
#######################################################
#                                                     #
#                        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   25 (  189),  selected   25 , name T0356TS013_1_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS013_1_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    G     323      E      34          1.193
LGA    R     324      I      35          1.967
LGA    P     325      T      36          3.923
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    P     326      A      39          3.163
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    D     327      N      65          3.959
LGA    E     328      L      66          4.631
LGA    P     329      F      67          3.691
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    A     330      P     329          1.927
LGA    V     331      A     330          2.956
LGA    L     332      V     331          2.038
LGA    G     333      L     332          1.532
LGA    V     334      G     333          1.346
LGA    A     335      V     334          0.743
LGA    L     336      A     335          0.620
LGA    N     337      L     336          1.301
LGA    E     338      N     337          1.358
LGA    V     339      E     338          2.378
LGA    F     340      -       -           -
LGA    V     341      -       -           -
LGA    P     342      V     339          4.507
LGA    I     343      F     340          2.573
LGA    L     344      V     341          1.334
LGA    Q     345      P     342          2.172
LGA    K     346      I     343          1.749
LGA    Q     347      L     344          2.738
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25  124    5.0     23    2.61     0.00     13.533     0.850

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.861643 * X  +   0.053144 * Y  +   0.504724 * Z  +  52.863152
  Y_new =   0.319183 * X  +  -0.829945 * Y  +  -0.457508 * Z  +  76.888062
  Z_new =   0.394580 * X  +   0.555308 * Y  +  -0.732079 * Z  +  75.248917 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.492651   -0.648942  [ DEG:   142.8184    -37.1816 ]
  Theta =  -0.405610   -2.735982  [ DEG:   -23.2398   -156.7603 ]
  Phi   =   0.354762   -2.786830  [ DEG:    20.3264   -159.6736 ]
 
# 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: T0356TS013_1_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS013_1_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  124   5.0   23   2.61    0.00  13.533
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS013_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT N/A
ATOM   2524  N   GLY   323      57.235  65.826  97.213  1.00  8.31
ATOM   2525  CA  GLY   323      56.935  64.491  96.686  1.00  8.31
ATOM   2526  C   GLY   323      58.034  63.842  95.847  1.00  8.31
ATOM   2527  O   GLY   323      58.352  62.668  96.039  1.00  8.31
ATOM   2528  N   ARG   324      58.596  64.586  94.909  1.00  8.97
ATOM   2529  CA  ARG   324      59.670  64.108  94.044  1.00  8.97
