
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_5_2-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      Q       3           -
LGA    R     317      P       4           -
LGA    K     318      L       5           -
LGA    G     319      N       6           -
LGA    -       -      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      19           -
LGA    -       -      L      20           -
LGA    -       -      V      21           -
LGA    -       -      G      22           -
LGA    -       -      L      23           -
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
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    A     320      F      62           #
LGA    A     321      D      63          5.139
LGA    L     322      F      64          1.106
LGA    N     323      S      65          2.483
LGA    A     324      S      66          2.768
LGA    -       -      V      67           -
LGA    V     325      G      68          2.100
LGA    L     326      L      69          2.783
LGA    L     327      A      70          1.513
LGA    -       -      F      71           -
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    G     328      V      93          4.555
LGA    E     329      I      94          1.157
LGA    L     330      D      95          2.796
LGA    L     331      L      96          2.091
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    I     332      A     321          3.181
LGA    -       -      L     322           -
LGA    K     333      N     323          2.493
LGA    H     334      A     324          3.531
LGA    -       -      V     325           -
LGA    -       -      L     326           -
LGA    Y     335      L     327          1.952
LGA    L     336      G     328          2.812
LGA    -       -      E     329           -
LGA    -       -      L     330           -
LGA    -       -      L     331           -
LGA    -       -      I     332           -
LGA    -       -      K     333           -
LGA    -       -      H     334           -
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  148    5.0     16    2.86    12.50      7.208     0.541

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.368777 * X  +  -0.380297 * Y  +   0.848161 * Z  +  38.228638
  Y_new =  -0.912061 * X  +   0.027966 * Y  +   0.409100 * Z  +  69.801239
  Z_new =  -0.179299 * X  +  -0.924441 * Y  +  -0.336541 * Z  +  15.352623 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.919931    1.221662  [ DEG:  -110.0039     69.9961 ]
  Theta =   0.180274    2.961318  [ DEG:    10.3290    169.6710 ]
  Phi   =  -1.186560    1.955033  [ DEG:   -67.9849    112.0151 ]
 
# 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_5_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_5_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   16   2.86   12.50   7.208
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4b_A
ATOM   2298  N   VAL   316     -20.619  70.380 -32.313  1.00  0.00
ATOM   2299  CA  VAL   316     -21.056  69.027 -32.093  1.00  0.00
ATOM   2300  C   VAL   316     -19.930  68.056 -32.282  1.00  0.00
ATOM   2301  O   VAL   316     -19.760  67.137 -31.482  1.00  0.00
ATOM   2302  CB  VAL   316     -22.179  68.631 -33.070  1.00  0.00
ATOM   2303  CG1 VAL   316     -22.485  67.146 -32.954  1.00  0.00
ATOM   2304  CG2 VAL   316     -23.450  69.410 -32.765  1.00  0.00
ATOM   2305  N   ARG   317     -19.117  68.221 -33.342  1.00  0.00
