
#######################################################
#                                                     #
#                        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   21 (  161),  selected   21 , name T0298TS268_4_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_4_2-D1.T0298_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    V     316      Q       3           -
LGA    R     317      P       4           -
LGA    K     318      L       5           -
LGA    G     319      N       6           -
LGA    A     320      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    -       -      T      13           -
LGA    -       -      G      14           -
LGA    -       -      S      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    A     321      A      19           #
LGA    -       -      L      20           -
LGA    -       -      V      21           -
LGA    L     322      G      22          3.311
LGA    N     323      L      23          2.967
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    A     324      R      27          2.062
LGA    V     325      D      28          2.630
LGA    L     326      F      29          3.021
LGA    L     327      P      30          4.320
LGA    -       -      L      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      H      35           -
LGA    -       -      L      36           -
LGA    -       -      L      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      A      40           -
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      Q      45           -
LGA    -       -      R      46           -
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      V      56           -
LGA    -       -      G      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    -       -      S      61           -
LGA    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    G     328      G      68          4.872
LGA    E     329      L      69          2.893
LGA    L     330      A      70          3.807
LGA    L     331      F      71          2.888
LGA    -       -      F      72           -
LGA    -       -      A      73           -
LGA    -       -      A      74           -
LGA    -       -      A      75           -
LGA    -       -      A      76           -
LGA    -       -      E      77           -
LGA    -       -      V      78           -
LGA    -       -      S      79           -
LGA    -       -      R      80           -
LGA    -       -      A      81           -
LGA    -       -      H      82           -
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      S      97           -
LGA    -       -      G      98           -
LGA    -       -      A      99           -
LGA    -       -      L     100           -
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    -       -      A     105           -
LGA    -       -      P     106           -
LGA    -       -      P     107           -
LGA    -       -      V     108           -
LGA    -       -      M     109           -
LGA    -       -      V     110           -
LGA    -       -      S     111           -
LGA    -       -      V     112           -
LGA    -       -      N     113           -
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    -       -      R     116           -
LGA    -       -      L     117           -
LGA    -       -      A     118           -
LGA    -       -      S     119           -
LGA    -       -      Q     120           -
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      L     125           -
LGA    -       -      L     126           -
LGA    -       -      S     127           -
LGA    -       -      S     128           -
LGA    -       -      P     129           -
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      L     322           -
LGA    -       -      N     323           -
LGA    I     332      A     324          5.220
LGA    -       -      V     325           -
LGA    -       -      L     326           -
