
#######################################################
#                                                     #
#                        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 T0298TS022_5_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_5_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    -       -      P       4           -
LGA    -       -      L       5           -
LGA    -       -      N       6           -
LGA    -       -      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    R     317      T      13          4.588
LGA    K     318      G      14          1.585
LGA    G     319      S      15          3.428
LGA    A     320      V      16          3.339
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    A     321      L      20          1.639
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    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      A      70           -
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    -       -      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    L     322      G     319           #
LGA    N     323      A     320          2.581
LGA    A     324      A     321          2.939
LGA    V     325      L     322          0.462
LGA    L     326      N     323          2.329
LGA    L     327      A     324          2.401
LGA    G     328      V     325          1.717
LGA    E     329      L     326          1.637
LGA    L     330      L     327          1.506
LGA    -       -      G     328           -
LGA    -       -      E     329           -
LGA    L     331      L     330          1.692
LGA    I     332      L     331          1.605
LGA    K     333      I     332          2.203
LGA    H     334      K     333          1.414
LGA    Y     335      H     334          2.314
LGA    L     336      Y     335          3.114
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  148    5.0     19    2.42    15.79      9.549     0.755

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.809044 * X  +  -0.434926 * Y  +  -0.395331 * Z  +  54.788525
  Y_new =   0.504169 * X  +  -0.859267 * Y  +  -0.086455 * Z  + 103.004608
  Z_new =  -0.302093 * X  +  -0.269260 * Y  +   0.914461 * Z  +  23.414150 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.286354    2.855239  [ DEG:   -16.4069    163.5931 ]
  Theta =   0.306888    2.834705  [ DEG:    17.5834    162.4166 ]
  Phi   =   2.584313   -0.557280  [ DEG:   148.0702    -31.9298 ]
 
# 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: T0298TS022_5_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_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   19   2.42   15.79   9.549
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1qor_A
ATOM   2316  N   VAL   316      -7.875  56.340  -8.561  1.00  0.00
ATOM   2317  CA  VAL   316      -8.141  55.916  -7.220  1.00  0.00
ATOM   2318  C   VAL   316      -9.626  55.941  -7.059  1.00  0.00
ATOM   2319  O   VAL   316     -10.342  56.454  -7.916  1.00  0.00
ATOM   2320  CB  VAL   316      -7.480  56.852  -6.191  1.00  0.00
ATOM   2321  CG1 VAL   316      -5.966  56.819  -6.335  1.00  0.00
ATOM   2322  CG2 VAL   316      -7.952  58.283  -6.393  1.00  0.00
ATOM   2323  N   ARG   317     -10.135  55.358  -5.957  1.00  0.00
ATOM   2324  CA  ARG   317     -11.551  55.372  -5.729  1.00  0.00
ATOM   2325  C   ARG   317     -11.816  56.474  -4.755  1.00  0.00