ATOM   2306  CA  ARG   317     -18.066  67.275 -33.571  1.00  0.00
ATOM   2307  C   ARG   317     -16.808  67.864 -33.034  1.00  0.00
ATOM   2308  O   ARG   317     -16.625  69.079 -33.022  1.00  0.00
ATOM   2309  CB  ARG   317     -17.915  66.993 -35.067  1.00  0.00
ATOM   2310  CG  ARG   317     -19.112  66.295 -35.692  1.00  0.00
ATOM   2311  CD  ARG   317     -18.878  66.010 -37.166  1.00  0.00
ATOM   2312  NE  ARG   317     -20.069  65.467 -37.814  1.00  0.00
ATOM   2313  CZ  ARG   317     -20.128  65.118 -39.095  1.00  0.00
ATOM   2314  NH1 ARG   317     -21.256  64.633 -39.599  1.00  0.00
ATOM   2315  NH2 ARG   317     -19.060  65.254 -39.870  1.00  0.00
ATOM   2316  N   LYS   318     -15.930  67.027 -32.472  1.00  0.00
ATOM   2317  CA  LYS   318     -14.670  67.462 -31.936  1.00  0.00
ATOM   2318  C   LYS   318     -14.883  68.526 -30.905  1.00  0.00
ATOM   2319  O   LYS   318     -13.944  69.203 -30.488  1.00  0.00
ATOM   2320  CB  LYS   318     -13.783  68.030 -33.045  1.00  0.00
ATOM   2321  CG  LYS   318     -13.391  67.016 -34.107  1.00  0.00
ATOM   2322  CD  LYS   318     -12.505  67.645 -35.170  1.00  0.00
ATOM   2323  CE  LYS   318     -12.214  66.666 -36.296  1.00  0.00
ATOM   2324  NZ  LYS   318     -11.387  67.284 -37.370  1.00  0.00
ATOM   2325  N   GLY   319     -16.132  68.656 -30.433  1.00  0.00
ATOM   2326  CA  GLY   319     -16.518  69.573 -29.410  1.00  0.00
ATOM   2327  C   GLY   319     -17.702  68.903 -28.804  1.00  0.00
ATOM   2328  O   GLY   319     -18.400  68.154 -29.486  1.00  0.00
ATOM   2329  N   ALA   320     -17.987  69.141 -27.516  1.00  0.00
ATOM   2330  CA  ALA   320     -19.106  68.408 -27.012  1.00  0.00
ATOM   2331  C   ALA   320     -19.821  69.228 -25.999  1.00  0.00
ATOM   2332  O   ALA   320     -19.278  70.181 -25.443  1.00  0.00
ATOM   2333  CB  ALA   320     -18.642  67.113 -26.363  1.00  0.00
ATOM   2334  N   ALA   321     -21.096  68.869 -25.764  1.00  0.00
ATOM   2335  CA  ALA   321     -21.889  69.514 -24.766  1.00  0.00
ATOM   2336  C   ALA   321     -22.460  68.409 -23.942  1.00  0.00
ATOM   2337  O   ALA   321     -22.656  67.298 -24.432  1.00  0.00
ATOM   2338  CB  ALA   321     -22.990  70.339 -25.415  1.00  0.00
ATOM   2339  N   LEU   322     -22.720  68.672 -22.647  1.00  0.00
ATOM   2340  CA  LEU   322     -23.253  67.628 -21.825  1.00  0.00
ATOM   2341  C   LEU   322     -24.732  67.827 -21.752  1.00  0.00
ATOM   2342  O   LEU   322     -25.211  68.909 -21.422  1.00  0.00
ATOM   2343  CB  LEU   322     -22.648  67.688 -20.421  1.00  0.00
ATOM   2344  CG  LEU   322     -21.130  67.514 -20.330  1.00  0.00
ATOM   2345  CD1 LEU   322     -20.656  67.671 -18.893  1.00  0.00
ATOM   2346  CD2 LEU   322     -20.717  66.133 -20.818  1.00  0.00
ATOM   2347  N   ASN   323     -25.495  66.765 -22.072  1.00  0.00
ATOM   2348  CA  ASN   323     -26.926  66.851 -22.070  1.00  0.00
ATOM   2349  C   ASN   323     -27.392  67.119 -20.675  1.00  0.00
ATOM   2350  O   ASN   323     -28.239  67.982 -20.447  1.00  0.00
ATOM   2351  CB  ASN   323     -27.543  65.542 -22.567  1.00  0.00
ATOM   2352  CG  ASN   323     -27.374  65.349 -24.061  1.00  0.00
ATOM   2353  OD1 ASN   323     -27.137  66.305 -24.797  1.00  0.00
ATOM   2354  ND2 ASN   323     -27.497  64.105 -24.513  1.00  0.00
ATOM   2355  N   ALA   324     -26.817  66.397 -19.695  1.00  0.00
ATOM   2356  CA  ALA   324     -27.227  66.513 -18.326  1.00  0.00
