
#######################################################
#                                                     #
#                        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   23 (  185),  selected   23 , name T0356TS135_3-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS135_3-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    F     348      R     380          2.799
LGA    P     349      V     381          2.853
LGA    E     350      M     382          3.430
LGA    -       -      M     383           -
LGA    -       -      G     384           -
LGA    -       -      V     385           -
LGA    I     351      W     386          1.371
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    V     352      F     392          4.655
LGA    D     353      M     393          1.808
LGA    F     354      Y     394          2.552
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    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
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    Y     355      D     436          2.469
LGA    L     356      Y     437          3.575
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    P     357      L     447          2.171
LGA    P     358      G     448          1.414
LGA    E     359      S     449          2.108
LGA    G     360      K     450          1.603
LGA    C     361      M     451          1.238
LGA    S     362      G     452          1.251
LGA    Y     363      L     453          1.154
LGA    R     364      D     454          1.111
LGA    L     365      A     455          1.384
LGA    A     366      T     456          2.322
LGA    V     367      N     457          2.089
LGA    V     368      K     458          3.824
LGA    -       -      W     459           -
LGA    T     369      P     460           #
LGA    I     370      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  120    5.0     21    2.45     0.00     13.967     0.825

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.740016 * X  +  -0.209684 * Y  +   0.639069 * Z  + -42.709507
  Y_new =   0.638915 * X  +  -0.077728 * Y  +  -0.765340 * Z  +  93.828766
  Z_new =   0.210153 * X  +   0.974675 * Y  +   0.076450 * Z  +  28.028643 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.492520   -1.649073  [ DEG:    85.5151    -94.4849 ]
  Theta =  -0.211732   -2.929861  [ DEG:   -12.1313   -167.8687 ]
  Phi   =   0.712211   -2.429382  [ DEG:    40.8067   -139.1933 ]
 
# 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: T0356TS135_3-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS135_3-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  120   5.0   21   2.45    0.00  13.967
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS135_3-D3
PFRMAT TS
TARGET T0356
MODEL 3 REFINED
PARENT 1gvhA
ATOM   2713  N   PHE   348      54.091  62.184  51.246  1.00  5.00
ATOM   2714  CA  PHE   348      55.033  63.248  51.344  1.00  5.00
ATOM   2715  C   PHE   348      55.333  63.398  52.808  1.00  5.00
ATOM   2716  O   PHE   348      55.845  62.415  53.335  1.00  5.00
ATOM   2717  CB  PHE   348      54.597  64.551  50.644  1.00  5.00
ATOM   2718  CG  PHE   348      54.385  64.303  49.199  1.00  5.00
ATOM   2719  CD1 PHE   348      53.162  63.859  48.751  1.00  5.00
ATOM   2720  CD2 PHE   348      55.397  64.521  48.294  1.00  5.00
ATOM   2721  CE1 PHE   348      52.947  63.636  47.414  1.00  5.00
ATOM   2722  CE2 PHE   348      55.187  64.298  46.956  1.00  5.00
ATOM   2723  CZ  PHE   348      53.961  63.855  46.515  1.00  5.00
ATOM   2724  N   PRO   349      55.144  64.496  53.523  1.00  5.00
ATOM   2725  CA  PRO   349      55.584  64.503  54.888  1.00  5.00
ATOM   2726  C   PRO   349      54.931  63.414  55.672  1.00  5.00
ATOM   2727  O   PRO   349      53.723  63.469  55.895  1.00  5.00