ATOM   2326  O   ARG   317     -11.266  56.482  -3.654  1.00  0.00
ATOM   2327  CB  ARG   317     -12.014  54.031  -5.156  1.00  0.00
ATOM   2328  CG  ARG   317     -13.522  53.906  -5.009  1.00  0.00
ATOM   2329  CD  ARG   317     -13.914  52.536  -4.483  1.00  0.00
ATOM   2330  NE  ARG   317     -15.364  52.368  -4.420  1.00  0.00
ATOM   2331  CZ  ARG   317     -15.974  51.368  -3.792  1.00  0.00
ATOM   2332  NH1 ARG   317     -17.298  51.298  -3.788  1.00  0.00
ATOM   2333  NH2 ARG   317     -15.259  50.442  -3.168  1.00  0.00
ATOM   2334  N   LYS   318     -12.655  57.454  -5.147  1.00  0.00
ATOM   2335  CA  LYS   318     -12.930  58.548  -4.260  1.00  0.00
ATOM   2336  C   LYS   318     -14.334  59.009  -4.471  1.00  0.00
ATOM   2337  O   LYS   318     -15.078  58.441  -5.271  1.00  0.00
ATOM   2338  CB  LYS   318     -11.975  59.712  -4.532  1.00  0.00
ATOM   2339  CG  LYS   318     -12.129  60.331  -5.911  1.00  0.00
ATOM   2340  CD  LYS   318     -11.155  61.482  -6.112  1.00  0.00
ATOM   2341  CE  LYS   318     -11.271  62.067  -7.510  1.00  0.00
ATOM   2342  NZ  LYS   318     -10.377  63.242  -7.697  1.00  0.00
ATOM   2343  N   GLY   319     -14.737  60.051  -3.712  1.00  0.00
ATOM   2344  CA  GLY   319     -16.064  60.571  -3.839  1.00  0.00
ATOM   2345  C   GLY   319     -16.016  62.062  -3.704  1.00  0.00
ATOM   2346  O   GLY   319     -15.321  62.616  -2.852  1.00  0.00
ATOM   2347  N   ALA   320     -16.785  62.733  -4.579  1.00  0.00
ATOM   2348  CA  ALA   320     -16.954  64.154  -4.655  1.00  0.00
ATOM   2349  C   ALA   320     -17.671  64.631  -3.429  1.00  0.00
ATOM   2350  O   ALA   320     -17.415  65.722  -2.922  1.00  0.00
ATOM   2351  CB  ALA   320     -17.767  64.528  -5.885  1.00  0.00
ATOM   2352  N   ALA   321     -18.574  63.784  -2.907  1.00  0.00
ATOM   2353  CA  ALA   321     -19.501  64.107  -1.860  1.00  0.00
ATOM   2354  C   ALA   321     -18.792  64.600  -0.641  1.00  0.00
ATOM   2355  O   ALA   321     -19.299  65.478   0.056  1.00  0.00
ATOM   2356  CB  ALA   321     -20.311  62.880  -1.471  1.00  0.00
ATOM   2357  N   LEU   322     -17.601  64.060  -0.336  1.00  0.00
ATOM   2358  CA  LEU   322     -16.945  64.496   0.857  1.00  0.00
ATOM   2359  C   LEU   322     -16.681  65.961   0.723  1.00  0.00
ATOM   2360  O   LEU   322     -16.635  66.667   1.732  1.00  0.00
ATOM   2361  CB  LEU   322     -15.624  63.748   1.047  1.00  0.00
ATOM   2362  CG  LEU   322     -15.732  62.256   1.371  1.00  0.00
ATOM   2363  CD1 LEU   322     -14.357  61.604   1.368  1.00  0.00
ATOM   2364  CD2 LEU   322     -16.352  62.047   2.744  1.00  0.00
ATOM   2365  N   ASN   323     -16.484  66.439  -0.528  1.00  0.00
ATOM   2366  CA  ASN   323     -16.301  67.840  -0.796  1.00  0.00
ATOM   2367  C   ASN   323     -17.449  68.487  -0.116  1.00  0.00
ATOM   2368  O   ASN   323     -18.538  67.917  -0.117  1.00  0.00
ATOM   2369  CB  ASN   323     -16.313  68.104  -2.302  1.00  0.00
ATOM   2370  CG  ASN   323     -15.070  67.581  -2.996  1.00  0.00
ATOM   2371  OD1 ASN   323     -14.023  67.411  -2.370  1.00  0.00
ATOM   2372  ND2 ASN   323     -15.182  67.323  -4.293  1.00  0.00
ATOM   2373  N   ALA   324     -17.215  69.688   0.458  1.00  0.00
ATOM   2374  CA  ALA   324     -18.123  70.337   1.363  1.00  0.00
ATOM   2375  C   ALA   324     -19.536  70.197   0.922  1.00  0.00
