
#######################################################
#                                                     #
#                        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   16 (  132),  selected   16 , name T0356TS105_1_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS105_1_1-D3.T0356_D3.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    -       -      F     348           -
LGA    -       -      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    -       -      V     352           -
LGA    -       -      D     353           -
LGA    -       -      F     354           -
LGA    -       -      Y     355           -
LGA    -       -      L     356           -
LGA    -       -      P     357           -
LGA    -       -      P     358           -
LGA    -       -      E     359           -
LGA    -       -      G     360           -
LGA    -       -      C     361           -
LGA    -       -      S     362           -
LGA    -       -      Y     363           -
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    -       -      A     366           -
LGA    -       -      V     367           -
LGA    -       -      V     368           -
LGA    -       -      T     369           -
LGA    -       -      I     370           -
LGA    -       -      K     371           -
LGA    -       -      K     372           -
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    -       -      R     380           -
LGA    -       -      V     381           -
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    -       -      W     386           -
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    F     348      N     406          5.335
LGA    P     349      A     407           #
LGA    E     350      R     408          3.413
LGA    I     351      D     409          1.176
LGA    V     352      W     410          2.596
LGA    D     353      N     411          1.886
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    F     354      I     414          2.101
LGA    Y     355      W     415          2.320
LGA    L     356      A     416          2.900
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    P     357      R     420          1.342
LGA    P     358      M     421          4.270
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    -       -      E     431           -
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    -       -      A     455           -
LGA    -       -      T     456           -
LGA    -       -      N     457           -
LGA    E     359      K     458          1.174
LGA    G     360      W     459          2.709
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    C     361      T     463          1.861
LGA    -       -      Q     464           -
LGA    S     362      R     465          4.122
LGA    -       -      E     466           -
LGA    Y     363      W     467          2.878

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  120    5.0     15    2.92     0.00      8.873     0.497

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.783388 * X  +   0.237822 * Y  +  -0.574234 * Z  +  -4.204200
  Y_new =   0.309190 * X  +   0.652353 * Y  +   0.691981 * Z  + -92.125534
  Z_new =   0.539171 * X  +  -0.719637 * Y  +   0.437513 * Z  + 114.518677 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.024542    2.117051  [ DEG:   -58.7019    121.2981 ]
  Theta =  -0.569453   -2.572140  [ DEG:   -32.6272   -147.3728 ]
  Phi   =   0.375914   -2.765678  [ DEG:    21.5383   -158.4617 ]
 