LGA    -       -      L     327           -
LGA    K     333      G     328          2.818
LGA    -       -      E     329           -
LGA    -       -      L     330           -
LGA    -       -      L     331           -
LGA    H     334      I     332          3.407
LGA    Y     335      K     333          1.458
LGA    L     336      H     334          3.271
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  148    5.0     15    3.40     6.67      6.121     0.429

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.193809 * X  +  -0.976011 * Y  +  -0.099200 * Z  + -35.264153
  Y_new =  -0.609342 * X  +  -0.040514 * Y  +  -0.791872 * Z  +  93.688698
  Z_new =   0.768857 * X  +   0.213918 * Y  +  -0.602576 * Z  + -54.052536 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.800465   -0.341128  [ DEG:   160.4548    -19.5452 ]
  Theta =  -0.877052   -2.264541  [ DEG:   -50.2514   -129.7486 ]
  Phi   =  -1.262852    1.878741  [ DEG:   -72.3561    107.6439 ]
 
# 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: T0298TS268_4_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_4_2-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  148   5.0   15   3.40    6.67   6.121
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4d_B
ATOM   2298  N   VAL   316     -32.590  53.462  -2.344  1.00  0.00
ATOM   2299  CA  VAL   316     -31.679  53.999  -1.373  1.00  0.00
ATOM   2300  C   VAL   316     -30.765  52.918  -0.895  1.00  0.00
ATOM   2301  O   VAL   316     -30.771  52.523   0.271  1.00  0.00
ATOM   2302  CB  VAL   316     -32.426  54.578  -0.158  1.00  0.00
ATOM   2303  CG1 VAL   316     -31.443  55.168   0.841  1.00  0.00
ATOM   2304  CG2 VAL   316     -33.383  55.677  -0.595  1.00  0.00
ATOM   2305  N   ARG   317     -29.890  52.469  -1.808  1.00  0.00
ATOM   2306  CA  ARG   317     -28.940  51.432  -1.561  1.00  0.00
ATOM   2307  C   ARG   317     -27.956  51.572  -2.666  1.00  0.00
ATOM   2308  O   ARG   317     -27.149  52.499  -2.691  1.00  0.00
ATOM   2309  CB  ARG   317     -29.622  50.063  -1.583  1.00  0.00
ATOM   2310  CG  ARG   317     -30.674  49.877  -0.501  1.00  0.00
ATOM   2311  CD  ARG   317     -30.037  49.723   0.870  1.00  0.00
ATOM   2312  NE  ARG   317     -31.033  49.494   1.914  1.00  0.00
ATOM   2313  CZ  ARG   317     -30.746  49.367   3.206  1.00  0.00
ATOM   2314  NH1 ARG   317     -31.717  49.161   4.083  1.00  0.00
ATOM   2315  NH2 ARG   317     -29.487  49.448   3.615  1.00  0.00
ATOM   2316  N   LYS   318     -28.022  50.633  -3.622  1.00  0.00
ATOM   2317  CA  LYS   318     -27.171  50.658  -4.770  1.00  0.00
ATOM   2318  C   LYS   318     -27.447  51.956  -5.458  1.00  0.00
ATOM   2319  O   LYS   318     -26.535  52.608  -5.966  1.00  0.00
ATOM   2320  CB  LYS   318     -27.484  49.479  -5.694  1.00  0.00
ATOM   2321  CG  LYS   318     -26.592  49.399  -6.923  1.00  0.00
ATOM   2322  CD  LYS   318     -26.904  48.165  -7.752  1.00  0.00
ATOM   2323  CE  LYS   318     -26.032  48.101  -8.997  1.00  0.00
ATOM   2324  NZ  LYS   318     -26.338  46.904  -9.827  1.00  0.00
ATOM   2325  N   GLY   319     -28.727  52.374  -5.468  1.00  0.00
ATOM   2326  CA  GLY   319     -29.093  53.576  -6.155  1.00  0.00
ATOM   2327  C   GLY   319     -28.298  54.709  -5.601  1.00  0.00
ATOM   2328  O   GLY   319     -28.381  55.032  -4.417  1.00  0.00
ATOM   2329  N   ALA   320     -27.539  55.373  -6.493  1.00  0.00
ATOM   2330  CA  ALA   320     -26.693  56.460  -6.103  1.00  0.00
ATOM   2331  C   ALA   320     -27.552  57.618  -5.733  1.00  0.00
ATOM   2332  O   ALA   320     -28.605  57.849  -6.324  1.00  0.00
ATOM   2333  CB  ALA   320     -25.774  56.854  -7.249  1.00  0.00
ATOM   2334  N   ALA   321     -27.113  58.369  -4.706  1.00  0.00
ATOM   2335  CA  ALA   321     -27.824  59.533  -4.281  1.00  0.00
ATOM   2336  C   ALA   321     -26.978  60.178  -3.240  1.00  0.00
ATOM   2337  O   ALA   321     -26.054  59.564  -2.710  1.00  0.00
ATOM   2338  CB  ALA   321     -29.179  59.147  -3.708  1.00  0.00