ATOM   2728  CB  PRO   349      55.179  65.866  55.445  1.00  5.00
ATOM   2729  CG  PRO   349      54.380  66.526  54.301  1.00  5.00
ATOM   2730  CD  PRO   349      53.968  65.346  53.427  1.00  5.00
ATOM   2731  N   GLU   350      55.725  62.419  56.098  1.00  5.00
ATOM   2732  CA  GLU   350      55.250  61.351  56.918  1.00  5.00
ATOM   2733  C   GLU   350      56.165  60.196  56.727  1.00  5.00
ATOM   2734  O   GLU   350      55.977  59.389  55.818  1.00  5.00
ATOM   2735  CB  GLU   350      53.846  60.830  56.559  1.00  5.00
ATOM   2736  CG  GLU   350      53.490  59.510  57.249  1.00  5.00
ATOM   2737  CD  GLU   350      53.081  59.769  58.691  1.00  5.00
ATOM   2738  OE1 GLU   350      52.728  60.936  59.010  1.00  5.00
ATOM   2739  OE2 GLU   350      53.106  58.797  59.493  1.00  5.00
ATOM   2740  N   ILE   351      57.196  60.087  57.576  1.00  5.00
ATOM   2741  CA  ILE   351      57.991  58.901  57.533  1.00  5.00
ATOM   2742  C   ILE   351      58.065  58.482  58.958  1.00  5.00
ATOM   2743  O   ILE   351      58.248  59.325  59.833  1.00  5.00
ATOM   2744  CB  ILE   351      59.411  59.060  57.064  1.00  5.00
ATOM   2745  CG1 ILE   351      60.229  59.920  58.035  1.00  5.00
ATOM   2746  CG2 ILE   351      59.388  59.590  55.621  1.00  5.00
ATOM   2747  CD1 ILE   351      61.732  59.722  57.854  1.00  5.00
ATOM   2748  N   VAL   352      57.905  57.181  59.252  1.00  5.00
ATOM   2749  CA  VAL   352      57.939  56.844  60.643  1.00  5.00
ATOM   2750  C   VAL   352      58.869  55.702  60.886  1.00  5.00
ATOM   2751  O   VAL   352      58.955  54.756  60.103  1.00  5.00
ATOM   2752  CB  VAL   352      56.612  56.422  61.186  1.00  5.00
ATOM   2753  CG1 VAL   352      56.102  55.250  60.333  1.00  5.00
ATOM   2754  CG2 VAL   352      56.795  56.060  62.670  1.00  5.00
ATOM   2755  N   ASP   353      59.602  55.792  62.010  1.00  5.00
ATOM   2756  CA  ASP   353      60.486  54.742  62.403  1.00  5.00
ATOM   2757  C   ASP   353      60.077  54.353  63.787  1.00  5.00
ATOM   2758  O   ASP   353      59.911  55.204  64.660  1.00  5.00
ATOM   2759  CB  ASP   353      61.962  55.169  62.452  1.00  5.00
ATOM   2760  CG  ASP   353      62.832  53.918  62.409  1.00  5.00
ATOM   2761  OD1 ASP   353      62.565  53.033  61.552  1.00  5.00
ATOM   2762  OD2 ASP   353      63.773  53.830  63.240  1.00  5.00
ATOM   2763  N   PHE   354      59.891  53.042  64.024  1.00  5.00
ATOM   2764  CA  PHE   354      59.449  52.609  65.314  1.00  5.00
ATOM   2765  C   PHE   354      60.584  51.862  65.926  1.00  5.00
ATOM   2766  O   PHE   354      61.193  51.013  65.278  1.00  5.00
ATOM   2767  CB  PHE   354      58.295  51.602  65.218  1.00  5.00
ATOM   2768  CG  PHE   354      57.229  52.223  64.386  1.00  5.00
ATOM   2769  CD1 PHE   354      57.266  52.108  63.015  1.00  5.00
ATOM   2770  CD2 PHE   354      56.202  52.920  64.976  1.00  5.00
ATOM   2771  CE1 PHE   354      56.284  52.680  62.242  1.00  5.00
ATOM   2772  CE2 PHE   354      55.219  53.489  64.207  1.00  5.00
ATOM   2773  CZ  PHE   354      55.257  53.375  62.840  1.00  5.00
ATOM   2774  N   TYR   355      60.945  52.183  67.182  1.00  5.00
ATOM   2775  CA  TYR   355      61.958  51.387  67.803  1.00  5.00
ATOM   2776  C   TYR   355      61.367  50.040  68.074  1.00  5.00
ATOM   2777  O   TYR   355      62.027  49.019  67.890  1.00  5.00
ATOM   2778  CB  TYR   355      62.543  51.986  69.086  1.00  5.00
ATOM   2779  CG  TYR   355      63.295  53.178  68.609  1.00  5.00
ATOM   2780  CD1 TYR   355      64.484  53.018  67.933  1.00  5.00
ATOM   2781  CD2 TYR   355      62.794  54.445  68.785  1.00  5.00
ATOM   2782  CE1 TYR   355      65.186  54.107  67.473  1.00  5.00
ATOM   2783  CE2 TYR   355      63.491  55.537  68.329  1.00  5.00
ATOM   2784  CZ  TYR   355      64.690  55.372  67.678  1.00  5.00