# 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: T0356TS105_1_1-D3                             
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS105_1_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  120   5.0   15   2.92    0.00   8.873
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS105_1_1-D3
REMARK PARENT number 1
PFRMAT TS
TARGET T0356
PARENT 1pg4_A
ATOM   2713  N   PHE   348      47.887  69.126  65.991  1.00107.55           N  
ATOM   2714  CA  PHE   348      48.172  70.523  66.170  1.00107.55           C  
ATOM   2715  CB  PHE   348      47.379  71.443  65.230  1.00107.55           C  
ATOM   2716  CG  PHE   348      47.814  71.115  63.848  1.00107.55           C  
ATOM   2717  CD1 PHE   348      47.254  70.047  63.188  1.00107.55           C  
ATOM   2718  CD2 PHE   348      48.777  71.871  63.221  1.00107.55           C  
ATOM   2719  CE1 PHE   348      47.648  69.732  61.912  1.00107.55           C  
ATOM   2720  CE2 PHE   348      49.176  71.561  61.944  1.00107.55           C  
ATOM   2721  CZ  PHE   348      48.611  70.492  61.294  1.00107.55           C  
ATOM   2722  C   PHE   348      47.765  70.873  67.568  1.00107.55           C  
ATOM   2723  O   PHE   348      46.698  70.480  68.037  1.00107.55           O  
ATOM   2724  N   PRO   349      48.601  71.602  68.254  1.00 76.80           N  
ATOM   2725  CA  PRO   349      48.305  71.909  69.623  1.00 76.80           C  
ATOM   2726  CD  PRO   349      50.034  71.555  68.005  1.00 76.80           C  
ATOM   2727  CB  PRO   349      49.580  72.527  70.193  1.00 76.80           C  
ATOM   2728  CG  PRO   349      50.695  71.868  69.361  1.00 76.80           C  
ATOM   2729  C   PRO   349      47.079  72.740  69.793  1.00 76.80           C  
ATOM   2730  O   PRO   349      46.449  72.654  70.846  1.00 76.80           O  
ATOM   2731  N   GLU   350      46.745  73.579  68.798  1.00 61.93           N  
ATOM   2732  CA  GLU   350      45.587  74.414  68.898  1.00 61.93           C  
ATOM   2733  CB  GLU   350      45.553  75.562  67.875  1.00 61.93           C  
ATOM   2734  CG  GLU   350      46.582  76.655  68.177  1.00 61.93           C  
ATOM   2735  CD  GLU   350      46.224  77.888  67.359  1.00 61.93           C  
ATOM   2736  OE1 GLU   350      45.204  77.837  66.623  1.00 61.93           O1-
ATOM   2737  OE2 GLU   350      46.962  78.903  67.468  1.00 61.93           O  
ATOM   2738  C   GLU   350      44.316  73.627  68.759  1.00 61.93           C  
ATOM   2739  O   GLU   350      43.322  73.949  69.405  1.00 61.93           O  
ATOM   2740  N   ILE   351      44.304  72.569  67.922  1.00 75.85           N  
ATOM   2741  CA  ILE   351      43.060  71.901  67.633  1.00 75.85           C  
ATOM   2742  CB  ILE   351      43.094  71.160  66.328  1.00 75.85           C  
ATOM   2743  CG2 ILE   351      41.779  70.378  66.185  1.00 75.85           C  
ATOM   2744  CG1 ILE   351      43.358  72.138  65.172  1.00 75.85           C  
ATOM   2745  CD1 ILE   351      43.697  71.446  63.852  1.00 75.85           C  
ATOM   2746  C   ILE   351      42.700  70.910  68.698  1.00 75.85           C  
ATOM   2747  O   ILE   351      43.468  69.999  69.004  1.00 75.85           O  
ATOM   2748  N   VAL   352      41.521  71.113  69.329  1.00125.51           N  
ATOM   2749  CA  VAL   352      41.015  70.212  70.328  1.00125.51           C  
ATOM   2750  CB  VAL   352      39.945  70.831  71.183  1.00125.51           C  
ATOM   2751  CG1 VAL   352      40.567  72.002  71.963  1.00125.51           C  
ATOM   2752  CG2 VAL   352      38.757  71.241  70.300  1.00125.51           C  
ATOM   2753  C   VAL   352      40.471  68.934  69.737  1.00125.51           C  
ATOM   2754  O   VAL   352      40.871  67.845  70.148  1.00125.51           O  