ATOM   2339  N   LEU   322     -27.256  61.457  -2.932  1.00  0.00
ATOM   2340  CA  LEU   322     -26.515  62.109  -1.898  1.00  0.00
ATOM   2341  C   LEU   322     -27.445  62.269  -0.748  1.00  0.00
ATOM   2342  O   LEU   322     -28.658  62.139  -0.901  1.00  0.00
ATOM   2343  CB  LEU   322     -26.016  63.474  -2.376  1.00  0.00
ATOM   2344  CG  LEU   322     -25.135  63.474  -3.627  1.00  0.00
ATOM   2345  CD1 LEU   322     -24.794  64.896  -4.044  1.00  0.00
ATOM   2346  CD2 LEU   322     -23.834  62.728  -3.369  1.00  0.00
ATOM   2347  N   ASN   323     -26.895  62.537   0.447  1.00  0.00
ATOM   2348  CA  ASN   323     -27.750  62.684   1.582  1.00  0.00
ATOM   2349  C   ASN   323     -28.673  63.815   1.282  1.00  0.00
ATOM   2350  O   ASN   323     -29.877  63.720   1.505  1.00  0.00
ATOM   2351  CB  ASN   323     -26.929  62.987   2.837  1.00  0.00
ATOM   2352  CG  ASN   323     -26.163  61.778   3.338  1.00  0.00
ATOM   2353  OD1 ASN   323     -26.490  60.641   3.000  1.00  0.00
ATOM   2354  ND2 ASN   323     -25.140  62.022   4.149  1.00  0.00
ATOM   2355  N   ALA   324     -28.124  64.923   0.750  1.00  0.00
ATOM   2356  CA  ALA   324     -28.969  66.017   0.382  1.00  0.00
ATOM   2357  C   ALA   324     -29.602  65.637  -0.915  1.00  0.00
ATOM   2358  O   ALA   324     -29.062  64.817  -1.655  1.00  0.00
ATOM   2359  CB  ALA   324     -28.152  67.290   0.228  1.00  0.00
ATOM   2360  N   VAL   325     -30.780  66.209  -1.224  1.00  0.00
ATOM   2361  CA  VAL   325     -31.371  65.859  -2.479  1.00  0.00
ATOM   2362  C   VAL   325     -30.483  66.436  -3.527  1.00  0.00
ATOM   2363  O   VAL   325     -30.050  67.582  -3.425  1.00  0.00
ATOM   2364  CB  VAL   325     -32.795  66.431  -2.612  1.00  0.00
ATOM   2365  CG1 VAL   325     -33.356  66.143  -3.996  1.00  0.00
ATOM   2366  CG2 VAL   325     -33.718  65.807  -1.579  1.00  0.00
ATOM   2367  N   LEU   326     -30.163  65.643  -4.565  1.00  0.00
ATOM   2368  CA  LEU   326     -29.289  66.174  -5.561  1.00  0.00
ATOM   2369  C   LEU   326     -30.138  66.628  -6.694  1.00  0.00
ATOM   2370  O   LEU   326     -30.959  65.875  -7.215  1.00  0.00
ATOM   2371  CB  LEU   326     -28.307  65.102  -6.037  1.00  0.00
ATOM   2372  CG  LEU   326     -27.329  65.519  -7.138  1.00  0.00
ATOM   2373  CD1 LEU   326     -26.352  66.564  -6.621  1.00  0.00
ATOM   2374  CD2 LEU   326     -26.528  64.322  -7.627  1.00  0.00
ATOM   2375  N   LEU   327     -29.977  67.901  -7.087  1.00  0.00
ATOM   2376  CA  LEU   327     -30.743  68.381  -8.191  1.00  0.00
ATOM   2377  C   LEU   327     -29.763  68.819  -9.223  1.00  0.00
ATOM   2378  O   LEU   327     -28.645  69.217  -8.905  1.00  0.00
ATOM   2379  CB  LEU   327     -31.627  69.553  -7.760  1.00  0.00
ATOM   2380  CG  LEU   327     -32.642  69.264  -6.651  1.00  0.00
ATOM   2381  CD1 LEU   327     -33.363  70.538  -6.239  1.00  0.00
ATOM   2382  CD2 LEU   327     -33.682  68.260  -7.121  1.00  0.00
ATOM   2383  N   GLY   328     -30.152  68.717 -10.505  1.00  0.00
ATOM   2384  CA  GLY   328     -29.289  69.178 -11.544  1.00  0.00
ATOM   2385  C   GLY   328     -28.058  68.335 -11.568  1.00  0.00
ATOM   2386  O   GLY   328     -28.115  67.110 -11.482  1.00  0.00
ATOM   2387  N   GLU   329     -26.899  69.008 -11.694  1.00  0.00
ATOM   2388  CA  GLU   329     -25.629  68.360 -11.811  1.00  0.00
ATOM   2389  C   GLU   329     -24.980  68.280 -10.468  1.00  0.00
ATOM   2390  O   GLU   329     -25.533  68.709  -9.455  1.00  0.00
ATOM   2391  CB  GLU   329     -24.713  69.143 -12.756  1.00  0.00
ATOM   2392  CG  GLU   329     -25.226  69.231 -14.184  1.00  0.00
ATOM   2393  CD  GLU   329     -24.261  69.949 -15.106  1.00  0.00
ATOM   2394  OE1 GLU   329     -23.249  70.484 -14.606  1.00  0.00
ATOM   2395  OE2 GLU   329     -24.517  69.978 -16.328  1.00  0.00
ATOM   2396  N   LEU   330     -23.772  67.684 -10.451  1.00  0.00
ATOM   2397  CA  LEU   330     -23.003  67.495  -9.259  1.00  0.00
ATOM   2398  C   LEU   330     -22.691  68.848  -8.712  1.00  0.00