ATOM   2530  C   ARG   324      60.152  65.304  93.254  1.00  8.97
ATOM   2531  O   ARG   324      59.714  66.420  93.513  1.00  8.97
ATOM   2532  CB  ARG   324      59.192  62.982  93.126  1.00  8.97
ATOM   2533  CG  ARG   324      58.940  61.692  93.921  1.00  8.97
ATOM   2534  CD  ARG   324      58.768  60.367  93.180  1.00  8.97
ATOM   2535  NE  ARG   324      57.493  60.256  92.478  1.00  8.97
ATOM   2536  CZ  ARG   324      57.241  59.329  91.516  1.00  8.97
ATOM   2537  NH1 ARG   324      58.210  58.460  91.121  1.00  8.97
ATOM   2538  NH2 ARG   324      56.013  59.291  90.942  1.00  8.97
ATOM   2539  N   PRO   325      61.054  65.105  92.300  1.00  8.11
ATOM   2540  CA  PRO   325      61.648  66.216  91.591  1.00  8.11
ATOM   2541  C   PRO   325      60.619  66.864  90.693  1.00  8.11
ATOM   2542  O   PRO   325      59.800  66.194  90.104  1.00  8.11
ATOM   2543  CB  PRO   325      62.852  65.774  90.799  1.00  8.11
ATOM   2544  CG  PRO   325      62.830  64.379  90.680  1.00  8.11
ATOM   2545  CD  PRO   325      61.987  63.807  91.799  1.00  8.11
ATOM   2546  N   PRO   326      60.735  68.177  90.558  1.00  7.38
ATOM   2547  CA  PRO   326      59.774  68.891  89.724  1.00  7.38
ATOM   2548  C   PRO   326      59.801  68.304  88.325  1.00  7.38
ATOM   2549  O   PRO   326      60.869  67.839  87.890  1.00  7.38
ATOM   2550  CB  PRO   326      60.115  70.373  89.616  1.00  7.38
ATOM   2551  CG  PRO   326      61.072  70.736  90.759  1.00  7.38
ATOM   2552  CD  PRO   326      61.523  69.441  91.431  1.00  7.38
ATOM   2553  N   ASP   327      58.671  68.348  87.651  1.00  9.54
ATOM   2554  CA  ASP   327      58.595  67.887  86.272  1.00  9.54
ATOM   2555  C   ASP   327      58.574  69.111  85.374  1.00  9.54
ATOM   2556  O   ASP   327      57.577  69.830  85.318  1.00  9.54
ATOM   2557  CB  ASP   327      57.370  66.986  86.040  1.00  9.54
ATOM   2558  CG  ASP   327      56.024  67.390  86.568  1.00  9.54
ATOM   2559  OD1 ASP   327      55.740  68.583  86.678  1.00  9.54
ATOM   2560  OD2 ASP   327      55.253  66.463  86.840  1.00  9.54
ATOM   2561  N   GLU   328      59.697  69.411  84.736  1.00  8.59
ATOM   2562  CA  GLU   328      59.866  70.655  84.006  1.00  8.59
ATOM   2563  C   GLU   328      60.499  70.422  82.641  1.00  8.59
ATOM   2564  O   GLU   328      61.170  69.414  82.418  1.00  8.59
ATOM   2565  CB  GLU   328      60.790  71.640  84.771  1.00  8.59
ATOM   2566  CG  GLU   328      60.875  72.937  84.001  1.00  8.59
ATOM   2567  CD  GLU   328      61.738  73.975  84.707  1.00  8.59
ATOM   2568  OE1 GLU   328      61.918  73.900  85.933  1.00  8.59
ATOM   2569  OE2 GLU   328      62.216  74.879  84.025  1.00  8.59
ATOM   2570  N   PRO   329      61.233  69.452  82.367  1.00 10.41
ATOM   2571  CA  PRO   329      61.849  69.268  81.055  1.00 10.41
ATOM   2572  C   PRO   329      61.354  68.013  80.344  1.00 10.41
ATOM   2573  O   PRO   329      62.026  67.484  79.468  1.00 10.41
ATOM   2574  CB  PRO   329      63.388  69.295  81.141  1.00 10.41
ATOM   2575  CG  PRO   329      63.737  69.117  82.473  1.00 10.41