ATOM   2376  O   ALA   324     -19.923  70.591  -0.177  1.00  0.00
ATOM   2377  CB  ALA   324     -17.809  71.822   1.456  1.00  0.00
ATOM   2378  N   VAL   325     -20.332  69.582   1.814  1.00  0.00
ATOM   2379  CA  VAL   325     -21.716  69.343   1.564  1.00  0.00
ATOM   2380  C   VAL   325     -22.327  70.684   1.408  1.00  0.00
ATOM   2381  O   VAL   325     -23.155  70.909   0.528  1.00  0.00
ATOM   2382  CB  VAL   325     -22.377  68.581   2.728  1.00  0.00
ATOM   2383  CG1 VAL   325     -23.884  68.514   2.533  1.00  0.00
ATOM   2384  CG2 VAL   325     -21.838  67.161   2.809  1.00  0.00
ATOM   2385  N   LEU   326     -21.907  71.622   2.271  1.00  0.00
ATOM   2386  CA  LEU   326     -22.430  72.950   2.209  1.00  0.00
ATOM   2387  C   LEU   326     -22.029  73.515   0.887  1.00  0.00
ATOM   2388  O   LEU   326     -22.801  74.217   0.236  1.00  0.00
ATOM   2389  CB  LEU   326     -21.861  73.804   3.344  1.00  0.00
ATOM   2390  CG  LEU   326     -22.332  73.454   4.757  1.00  0.00
ATOM   2391  CD1 LEU   326     -21.558  74.252   5.795  1.00  0.00
ATOM   2392  CD2 LEU   326     -23.812  73.767   4.924  1.00  0.00
ATOM   2393  N   LEU   327     -20.803  73.186   0.446  1.00  0.00
ATOM   2394  CA  LEU   327     -20.297  73.644  -0.813  1.00  0.00
ATOM   2395  C   LEU   327     -21.228  73.138  -1.866  1.00  0.00
ATOM   2396  O   LEU   327     -21.594  73.856  -2.796  1.00  0.00
ATOM   2397  CB  LEU   327     -18.886  73.105  -1.051  1.00  0.00
ATOM   2398  CG  LEU   327     -18.210  73.527  -2.357  1.00  0.00
ATOM   2399  CD1 LEU   327     -18.048  75.039  -2.414  1.00  0.00
ATOM   2400  CD2 LEU   327     -16.831  72.897  -2.478  1.00  0.00
ATOM   2401  N   GLY   328     -21.659  71.878  -1.702  1.00  0.00
ATOM   2402  CA  GLY   328     -22.504  71.175  -2.621  1.00  0.00
ATOM   2403  C   GLY   328     -23.823  71.866  -2.734  1.00  0.00
ATOM   2404  O   GLY   328     -24.509  71.741  -3.746  1.00  0.00
ATOM   2405  N   GLU   329     -24.242  72.581  -1.676  1.00  0.00
ATOM   2406  CA  GLU   329     -25.557  73.138  -1.710  1.00  0.00
ATOM   2407  C   GLU   329     -25.739  74.045  -2.885  1.00  0.00
ATOM   2408  O   GLU   329     -26.719  73.903  -3.613  1.00  0.00
ATOM   2409  CB  GLU   329     -25.828  73.950  -0.443  1.00  0.00
ATOM   2410  CG  GLU   329     -27.225  74.544  -0.373  1.00  0.00
ATOM   2411  CD  GLU   329     -27.468  75.313   0.912  1.00  0.00
ATOM   2412  OE1 GLU   329     -26.546  75.371   1.753  1.00  0.00
ATOM   2413  OE2 GLU   329     -28.580  75.858   1.076  1.00  0.00
ATOM   2414  N   LEU   330     -24.822  74.997  -3.151  1.00  0.00
ATOM   2415  CA  LEU   330     -25.096  75.851  -4.278  1.00  0.00
ATOM   2416  C   LEU   330     -26.380  76.597  -4.025  1.00  0.00
ATOM   2417  O   LEU   330     -27.046  76.419  -3.006  1.00  0.00
ATOM   2418  CB  LEU   330     -25.239  75.022  -5.557  1.00  0.00
ATOM   2419  CG  LEU   330     -26.317  73.936  -5.544  1.00  0.00
ATOM   2420  CD1 LEU   330     -27.690  74.538  -5.800  1.00  0.00
ATOM   2421  CD2 LEU   330     -26.044  72.895  -6.619  1.00  0.00
ATOM   2422  N   LEU   331     -26.758  77.524  -4.925  1.00  0.00
ATOM   2423  CA  LEU   331     -27.982  78.215  -4.644  1.00  0.00
ATOM   2424  C   LEU   331     -28.940  77.935  -5.757  1.00  0.00
ATOM   2425  O   LEU   331     -29.838  78.732  -6.020  1.00  0.00
ATOM   2426  CB  LEU   331     -27.736  79.722  -4.544  1.00  0.00