ATOM   2755  N   ASP   353      39.551  69.022  68.746  1.00127.50           N  
ATOM   2756  CA  ASP   353      38.949  67.828  68.200  1.00127.50           C  
ATOM   2757  CB  ASP   353      37.614  67.421  68.852  1.00127.50           C  
ATOM   2758  CG  ASP   353      36.596  68.527  68.629  1.00127.50           C  
ATOM   2759  OD1 ASP   353      36.798  69.627  69.206  1.00127.50           O  
ATOM   2760  OD2 ASP   353      35.608  68.292  67.882  1.00127.50           O1-
ATOM   2761  C   ASP   353      38.699  68.025  66.739  1.00127.50           C  
ATOM   2762  O   ASP   353      38.692  69.153  66.250  1.00127.50           O  
ATOM   2763  N   PHE   354      38.489  66.914  65.995  1.00128.63           N  
ATOM   2764  CA  PHE   354      38.367  67.053  64.573  1.00128.63           C  
ATOM   2765  CB  PHE   354      39.771  66.963  63.957  1.00128.63           C  
ATOM   2766  CG  PHE   354      39.742  67.153  62.490  1.00128.63           C  
ATOM   2767  CD1 PHE   354      39.866  68.416  61.966  1.00128.63           C  
ATOM   2768  CD2 PHE   354      39.614  66.075  61.648  1.00128.63           C  
ATOM   2769  CE1 PHE   354      39.851  68.601  60.609  1.00128.63           C  
ATOM   2770  CE2 PHE   354      39.599  66.261  60.287  1.00128.63           C  
ATOM   2771  CZ  PHE   354      39.716  67.527  59.766  1.00128.63           C  
ATOM   2772  C   PHE   354      37.545  65.921  64.014  1.00128.63           C  
ATOM   2773  O   PHE   354      37.620  64.791  64.496  1.00128.63           O  
ATOM   2774  N   TYR   355      36.714  66.211  62.984  1.00133.96           N  
ATOM   2775  CA  TYR   355      35.972  65.194  62.277  1.00133.96           C  
ATOM   2776  CB  TYR   355      34.462  65.150  62.571  1.00133.96           C  
ATOM   2777  CG  TYR   355      33.913  64.177  61.583  1.00133.96           C  
ATOM   2778  CD1 TYR   355      33.999  62.822  61.803  1.00133.96           C  
ATOM   2779  CD2 TYR   355      33.318  64.624  60.425  1.00133.96           C  
ATOM   2780  CE1 TYR   355      33.505  61.924  60.885  1.00133.96           C  
ATOM   2781  CE2 TYR   355      32.822  63.733  59.504  1.00133.96           C  
ATOM   2782  CZ  TYR   355      32.916  62.382  59.731  1.00133.96           C  
ATOM   2783  OH  TYR   355      32.411  61.470  58.781  1.00133.96           O  
ATOM   2784  C   TYR   355      36.101  65.507  60.813  1.00133.96           C  
ATOM   2785  O   TYR   355      36.021  66.674  60.436  1.00133.96           O  
ATOM   2786  N   LEU   356      36.300  64.499  59.925  1.00219.85           N  
ATOM   2787  CA  LEU   356      36.427  64.946  58.561  1.00219.85           C  
ATOM   2788  CB  LEU   356      37.889  65.208  58.125  1.00219.85           C  
ATOM   2789  CG  LEU   356      38.645  64.007  57.511  1.00219.85           C  
ATOM   2790  CD1 LEU   356      38.480  62.759  58.373  1.00219.85           C  
ATOM   2791  CD2 LEU   356      38.328  63.765  56.029  1.00219.85           C  
ATOM   2792  C   LEU   356      35.819  64.009  57.546  1.00219.85           C  
ATOM   2793  O   LEU   356      35.848  62.786  57.676  1.00219.85           O  
ATOM   2794  N   PRO   357      35.156  64.611  56.580  1.00152.76           N  
ATOM   2795  CA  PRO   357      34.818  63.912  55.358  1.00152.76           C  
ATOM   2796  CD  PRO   357      34.066  65.490  56.978  1.00152.76           C  
ATOM   2797  CB  PRO   357      33.450  64.425  54.903  1.00152.76           C  
ATOM   2798  CG  PRO   357      33.247  65.719  55.700  1.00152.76           C  
ATOM   2799  C   PRO   357      35.935  64.127  54.334  1.00152.76           C  