ATOM   2399  O   LEU   330     -22.730  69.060  -7.501  1.00  0.00
ATOM   2400  CB  LEU   330     -21.707  66.744  -9.571  1.00  0.00
ATOM   2401  CG  LEU   330     -21.854  65.274  -9.967  1.00  0.00
ATOM   2402  CD1 LEU   330     -20.519  64.704 -10.422  1.00  0.00
ATOM   2403  CD2 LEU   330     -22.347  64.447  -8.790  1.00  0.00
ATOM   2404  N   LEU   331     -22.389  69.813  -9.600  1.00  0.00
ATOM   2405  CA  LEU   331     -22.061  71.118  -9.118  1.00  0.00
ATOM   2406  C   LEU   331     -23.257  71.612  -8.377  1.00  0.00
ATOM   2407  O   LEU   331     -24.396  71.329  -8.747  1.00  0.00
ATOM   2408  CB  LEU   331     -21.730  72.053 -10.283  1.00  0.00
ATOM   2409  CG  LEU   331     -20.455  71.736 -11.066  1.00  0.00
ATOM   2410  CD1 LEU   331     -20.319  72.657 -12.269  1.00  0.00
ATOM   2411  CD2 LEU   331     -19.226  71.917 -10.187  1.00  0.00
ATOM   2412  N   ILE   332     -23.015  72.359  -7.285  1.00  0.00
ATOM   2413  CA  ILE   332     -24.091  72.810  -6.459  1.00  0.00
ATOM   2414  C   ILE   332     -24.896  73.797  -7.232  1.00  0.00
ATOM   2415  O   ILE   332     -24.364  74.756  -7.789  1.00  0.00
ATOM   2416  CB  ILE   332     -23.573  73.482  -5.174  1.00  0.00
ATOM   2417  CG1 ILE   332     -22.809  72.473  -4.315  1.00  0.00
ATOM   2418  CG2 ILE   332     -24.732  74.032  -4.356  1.00  0.00
ATOM   2419  CD1 ILE   332     -22.066  73.098  -3.154  1.00  0.00
ATOM   2420  N   LYS   333     -26.217  73.557  -7.294  1.00  0.00
ATOM   2421  CA  LYS   333     -27.112  74.460  -7.944  1.00  0.00
ATOM   2422  C   LYS   333     -27.883  75.098  -6.844  1.00  0.00
ATOM   2423  O   LYS   333     -28.059  74.505  -5.782  1.00  0.00
ATOM   2424  CB  LYS   333     -28.036  73.703  -8.900  1.00  0.00
ATOM   2425  CG  LYS   333     -27.320  73.061 -10.078  1.00  0.00
ATOM   2426  CD  LYS   333     -28.299  72.356 -11.001  1.00  0.00
ATOM   2427  CE  LYS   333     -27.584  71.721 -12.182  1.00  0.00
ATOM   2428  NZ  LYS   333     -28.534  71.045 -13.109  1.00  0.00
ATOM   2429  N   HIS   334     -28.350  76.340  -7.055  1.00  0.00
ATOM   2430  CA  HIS   334     -29.057  76.971  -5.985  1.00  0.00
ATOM   2431  C   HIS   334     -30.522  76.831  -6.204  1.00  0.00
ATOM   2432  O   HIS   334     -31.017  76.859  -7.329  1.00  0.00
ATOM   2433  CB  HIS   334     -28.707  78.459  -5.915  1.00  0.00
ATOM   2434  CG  HIS   334     -27.276  78.727  -5.568  1.00  0.00
ATOM   2435  ND1 HIS   334     -26.807  78.703  -4.271  1.00  0.00
ATOM   2436  CD2 HIS   334     -26.070  79.050  -6.315  1.00  0.00
ATOM   2437  CE1 HIS   334     -25.491  78.980  -4.277  1.00  0.00
ATOM   2438  NE2 HIS   334     -25.041  79.190  -5.500  1.00  0.00
ATOM   2439  N   TYR   335     -31.239  76.640  -5.083  1.00  0.00
ATOM   2440  CA  TYR   335     -32.665  76.563  -5.063  1.00  0.00
ATOM   2441  C   TYR   335     -33.081  77.636  -4.117  1.00  0.00
ATOM   2442  O   TYR   335     -32.449  77.835  -3.082  1.00  0.00
ATOM   2443  CB  TYR   335     -33.120  75.183  -4.583  1.00  0.00
ATOM   2444  CG  TYR   335     -34.622  75.033  -4.486  1.00  0.00
ATOM   2445  CD1 TYR   335     -35.389  74.819  -5.624  1.00  0.00
ATOM   2446  CD2 TYR   335     -35.266  75.105  -3.258  1.00  0.00
ATOM   2447  CE1 TYR   335     -36.763  74.680  -5.546  1.00  0.00
ATOM   2448  CE2 TYR   335     -36.638  74.968  -3.161  1.00  0.00
ATOM   2449  CZ  TYR   335     -37.385  74.754  -4.319  1.00  0.00
ATOM   2450  OH  TYR   335     -38.752  74.616  -4.238  1.00  0.00
ATOM   2451  N   LEU   336     -34.143  78.384  -4.460  1.00  0.00
ATOM   2452  CA  LEU   336     -34.534  79.461  -3.599  1.00  0.00
ATOM   2453  C   LEU   336     -34.884  78.826  -2.264  1.00  0.00
ATOM   2454  O   LEU   336     -34.147  79.081  -1.270  1.00  0.00
ATOM   2455  CB  LEU   336     -35.742  80.199  -4.180  1.00  0.00
ATOM   2456  CG  LEU   336     -35.560  80.807  -5.573  1.00  0.00
ATOM   2457  CD1 LEU   336     -36.867  81.400  -6.075  1.00  0.00
ATOM   2458  CD2 LEU   336     -34.516  81.915  -5.543  1.00  0.00
TER
END