ATOM   2357  C   ALA   324     -26.782  67.829 -17.784  1.00  0.00
ATOM   2358  O   ALA   324     -25.966  68.528 -18.381  1.00  0.00
ATOM   2359  CB  ALA   324     -26.613  65.400 -17.492  1.00  0.00
ATOM   2360  N   VAL   325     -27.366  68.199 -16.630  1.00  0.00
ATOM   2361  CA  VAL   325     -27.075  69.429 -15.963  1.00  0.00
ATOM   2362  C   VAL   325     -25.706  69.340 -15.378  1.00  0.00
ATOM   2363  O   VAL   325     -25.234  68.261 -15.024  1.00  0.00
ATOM   2364  CB  VAL   325     -28.084  69.711 -14.834  1.00  0.00
ATOM   2365  CG1 VAL   325     -27.642  70.915 -14.016  1.00  0.00
ATOM   2366  CG2 VAL   325     -29.461  70.000 -15.410  1.00  0.00
ATOM   2367  N   LEU   326     -25.026  70.499 -15.288  1.00  0.00
ATOM   2368  CA  LEU   326     -23.726  70.518 -14.690  1.00  0.00
ATOM   2369  C   LEU   326     -23.939  70.196 -13.259  1.00  0.00
ATOM   2370  O   LEU   326     -24.919  70.629 -12.653  1.00  0.00
ATOM   2371  CB  LEU   326     -23.085  71.898 -14.848  1.00  0.00
ATOM   2372  CG  LEU   326     -22.765  72.337 -16.279  1.00  0.00
ATOM   2373  CD1 LEU   326     -22.242  73.765 -16.299  1.00  0.00
ATOM   2374  CD2 LEU   326     -21.707  71.434 -16.895  1.00  0.00
ATOM   2375  N   LEU   327     -23.031  69.400 -12.674  1.00  0.00
ATOM   2376  CA  LEU   327     -23.265  69.047 -11.315  1.00  0.00
ATOM   2377  C   LEU   327     -22.543  70.044 -10.481  1.00  0.00
ATOM   2378  O   LEU   327     -21.345  69.898 -10.241  1.00  0.00
ATOM   2379  CB  LEU   327     -22.740  67.638 -11.029  1.00  0.00
ATOM   2380  CG  LEU   327     -23.371  66.504 -11.838  1.00  0.00
ATOM   2381  CD1 LEU   327     -22.712  65.174 -11.504  1.00  0.00
ATOM   2382  CD2 LEU   327     -24.857  66.387 -11.532  1.00  0.00
ATOM   2383  N   GLY   328     -23.277  71.091 -10.046  1.00  0.00
ATOM   2384  CA  GLY   328     -22.761  72.115  -9.182  1.00  0.00
ATOM   2385  C   GLY   328     -21.451  72.570  -9.728  1.00  0.00
ATOM   2386  O   GLY   328     -21.357  73.106 -10.830  1.00  0.00
ATOM   2387  N   GLU   329     -20.397  72.359  -8.922  1.00  0.00
ATOM   2388  CA  GLU   329     -19.055  72.660  -9.306  1.00  0.00
ATOM   2389  C   GLU   329     -18.292  71.425  -8.975  1.00  0.00
ATOM   2390  O   GLU   329     -18.806  70.541  -8.291  1.00  0.00
ATOM   2391  CB  GLU   329     -18.533  73.869  -8.526  1.00  0.00
ATOM   2392  CG  GLU   329     -19.287  75.160  -8.806  1.00  0.00
ATOM   2393  CD  GLU   329     -18.728  76.338  -8.033  1.00  0.00
ATOM   2394  OE1 GLU   329     -17.724  76.155  -7.314  1.00  0.00
ATOM   2395  OE2 GLU   329     -19.296  77.445  -8.147  1.00  0.00
ATOM   2396  N   LEU   330     -17.041  71.308  -9.451  1.00  0.00
ATOM   2397  CA  LEU   330     -16.340  70.096  -9.159  1.00  0.00
ATOM   2398  C   LEU   330     -15.786  70.226  -7.778  1.00  0.00
ATOM   2399  O   LEU   330     -14.625  69.901  -7.535  1.00  0.00
ATOM   2400  CB  LEU   330     -15.205  69.880 -10.161  1.00  0.00
ATOM   2401  CG  LEU   330     -15.608  69.796 -11.635  1.00  0.00
ATOM   2402  CD1 LEU   330     -14.382  69.627 -12.519  1.00  0.00
ATOM   2403  CD2 LEU   330     -16.533  68.611 -11.872  1.00  0.00
ATOM   2404  N   LEU   331     -16.612  70.700  -6.826  1.00  0.00
ATOM   2405  CA  LEU   331     -16.171  70.795  -5.468  1.00  0.00
ATOM   2406  C   LEU   331     -17.411  70.641  -4.659  1.00  0.00
ATOM   2407  O   LEU   331     -18.426  71.271  -4.954  1.00  0.00