ATOM   2785  OH  TYR   355      65.402  56.496  67.210  1.00  5.00
ATOM   2786  N   LEU   356      60.091  50.018  68.519  1.00  5.00
ATOM   2787  CA  LEU   356      59.382  48.798  68.802  1.00  5.00
ATOM   2788  C   LEU   356      58.861  48.236  67.513  1.00  5.00
ATOM   2789  O   LEU   356      58.906  48.869  66.458  1.00  5.00
ATOM   2790  CB  LEU   356      58.198  48.949  69.780  1.00  5.00
ATOM   2791  CG  LEU   356      58.632  49.286  71.220  1.00  5.00
ATOM   2792  CD1 LEU   356      59.337  50.647  71.280  1.00  5.00
ATOM   2793  CD2 LEU   356      57.457  49.184  72.208  1.00  5.00
ATOM   2794  N   PRO   357      58.410  47.015  67.600  1.00  5.00
ATOM   2795  CA  PRO   357      57.977  46.265  66.448  1.00  5.00
ATOM   2796  C   PRO   357      56.834  46.756  65.612  1.00  5.00
ATOM   2797  O   PRO   357      56.940  46.649  64.390  1.00  5.00
ATOM   2798  CB  PRO   357      57.746  44.842  66.957  1.00  5.00
ATOM   2799  CG  PRO   357      58.706  44.716  68.153  1.00  5.00
ATOM   2800  CD  PRO   357      58.830  46.151  68.689  1.00  5.00
ATOM   2801  N   PRO   358      55.784  47.284  66.152  1.00  5.00
ATOM   2802  CA  PRO   358      54.659  47.553  65.293  1.00  5.00
ATOM   2803  C   PRO   358      54.744  48.752  64.424  1.00  5.00
ATOM   2804  O   PRO   358      55.522  49.652  64.722  1.00  5.00
ATOM   2805  CB  PRO   358      53.418  47.530  66.194  1.00  5.00
ATOM   2806  CG  PRO   358      53.967  47.513  67.632  1.00  5.00
ATOM   2807  CD  PRO   358      55.357  46.881  67.480  1.00  5.00
ATOM   2808  N   GLU   359      53.950  48.763  63.334  1.00  5.00
ATOM   2809  CA  GLU   359      53.881  49.881  62.438  1.00  5.00
ATOM   2810  C   GLU   359      52.772  50.745  62.930  1.00  5.00
ATOM   2811  O   GLU   359      52.128  50.426  63.926  1.00  5.00
ATOM   2812  CB  GLU   359      53.559  49.544  60.971  1.00  5.00
ATOM   2813  CG  GLU   359      52.160  48.968  60.740  1.00  5.00
ATOM   2814  CD  GLU   359      51.893  48.979  59.240  1.00  5.00
ATOM   2815  OE1 GLU   359      52.842  49.285  58.468  1.00  5.00
ATOM   2816  OE2 GLU   359      50.731  48.688  58.846  1.00  5.00
ATOM   2817  N   GLY   360      52.528  51.884  62.257  1.00  5.00
ATOM   2818  CA  GLY   360      51.512  52.759  62.761  1.00  5.00
ATOM   2819  C   GLY   360      50.333  52.751  61.850  1.00  5.00
ATOM   2820  O   GLY   360      50.409  52.343  60.692  1.00  5.00
ATOM   2821  N   CYS   361      49.190  53.216  62.386  1.00  5.00
ATOM   2822  CA  CYS   361      47.993  53.282  61.614  1.00  5.00
ATOM   2823  C   CYS   361      47.853  54.701  61.199  1.00  5.00
ATOM   2824  O   CYS   361      47.908  55.609  62.024  1.00  5.00
ATOM   2825  CB  CYS   361      46.737  52.892  62.413  1.00  5.00
ATOM   2826  SG  CYS   361      46.802  51.168  62.992  1.00  5.00
ATOM   2827  N   SER   362      47.691  54.930  59.888  1.00  5.00
ATOM   2828  CA  SER   362      47.559  56.280  59.455  1.00  5.00
ATOM   2829  C   SER   362      46.156  56.441  58.991  1.00  5.00
ATOM   2830  O   SER   362      45.647  55.640  58.208  1.00  5.00
ATOM   2831  CB  SER   362      48.496  56.635  58.287  1.00  5.00
ATOM   2832  OG  SER   362      49.849  56.541  58.710  1.00  5.00
ATOM   2833  N   TYR   363      45.483  57.487  59.498  1.00  5.00
ATOM   2834  CA  TYR   363      44.139  57.733  59.086  1.00  5.00
ATOM   2835  C   TYR   363      44.180  59.051  58.391  1.00  5.00
ATOM   2836  O   TYR   363      44.536  60.065  58.987  1.00  5.00
ATOM   2837  CB  TYR   363      43.165  57.850  60.272  1.00  5.00
ATOM   2838  CG  TYR   363      41.789  57.919  59.716  1.00  5.00
ATOM   2839  CD1 TYR   363      41.180  56.772  59.266  1.00  5.00
ATOM   2840  CD2 TYR   363      41.105  59.111  59.647  1.00  5.00
