291  C   PHE   260      20.006  29.224  -6.629  1.00  9.99
ATOM   1292  O   PHE   260      20.896  29.420  -5.796  1.00  9.99
ATOM   1293  CB  PHE   260      20.673  27.802  -8.613  1.00  9.99
ATOM   1294  N   LEU   261      19.100  30.150  -6.934  1.00  9.99
ATOM   1295  CA  LEU   261      19.120  31.438  -6.215  1.00  9.99
ATOM   1296  C   LEU   261      18.886  31.188  -4.719  1.00  9.99
ATOM   1297  O   LEU   261      19.611  31.717  -3.873  1.00  9.99
ATOM   1298  CB  LEU   261      18.091  32.448  -6.778  1.00  9.99
ATOM   1299  N   LYS   262      17.869  30.393  -4.398  1.00  9.99
ATOM   1300  CA  LYS   262      17.598  30.029  -2.991  1.00  9.99
ATOM   1301  C   LYS   262      18.822  29.390  -2.300  1.00  9.99
ATOM   1302  O   LYS   262      19.189  29.753  -1.159  1.00  9.99
ATOM   1303  CB  LYS   262      16.392  29.093  -2.887  1.00  9.99
ATOM   1304  N   LEU   263      19.422  28.418  -2.984  1.00  9.99
ATOM   1305  CA  LEU   263      20.608  27.741  -2.490  1.00  9.99
ATOM   1306  C   LEU   263      21.763  28.704  -2.268  1.00  9.99
ATOM   1307  O   LEU   263      22.433  28.628  -1.240  1.00  9.99
ATOM   1308  CB  LEU   263      21.045  26.629  -3.446  1.00  9.99
ATOM   1309  N   LEU   264      22.011  29.578  -3.239  1.00  9.99
ATOM   1310  CA  LEU   264      23.111  30.539  -3.137  1.00  9.99
ATOM   1311  C   LEU   264      22.874  31.448  -1.935  1.00  9.99
ATOM   1312  O   LEU   264      23.766  31.644  -1.102  1.00  9.99
ATOM   1313  CB  LEU   264      23.248  31.362  -4.414  1.00  9.99
ATOM   1314  N   LEU   265      21.661  32.000  -1.865  1.00  9.99
ATOM   1315  CA  LEU   265      21.241  32.847  -0.725  1.00  9.99
ATOM   1316  C   LEU   265      21.509  32.150   0.600  1.00  9.99
ATOM   1317  O   LEU   265      22.055  32.751   1.540  1.00  9.99
ATOM   1318  CB  LEU   265      19.747  33.233  -0.849  1.00  9.99
ATOM   1319  N   GLU   266      21.161  30.870   0.666  1.00  9.99
ATOM   1320  CA  GLU   266      21.292  30.101   1.888  1.00  9.99
ATOM   1321  C   GLU   266      22.728  29.803   2.294  1.00  9.99
ATOM   1322  O   GLU   266      23.022  29.670   3.481  1.00  9.99
ATOM   1323  CB  GLU   266      20.498  28.794   1.719  1.00  9.99
ATOM   1324  N   PHE   267      23.621  29.639   1.309  1.00  9.99
ATOM   1325  CA  PHE   267      25.049  29.514   1.607  1.00  9.99
ATOM   1326  C   PHE   267      25.597  30.846   2.110  1.00  9.99
ATOM   1327  O   PHE   267      26.306  30.871   3.105  1.00  9.99
ATOM   1328  CB  PHE   267      25.846  29.052   0.373  1.00  9.99
ATOM   1329  N   ASN   268      25.251  31.936   1.420  1.00  9.99
ATOM   1330  CA  ASN   268      25.744  33.287   1.698  1.00  9.99
ATOM   1331  C   ASN   268      25.351  33.779   3.103  1.00  9.99
ATOM   1332  O   ASN   268      26.156  34.395   3.807  1.00  9.99
ATOM   1333  CB  ASN   268      25.244  34.295   0.639  1.00  9.99
ATOM   1334  N   LYS   269      24.113  33.509   3.488  1.00  9.99
ATOM   1335  CA  LYS   269      23.595  33.842   4.808  1.00  9.99
ATOM   1336  C   LYS   269      24.408  33.183   5.934  1.00  9.99
ATOM   1337  O   LYS   269      24.373  33.654   7.068  1.00  9.99
ATOM   1338  CB  LYS   269      22.152  33.424   4.911  1.00  9.99
ATOM   1339  N   LYS   270      25.108  32.087   5.624  1.00  9.99
ATOM   1340  CA  LYS   270      25.894  31.379   6.610  1.00  9.99
ATOM   1341  C   LYS   270      27.402  31.597   6.452  1.00  9.99
ATOM   1342  O   LYS   270      28.186  30.888   7.073  1.00  9.99
ATOM   1343  CB  LYS   270      25.586  29.892   6.557  1.00  9.99
ATOM   1344  N   GLY   271      27.793  32.560   5.624  1.00  9.99
ATOM   1345  CA  GLY   271      29.211  32.902   5.470  1.00  9.99
ATOM   1346  C   GLY   271      29.972  32.149   4.400  1.00  9.99
ATOM   1347  O   GLY   271      31.182  32.333   4.258  1.00  9.99
ATOM   1348  N   ILE   272      29.273  31.310   3.644  1.00  9.99
ATOM   1349  CA  ILE   272      29.911  30.596   2.509  1.00  9.99
ATOM   1350  C   ILE   272      29.700  31.356   1.214  1.00  9.99
ATOM   1351  O   ILE   272      28.560  31.524   0.736  1.00  9.99
ATOM   1352  CB  ILE   272      29.487  29.109   2.425  1.00  9.99
ATOM   1353  N   HIS   273      30.817  31.854   0.692  1.00  9.99
ATOM   1354  CA  HIS   273      30.861  32.628  -0.533  1.00  9.99
ATOM   1355  C   HIS   273      31.748  31.930  -1.575  1.00  9.99
ATOM   1356  O   HIS   273      32.914  31.610  -1.275  1.00  9.99
ATOM   1357  CB  HIS   273      31.367  34.044  -0.229  1.00  9.99
ATOM   1358  N   PHE   274      31.201  31.719  -2.780  1.00  9.99
ATOM   1359  CA  PHE   274      31.874  30.947  -3.852  1.00  9.99
ATOM   1360  C   PHE   274      32.745  31.814  -4.756  1.00  9.99
ATOM   1361  O   PHE   274      32.435  32.972  -5.014  1.00  9.99
ATOM   1362  CB  PHE   274      30.839  30.206  -4.718  1.00  9.99
ATOM   1363  N   PHE   275      33.840  31.241  -5.249  1.00  9.99
ATOM   1364  CA  PHE   275      34.720  31.916  -6.218  1.00  9.99
ATOM   1365  C   PHE   275      34.672  31.180  -7.559  1.00  9.99
ATOM   1366  O   PHE   275      34.054  30.102  -7.632  1.00  9.99
ATOM   1367  CB  PHE   275      36.150  31.907  -5.700  1.00  9.99
TER
END