ATOM   2576  CD  PRO   329      62.585  69.516  83.369  1.00 10.41
ATOM   2577  N   ALA   330      60.139  67.548  80.705  1.00  8.83
ATOM   2578  CA  ALA   330      59.561  66.308  80.273  1.00  8.83
ATOM   2579  C   ALA   330      58.350  66.487  79.357  1.00  8.83
ATOM   2580  O   ALA   330      58.086  65.622  78.527  1.00  8.83
ATOM   2581  CB  ALA   330      59.121  65.499  81.505  1.00  8.83
ATOM   2582  N   VAL   331      57.592  67.570  79.527  1.00  8.22
ATOM   2583  CA  VAL   331      56.444  67.888  78.689  1.00  8.22
ATOM   2584  C   VAL   331      56.665  69.087  77.744  1.00  8.22
ATOM   2585  O   VAL   331      56.042  69.193  76.726  1.00  8.22
ATOM   2586  CB  VAL   331      55.182  68.170  79.531  1.00  8.22
ATOM   2587  CG1 VAL   331      54.028  68.768  78.749  1.00  8.22
ATOM   2588  CG2 VAL   331      54.726  66.813  80.051  1.00  8.22
ATOM   2589  N   LEU   332      57.543  70.010  78.169  1.00  6.70
ATOM   2590  CA  LEU   332      57.675  71.301  77.551  1.00  6.70
ATOM   2591  C   LEU   332      58.899  71.416  76.631  1.00  6.70
ATOM   2592  O   LEU   332      58.997  72.375  75.879  1.00  6.70
ATOM   2593  CB  LEU   332      57.788  72.387  78.610  1.00  6.70
ATOM   2594  CG  LEU   332      56.514  72.659  79.382  1.00  6.70
ATOM   2595  CD1 LEU   332      56.783  73.756  80.377  1.00  6.70
ATOM   2596  CD2 LEU   332      55.391  73.066  78.431  1.00  6.70
ATOM   2597  N   GLY   333      60.029  70.964  77.154  1.00  9.58
ATOM   2598  CA  GLY   333      61.252  70.991  76.389  1.00  9.58
ATOM   2599  C   GLY   333      61.170  70.168  75.144  1.00  9.58
ATOM   2600  O   GLY   333      61.563  70.542  74.084  1.00  9.58
ATOM   2601  N   VAL   334      60.645  68.929  75.254  1.00  9.91
ATOM   2602  CA  VAL   334      60.554  68.068  74.044  1.00  9.91
ATOM   2603  C   VAL   334      59.577  68.648  73.040  1.00  9.91
ATOM   2604  O   VAL   334      59.765  68.560  71.829  1.00  9.91
ATOM   2605  CB  VAL   334      60.040  66.691  74.493  1.00  9.91
ATOM   2606  CG1 VAL   334      59.628  65.769  73.358  1.00  9.91
ATOM   2607  CG2 VAL   334      61.208  66.027  75.213  1.00  9.91
ATOM   2608  N   ALA   335      58.467  69.253  73.521  1.00  5.25
ATOM   2609  CA  ALA   335      57.484  69.870  72.637  1.00  5.25
ATOM   2610  C   ALA   335      58.077  71.103  71.959  1.00  5.25
ATOM   2611  O   ALA   335      57.923  71.311  70.754  1.00  5.25
ATOM   2612  CB  ALA   335      56.246  70.207  73.449  1.00  5.25
ATOM   2613  N   LEU   336      58.737  71.966  72.646  1.00  4.44
ATOM   2614  CA  LEU   336      59.227  73.215  72.067  1.00  4.44
ATOM   2615  C   LEU   336      60.070  73.019  70.813  1.00  4.44
ATOM   2616  O   LEU   336      60.057  73.875  69.924  1.00  4.44
ATOM   2617  CB  LEU   336      59.997  74.043  73.114  1.00  4.44
ATOM   2618  CG  LEU   336      60.579  75.347  72.612  1.00  4.44
ATOM   2619  CD1 LEU   336      59.484  76.363  72.449  1.00  4.44
ATOM   2620  CD2 LEU   336      61.624  75.841  73.590  1.00  4.44
ATOM   2621  N   ASN   337      60.801  71.912  70.719  1.00 12.92