ATOM   2427  CG  LEU   331     -26.810  80.184  -3.418  1.00  0.00
ATOM   2428  CD1 LEU   331     -26.511  81.670  -3.543  1.00  0.00
ATOM   2429  CD2 LEU   331     -27.450  79.941  -2.060  1.00  0.00
ATOM   2430  N   ILE   332     -28.780  76.781  -6.435  1.00  0.00
ATOM   2431  CA  ILE   332     -29.655  76.426  -7.516  1.00  0.00
ATOM   2432  C   ILE   332     -31.018  76.123  -6.981  1.00  0.00
ATOM   2433  O   ILE   332     -32.025  76.512  -7.569  1.00  0.00
ATOM   2434  CB  ILE   332     -29.143  75.185  -8.271  1.00  0.00
ATOM   2435  CG1 ILE   332     -27.843  75.508  -9.008  1.00  0.00
ATOM   2436  CG2 ILE   332     -30.173  74.720  -9.290  1.00  0.00
ATOM   2437  CD1 ILE   332     -27.133  74.290  -9.558  1.00  0.00
ATOM   2438  N   LYS   333     -31.081  75.415  -5.840  1.00  0.00
ATOM   2439  CA  LYS   333     -32.343  75.037  -5.274  1.00  0.00
ATOM   2440  C   LYS   333     -33.084  76.297  -4.974  1.00  0.00
ATOM   2441  O   LYS   333     -34.300  76.372  -5.134  1.00  0.00
ATOM   2442  CB  LYS   333     -32.134  74.230  -3.991  1.00  0.00
ATOM   2443  CG  LYS   333     -31.569  72.837  -4.218  1.00  0.00
ATOM   2444  CD  LYS   333     -31.390  72.092  -2.906  1.00  0.00
ATOM   2445  CE  LYS   333     -30.801  70.710  -3.132  1.00  0.00
ATOM   2446  NZ  LYS   333     -30.588  69.980  -1.850  1.00  0.00
ATOM   2447  N   HIS   334     -32.350  77.327  -4.526  1.00  0.00
ATOM   2448  CA  HIS   334     -32.933  78.599  -4.224  1.00  0.00
ATOM   2449  C   HIS   334     -33.465  79.158  -5.504  1.00  0.00
ATOM   2450  O   HIS   334     -34.475  79.860  -5.516  1.00  0.00
ATOM   2451  CB  HIS   334     -31.882  79.542  -3.635  1.00  0.00
ATOM   2452  CG  HIS   334     -31.444  79.171  -2.252  1.00  0.00
ATOM   2453  ND1 HIS   334     -30.321  79.705  -1.658  1.00  0.00
ATOM   2454  CD2 HIS   334     -31.937  78.280  -1.211  1.00  0.00
ATOM   2455  CE1 HIS   334     -30.187  79.183  -0.426  1.00  0.00
ATOM   2456  NE2 HIS   334     -31.152  78.327  -0.151  1.00  0.00
ATOM   2457  N   TYR   335     -32.797  78.834  -6.628  1.00  0.00
ATOM   2458  CA  TYR   335     -33.151  79.384  -7.902  1.00  0.00
ATOM   2459  C   TYR   335     -32.861  80.845  -7.864  1.00  0.00
ATOM   2460  O   TYR   335     -33.494  81.640  -8.557  1.00  0.00
ATOM   2461  CB  TYR   335     -34.638  79.158  -8.189  1.00  0.00
ATOM   2462  CG  TYR   335     -35.059  77.707  -8.129  1.00  0.00
ATOM   2463  CD1 TYR   335     -35.807  77.227  -7.062  1.00  0.00
ATOM   2464  CD2 TYR   335     -34.706  76.822  -9.140  1.00  0.00
ATOM   2465  CE1 TYR   335     -36.197  75.902  -6.999  1.00  0.00
ATOM   2466  CE2 TYR   335     -35.086  75.494  -9.093  1.00  0.00
ATOM   2467  CZ  TYR   335     -35.839  75.038  -8.011  1.00  0.00
ATOM   2468  OH  TYR   335     -36.225  73.719  -7.950  1.00  0.00
ATOM   2469  N   LEU   336     -31.866  81.234  -7.046  1.00  0.00
ATOM   2470  CA  LEU   336     -31.483  82.611  -6.974  1.00  0.00
ATOM   2471  C   LEU   336     -30.352  82.816  -7.975  1.00  0.00
ATOM   2472  O   LEU   336     -29.411  81.978  -7.988  1.00  0.00
ATOM   2473  CB  LEU   336     -31.008  82.962  -5.563  1.00  0.00
ATOM   2474  CG  LEU   336     -32.010  82.725  -4.431  1.00  0.00
ATOM   2475  CD1 LEU   336     -31.394  83.078  -3.086  1.00  0.00
ATOM   2476  CD2 LEU   336     -33.252  83.581  -4.625  1.00  0.00
TER
END