ATOM   2841  CE1 TYR   363      39.905  56.812  58.752  1.00  5.00
ATOM   2842  CE2 TYR   363      39.829  59.156  59.135  1.00  5.00
ATOM   2843  CZ  TYR   363      39.231  58.007  58.678  1.00  5.00
ATOM   2844  OH  TYR   363      37.924  58.048  58.149  1.00  5.00
ATOM   2845  N   ARG   364      43.818  59.070  57.094  1.00  5.00
ATOM   2846  CA  ARG   364      43.890  60.292  56.353  1.00  5.00
ATOM   2847  C   ARG   364      42.493  60.735  56.102  1.00  5.00
ATOM   2848  O   ARG   364      41.603  59.915  55.883  1.00  5.00
ATOM   2849  CB  ARG   364      44.543  60.141  54.969  1.00  5.00
ATOM   2850  CG  ARG   364      46.041  59.833  55.003  1.00  5.00
ATOM   2851  CD  ARG   364      46.630  59.571  53.615  1.00  5.00
ATOM   2852  NE  ARG   364      46.072  58.274  53.138  1.00  5.00
ATOM   2853  CZ  ARG   364      46.693  57.102  53.459  1.00  5.00
ATOM   2854  NH1 ARG   364      47.848  57.117  54.190  1.00  5.00
ATOM   2855  NH2 ARG   364      46.160  55.913  53.055  1.00  5.00
ATOM   2856  N   LEU   365      42.254  62.055  56.167  1.00  5.00
ATOM   2857  CA  LEU   365      40.930  62.507  55.874  1.00  5.00
ATOM   2858  C   LEU   365      41.085  63.568  54.829  1.00  5.00
ATOM   2859  O   LEU   365      41.647  64.627  55.101  1.00  5.00
ATOM   2860  CB  LEU   365      40.238  63.139  57.098  1.00  5.00
ATOM   2861  CG  LEU   365      38.716  63.368  56.967  1.00  5.00
ATOM   2862  CD1 LEU   365      38.165  64.059  58.224  1.00  5.00
ATOM   2863  CD2 LEU   365      38.320  64.094  55.672  1.00  5.00
ATOM   2864  N   ALA   366      40.589  63.314  53.600  1.00  5.00
ATOM   2865  CA  ALA   366      40.691  64.304  52.564  1.00  5.00
ATOM   2866  C   ALA   366      39.353  64.393  51.902  1.00  5.00
ATOM   2867  O   ALA   366      38.650  63.392  51.778  1.00  5.00
ATOM   2868  CB  ALA   366      41.712  63.955  51.467  1.00  5.00
ATOM   2869  N   VAL   367      38.964  65.609  51.465  1.00  5.00
ATOM   2870  CA  VAL   367      37.679  65.752  50.842  1.00  5.00
ATOM   2871  C   VAL   367      37.818  66.794  49.774  1.00  5.00
ATOM   2872  O   VAL   367      38.764  67.580  49.773  1.00  5.00
ATOM   2873  CB  VAL   367      36.624  66.208  51.811  1.00  5.00
ATOM   2874  CG1 VAL   367      35.279  66.342  51.081  1.00  5.00
ATOM   2875  CG2 VAL   367      36.600  65.231  52.997  1.00  5.00
ATOM   2876  N   VAL   368      36.876  66.808  48.803  1.00  5.00
ATOM   2877  CA  VAL   368      36.945  67.768  47.743  1.00  5.00
ATOM   2878  C   VAL   368      35.553  68.260  47.485  1.00  5.00
ATOM   2879  O   VAL   368      34.577  67.591  47.820  1.00  5.00
ATOM   2880  CB  VAL   368      37.466  67.178  46.459  1.00  5.00
ATOM   2881  CG1 VAL   368      37.457  68.257  45.364  1.00  5.00
ATOM   2882  CG2 VAL   368      38.863  66.592  46.724  1.00  5.00
ATOM   2883  N   THR   369      35.434  69.474  46.905  1.00  5.00
ATOM   2884  CA  THR   369      34.153  70.024  46.572  1.00  5.00
ATOM   2885  C   THR   369      34.180  70.294  45.101  1.00  5.00
ATOM   2886  O   THR   369      35.241  70.543  44.531  1.00  5.00
ATOM   2887  CB  THR   369      33.871  71.333  47.248  1.00  5.00
ATOM   2888  OG1 THR   369      33.950  71.183  48.658  1.00  5.00
ATOM   2889  CG2 THR   369      32.461  71.804  46.844  1.00  5.00
ATOM   2890  N   ILE   370      33.004  70.214  44.444  1.00  5.00
ATOM   2891  CA  ILE   370      32.912  70.480  43.036  1.00  5.00
ATOM   2892  C   ILE   370      31.840  71.509  42.850  1.00  5.00
ATOM   2893  O   ILE   370      30.793  71.455  43.494  1.00  5.00
ATOM   2894  CB  ILE   370      32.532  69.274  42.227  1.00  5.00
ATOM   2895  CG1 ILE   370      31.130  68.783  42.631  1.00  5.00
ATOM   2896  CG2 ILE   370      33.635  68.216  42.401  1.00  5.00
ATOM   2897  CD1 ILE   370      30.543  67.756  41.664  1.00  5.00
TER
END