ATOM   2800  O   PRO   357      36.606  65.151  54.427  1.00152.76           O  
ATOM   2801  N   PRO   358      36.079  63.230  53.369  1.00203.95           N  
ATOM   2802  CA  PRO   358      37.160  63.068  52.378  1.00203.95           C  
ATOM   2803  CD  PRO   358      34.958  62.350  53.095  1.00203.95           C  
ATOM   2804  CB  PRO   358      36.746  61.853  51.554  1.00203.95           C  
ATOM   2805  CG  PRO   358      35.226  61.786  51.701  1.00203.95           C  
ATOM   2806  C   PRO   358      37.876  64.047  51.434  1.00203.95           C  
ATOM   2807  O   PRO   358      39.027  64.359  51.727  1.00203.95           O  
ATOM   2808  N   GLU   359      37.300  64.489  50.278  1.00330.54           N  
ATOM   2809  CA  GLU   359      37.967  65.384  49.336  1.00330.54           C  
ATOM   2810  CB  GLU   359      39.435  65.026  49.065  1.00330.54           C  
ATOM   2811  CG  GLU   359      40.162  66.064  48.210  1.00330.54           C  
ATOM   2812  CD  GLU   359      41.651  65.743  48.238  1.00330.54           C  
ATOM   2813  OE1 GLU   359      42.071  64.820  47.491  1.00330.54           O1-
ATOM   2814  OE2 GLU   359      42.387  66.411  49.013  1.00330.54           O  
ATOM   2815  C   GLU   359      37.226  65.405  48.015  1.00330.54           C  
ATOM   2816  O   GLU   359      36.387  66.272  47.780  1.00330.54           O  
ATOM   2817  N   GLY   360      37.552  64.465  47.092  1.00217.57           N  
ATOM   2818  CA  GLY   360      36.861  64.321  45.828  1.00217.57           C  
ATOM   2819  C   GLY   360      36.112  63.013  45.868  1.00217.57           C  
ATOM   2820  O   GLY   360      36.524  62.074  46.544  1.00217.57           O  
ATOM   2821  N   CYS   361      34.981  62.919  45.124  1.00160.13           N  
ATOM   2822  CA  CYS   361      34.084  61.781  45.070  1.00160.13           C  
ATOM   2823  CB  CYS   361      34.830  60.437  45.026  1.00160.13           C  
ATOM   2824  SG  CYS   361      35.829  60.250  43.521  1.00160.13           S  
ATOM   2825  C   CYS   361      33.249  61.806  46.309  1.00160.13           C  
ATOM   2826  O   CYS   361      32.167  61.226  46.386  1.00160.13           O  
ATOM   2827  N   SER   362      33.756  62.548  47.293  1.00126.73           N  
ATOM   2828  CA  SER   362      33.169  62.892  48.537  1.00126.73           C  
ATOM   2829  CB  SER   362      33.126  61.736  49.542  1.00126.73           C  
ATOM   2830  OG  SER   362      32.260  60.714  49.071  1.00126.73           O  
ATOM   2831  C   SER   362      34.153  63.910  48.967  1.00126.73           C  
ATOM   2832  O   SER   362      35.336  63.634  48.820  1.00126.73           O  
ATOM   2833  N   TYR   363      33.698  65.075  49.475  1.00154.75           N  
ATOM   2834  CA  TYR   363      34.496  66.246  49.769  1.00154.75           C  
ATOM   2835  CB  TYR   363      33.686  67.554  49.866  1.00154.75           C  
ATOM   2836  CG  TYR   363      33.155  67.956  48.535  1.00154.75           C  
ATOM   2837  CD1 TYR   363      32.007  67.387  48.037  1.00154.75           C  
ATOM   2838  CD2 TYR   363      33.802  68.920  47.796  1.00154.75           C  
ATOM   2839  CE1 TYR   363      31.514  67.769  46.813  1.00154.75           C  
ATOM   2840  CE2 TYR   363      33.316  69.308  46.571  1.00154.75           C  
ATOM   2841  CZ  TYR   363      32.170  68.731  46.080  1.00154.75           C  
ATOM   2842  OH  TYR   363      31.670  69.131  44.824  1.00154.75           O  
ATOM   2843  C   TYR   363      35.192  66.157  51.084  1.00154.75           C  
ATOM   2844  O   TYR   363      34.729  65.497  52.012  1.00154.75           O  
TER
END