ATOM   2408  CB  LEU   331     -15.504  72.149  -5.214  1.00  0.00
ATOM   2409  CG  LEU   331     -15.034  72.416  -3.783  1.00  0.00
ATOM   2410  CD1 LEU   331     -13.897  71.478  -3.407  1.00  0.00
ATOM   2411  CD2 LEU   331     -14.539  73.847  -3.639  1.00  0.00
ATOM   2412  N   ILE   332     -17.382  69.790  -3.619  1.00  0.00
ATOM   2413  CA  ILE   332     -18.588  69.691  -2.862  1.00  0.00
ATOM   2414  C   ILE   332     -18.405  70.561  -1.669  1.00  0.00
ATOM   2415  O   ILE   332     -17.872  70.147  -0.640  1.00  0.00
ATOM   2416  CB  ILE   332     -18.861  68.240  -2.423  1.00  0.00
ATOM   2417  CG1 ILE   332     -18.928  67.317  -3.642  1.00  0.00
ATOM   2418  CG2 ILE   332     -20.183  68.150  -1.677  1.00  0.00
ATOM   2419  CD1 ILE   332     -18.990  65.847  -3.291  1.00  0.00
ATOM   2420  N   LYS   333     -18.858  71.816  -1.831  1.00  0.00
ATOM   2421  CA  LYS   333     -18.824  72.861  -0.854  1.00  0.00
ATOM   2422  C   LYS   333     -20.198  73.430  -0.918  1.00  0.00
ATOM   2423  O   LYS   333     -21.176  72.773  -0.565  1.00  0.00
ATOM   2424  CB  LYS   333     -17.757  73.897  -1.214  1.00  0.00
ATOM   2425  CG  LYS   333     -17.595  75.004  -0.184  1.00  0.00
ATOM   2426  CD  LYS   333     -16.477  75.959  -0.572  1.00  0.00
ATOM   2427  CE  LYS   333     -16.325  77.074   0.448  1.00  0.00
ATOM   2428  NZ  LYS   333     -15.238  78.022   0.079  1.00  0.00
ATOM   2429  N   HIS   334     -20.300  74.692  -1.368  1.00  0.00
ATOM   2430  CA  HIS   334     -21.573  75.320  -1.521  1.00  0.00
ATOM   2431  C   HIS   334     -22.261  74.686  -2.687  1.00  0.00
ATOM   2432  O   HIS   334     -21.628  74.331  -3.679  1.00  0.00
ATOM   2433  CB  HIS   334     -21.404  76.820  -1.773  1.00  0.00
ATOM   2434  CG  HIS   334     -22.683  77.592  -1.703  1.00  0.00
ATOM   2435  ND1 HIS   334     -23.596  77.618  -2.735  1.00  0.00
ATOM   2436  CD2 HIS   334     -23.329  78.445  -0.715  1.00  0.00
ATOM   2437  CE1 HIS   334     -24.637  78.392  -2.380  1.00  0.00
ATOM   2438  NE2 HIS   334     -24.483  78.891  -1.169  1.00  0.00
ATOM   2439  N   TYR   335     -23.591  74.511  -2.572  1.00  0.00
ATOM   2440  CA  TYR   335     -24.368  73.931  -3.630  1.00  0.00
ATOM   2441  C   TYR   335     -25.243  75.003  -4.182  1.00  0.00
ATOM   2442  O   TYR   335     -26.013  75.628  -3.452  1.00  0.00
ATOM   2443  CB  TYR   335     -25.223  72.780  -3.097  1.00  0.00
ATOM   2444  CG  TYR   335     -26.078  72.113  -4.152  1.00  0.00
ATOM   2445  CD1 TYR   335     -25.520  71.228  -5.065  1.00  0.00
ATOM   2446  CD2 TYR   335     -27.440  72.371  -4.230  1.00  0.00
ATOM   2447  CE1 TYR   335     -26.292  70.614  -6.031  1.00  0.00
ATOM   2448  CE2 TYR   335     -28.230  71.766  -5.191  1.00  0.00
ATOM   2449  CZ  TYR   335     -27.643  70.882  -6.095  1.00  0.00
ATOM   2450  OH  TYR   335     -28.414  70.271  -7.056  1.00  0.00
ATOM   2451  N   LEU   336     -25.132  75.250  -5.500  1.00  0.00
ATOM   2452  CA  LEU   336     -25.908  76.285  -6.114  1.00  0.00
ATOM   2453  C   LEU   336     -27.355  75.818  -6.089  1.00  0.00
ATOM   2454  O   LEU   336     -28.197  76.538  -5.491  1.00  0.00
ATOM   2455  CB  LEU   336     -25.447  76.517  -7.555  1.00  0.00
ATOM   2456  CG  LEU   336     -23.986  76.930  -7.741  1.00  0.00
ATOM   2457  CD1 LEU   336     -23.639  77.026  -9.219  1.00  0.00
ATOM   2458  CD2 LEU   336     -23.726  78.286  -7.104  1.00  0.00
TER
END