ATOM   2622  CA  ASN   337      61.601  71.671  69.511  1.00 12.92
ATOM   2623  C   ASN   337      60.666  71.579  68.300  1.00 12.92
ATOM   2624  O   ASN   337      60.923  72.174  67.251  1.00 12.92
ATOM   2625  CB  ASN   337      62.417  70.377  69.649  1.00 12.92
ATOM   2626  CG  ASN   337      63.356  70.371  70.842  1.00 12.92
ATOM   2627  OD1 ASN   337      64.239  71.209  70.889  1.00 12.92
ATOM   2628  ND2 ASN   337      63.162  69.492  71.811  1.00 12.92
ATOM   2629  N   GLU   338      59.584  70.822  68.450  1.00 15.01
ATOM   2630  CA  GLU   338      58.590  70.687  67.392  1.00 15.01
ATOM   2631  C   GLU   338      57.895  72.023  67.125  1.00 15.01
ATOM   2632  O   GLU   338      57.663  72.390  65.966  1.00 15.01
ATOM   2633  CB  GLU   338      57.540  69.639  67.774  1.00 15.01
ATOM   2634  CG  GLU   338      58.216  68.290  67.894  1.00 15.01
ATOM   2635  CD  GLU   338      57.341  67.186  68.478  1.00 15.01
ATOM   2636  OE1 GLU   338      56.440  67.468  69.255  1.00 15.01
ATOM   2637  OE2 GLU   338      57.564  66.028  68.150  1.00 15.01
ATOM   2638  N   VAL   339      57.547  72.757  68.178  1.00  1.52
ATOM   2639  CA  VAL   339      56.861  74.028  67.951  1.00  1.52
ATOM   2640  C   VAL   339      57.712  74.941  67.076  1.00  1.52
ATOM   2641  O   VAL   339      57.210  75.547  66.117  1.00  1.52
ATOM   2642  CB  VAL   339      56.515  74.722  69.274  1.00  1.52
ATOM   2643  CG1 VAL   339      56.049  76.163  69.133  1.00  1.52
ATOM   2644  CG2 VAL   339      55.356  73.931  69.870  1.00  1.52
ATOM   2645  N   PHE   340      59.015  74.965  67.288  1.00  7.22
ATOM   2646  CA  PHE   340      59.908  75.764  66.473  1.00  7.22
ATOM   2647  C   PHE   340      59.767  75.458  64.992  1.00  7.22
ATOM   2648  O   PHE   340      59.706  76.372  64.175  1.00  7.22
ATOM   2649  CB  PHE   340      61.353  75.534  66.946  1.00  7.22
ATOM   2650  CG  PHE   340      62.361  76.424  66.296  1.00  7.22
ATOM   2651  CD1 PHE   340      62.941  76.054  65.089  1.00  7.22
ATOM   2652  CD2 PHE   340      62.760  77.610  66.911  1.00  7.22
ATOM   2653  CE1 PHE   340      63.909  76.855  64.490  1.00  7.22
ATOM   2654  CE2 PHE   340      63.706  78.441  66.317  1.00  7.22
ATOM   2655  CZ  PHE   340      64.269  78.056  65.089  1.00  7.22
ATOM   2656  N   VAL   341      59.203  76.363  64.185  1.00  3.78
ATOM   2657  CA  VAL   341      58.931  76.048  62.780  1.00  3.78
ATOM   2658  C   VAL   341      60.231  75.680  62.032  1.00  3.78
ATOM   2659  O   VAL   341      60.173  74.855  61.119  1.00  3.78
ATOM   2660  CB  VAL   341      58.164  77.186  62.135  1.00  3.78
ATOM   2661  CG1 VAL   341      56.804  77.466  62.850  1.00  3.78
ATOM   2662  CG2 VAL   341      58.957  78.520  62.076  1.00  3.78
ATOM   2663  N   PRO   342      61.361  76.268  62.409  1.00 13.89
ATOM   2664  CA  PRO   342      62.607  75.871  61.729  1.00 13.89
ATOM   2665  C   PRO   342      62.951  74.410  62.017  1.00 13.89
ATOM   2666  O   PRO   342      63.428  73.673  61.148  1.00 13.89
ATOM   2667  CB  PRO   342      63.718  76.896  61.972  1.00 13.89
ATOM   2668  CG  PRO   342      63.340  77.693  63.049  1.00 13.89
ATOM   2669  CD  PRO   342      61.836  77.652  63.210  1.00 13.89
ATOM   2670  N   ILE   343      62.707  73.989  63.276  1.00  7.55
ATOM   2671  CA  ILE   343      62.954  72.582  63.614  1.00  7.55
ATOM   2672  C   ILE   343      61.974  71.654  62.925  1.00  7.55
ATOM   2673  O   ILE   343      62.309  70.592  62.447  1.00  7.55
ATOM   2674  CB  ILE   343      62.875  72.386  65.126  1.00  7.55
ATOM   2675  CG1 ILE   343      63.874  73.290  65.853  1.00  7.55
ATOM   2676  CG2 ILE   343      63.182  70.939  65.508  1.00  7.55
ATOM   2677  CD1 ILE   343      63.740  73.277  67.382  1.00  7.55
ATOM   2678  N   LEU   344      60.707  72.082  62.844  1.00  6.23
ATOM   2679  CA  LEU   344      59.700  71.299  62.174  1.00  6.23
ATOM   2680  C   LEU   344      59.990  71.188  60.655  1.00  6.23
ATOM   2681  O   LEU   344      59.795  70.115  60.058  1.00  6.23
ATOM   2682  CB  LEU   344      58.293  71.858  62.424  1.00  6.23
ATOM   2683  CG  LEU   344      57.162  71.122  61.731  1.00  6.23
ATOM   2684  CD1 LEU   344      56.894  69.825  62.441  1.00  6.23
ATOM   2685  CD2 LEU   344      55.920  71.990  61.722  1.00  6.23
ATOM   2686  N   GLN   345      60.430  72.272  60.051  1.00 12.04
ATOM   2687  CA  GLN   345      60.803  72.203  58.649  1.00 12.04
ATOM   2688  C   GLN   345      61.984  71.317  58.409  1.00 12.04
ATOM   2689  O   GLN   345      62.042  70.636  57.374  1.00 12.04
ATOM   2690  CB  GLN   345      61.081  73.625  58.131  1.00 12.04
ATOM   2691  CG  GLN   345      59.788  74.224  57.667  1.00 12.04
ATOM   2692  CD  GLN   345      59.084  73.436  56.561  1.00 12.04
ATOM   2693  OE1 GLN   345      57.970  72.934  56.705  1.00 12.04
ATOM   2694  NE2 GLN   345      59.710  73.268  55.402  1.00 12.04
ATOM   2695  N   LYS   346      62.721  70.867  59.405  1.00 10.85
ATOM   2696  CA  LYS   346      63.740  69.849  59.193  1.00 10.85
ATOM   2697  C   LYS   346      63.186  68.624  58.485  1.00 10.85
ATOM   2698  O   LYS   346      63.825  68.060  57.571  1.00 10.85
ATOM   2699  CB  LYS   346      64.331  69.404  60.528  1.00 10.85
ATOM   2700  CG  LYS   346      65.042  70.579  61.171  1.00 10.85
ATOM   2701  CD  LYS   346      65.660  70.160  62.450  1.00 10.85
ATOM   2702  CE  LYS   346      66.256  71.423  63.059  1.00 10.85
ATOM   2703  NZ  LYS   346      67.041  71.031  64.204  1.00 10.85
ATOM   2704  N   GLN   347      62.028  68.100  58.850  1.00 11.25
ATOM   2705  CA  GLN   347      61.370  67.018  58.112  1.00 11.25
ATOM   2706  C   GLN   347      61.165  67.420  56.664  1.00 11.25
ATOM   2707  O   GLN   347      61.409  66.651  55.736  1.00 11.25
ATOM   2708  CB  GLN   347      60.038  66.669  58.764  1.00 11.25
ATOM   2709  CG  GLN   347      60.271  65.652  59.845  1.00 11.25
ATOM   2710  CD  GLN   347      60.924  64.358  59.359  1.00 11.25
ATOM   2711  OE1 GLN   347      62.029  63.979  59.748  1.00 11.25
ATOM   2712  NE2 GLN   347      60.281  63.617  58.462  1.00 11.25
TER
END
