
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0356AL380_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356AL380_1-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    A     441      E     350          2.598
LGA    S     442      I     351          1.116
LGA    -       -      V     352           -
LGA    P     443      D     353          3.476
LGA    V     444      F     354          1.921
LGA    S     445      Y     355          0.894
LGA    G     446      L     356          3.085
LGA    L     447      P     357          0.470
LGA    G     448      P     358          3.036
LGA    S     449      E     359          2.268
LGA    K     450      G     360          4.543
LGA    M     451      C     361          1.399
LGA    G     452      S     362          2.333
LGA    L     453      Y     363          3.813
LGA    -       -      R     364           -
LGA    -       -      L     365           -
LGA    D     454      A     366          4.320
LGA    A     455      V     367           #
LGA    T     456      V     368          5.978
LGA    N     457      T     369           #
LGA    K     458      I     370          3.740
LGA    W     459      K     371          2.871
LGA    P     460      K     372          3.371
LGA    -       -      Q     373           -
LGA    -       -      Y     374           -
LGA    -       -      A     375           -
LGA    -       -      G     376           -
LGA    -       -      H     377           -
LGA    G     461      A     378          2.933
LGA    E     462      K     379          3.414
LGA    -       -      R     380           -
LGA    -       -      V     381           -
LGA    T     463      M     382          1.877
LGA    -       -      M     383           -
LGA    Q     464      G     384          1.995
LGA    R     465      V     385          1.741
LGA    E     466      W     386          3.874
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    W     467      Q     391          4.406
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    -       -      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    -       -      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    -       -      K     458           -
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      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)   27  120    5.0     25    3.13     0.00     12.570     0.775

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.938879 * X  +   0.338346 * Y  +   0.063474 * Z  +  35.608143
  Y_new =  -0.183264 * X  +  -0.647335 * Y  +   0.739846 * Z  + 104.565872
  Z_new =   0.291413 * X  +   0.682993 * Y  +   0.669775 * Z  +  31.142712 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.795169   -2.346424  [ DEG:    45.5598   -134.4402 ]
  Theta =  -0.295704   -2.845889  [ DEG:   -16.9426   -163.0574 ]
  Phi   =  -2.948822    0.192770  [ DEG:  -168.9551     11.0449 ]
 
# 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: T0356AL380_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL380_1-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  120   5.0   25   3.13    0.00  12.570
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL380_1-D3
REMARK Aligment from pdb entry: 1xc3A
ATOM      1  N   ALA   441      54.801  72.742  51.922  1.00  0.00              
ATOM      2  CA  ALA   441      54.972  71.723  52.934  1.00  0.00              
ATOM      3  C   ALA   441      54.495  72.178  54.303  1.00  0.00              
ATOM      4  O   ALA   441      54.765  73.300  54.724  1.00  0.00              
ATOM      5  N   SER   442      53.774  71.288  54.977  1.00  0.00              
ATOM      6  CA  SER   442      53.149  71.586  56.270  1.00  0.00              
ATOM      7  C   SER   442      53.675  70.654  57.351  1.00  0.00              
ATOM      8  O   SER   442      53.961  69.487  57.083  1.00  0.00              
ATOM      9  N   PRO   443      53.799  71.180  58.568  1.00  0.00              
ATOM     10  CA  PRO   443      54.143  70.365  59.732  1.00  0.00              
ATOM     11  C   PRO   443      52.923  70.079  60.605  1.00  0.00              
ATOM     12  O   PRO   443      52.010  70.902  60.705  1.00  0.00              
ATOM     13  N   VAL   444      52.915  68.911  61.236  1.00  0.00              
ATOM     14  CA  VAL   444      51.876  68.554  62.188  1.00  0.00              
ATOM     15  C   VAL   444      52.468  68.021  63.472  1.00  0.00              
ATOM     16  O   VAL   444      53.445  67.254  63.453  1.00  0.00              
ATOM     17  N   SER   445      51.897  68.440  64.592  1.00  0.00              
ATOM     18  CA  SER   445      52.278  67.922  65.894  1.00  0.00              
ATOM     19  C   SER   445      51.025  67.362  66.555  1.00  0.00              
ATOM     20  O   SER   445      50.064  68.098  66.800  1.00  0.00              
ATOM     21  N   GLY   446      51.019  66.062  66.813  1.00  0.00              
ATOM     22  CA  GLY   446      49.987  65.473  67.651  1.00  0.00              
ATOM     23  C   GLY   446      50.610  65.206  69.007  1.00  0.00              
ATOM     24  O   GLY   446      51.419  64.275  69.172  1.00  0.00              
ATOM     25  N   LEU   447      50.253  66.066  69.955  1.00  0.00              
ATOM     26  CA  LEU   447      50.829  66.062  71.293  1.00  0.00              
ATOM     27  C   LEU   447      49.973  65.198  72.200  1.00  0.00              
ATOM     28  O   LEU   447      48.822  65.537  72.482  1.00  0.00              
ATOM     29  N   GLY   448      50.540  64.079  72.639  1.00  0.00              
ATOM     30  CA  GLY   448      49.867  63.147  73.531  1.00  0.00              
ATOM     31  C   GLY   448      50.521  63.148  74.887  1.00  0.00              
ATOM     32  O   GLY   448      51.634  63.660  75.060  1.00  0.00              
ATOM     33  N   SER   449      49.822  62.579  75.861  1.00  0.00              
ATOM     34  CA  SER   449      50.350  62.464  77.222  1.00  0.00              
ATOM     35  C   SER   449      51.519  61.495  77.312  1.00  0.00              
ATOM     36  O   SER   449      52.415  61.674  78.143  1.00  0.00              
ATOM     37  N   LYS   450      51.523  60.480  76.443  1.00  0.00              
ATOM     38  CA  LYS   450      52.586  59.462  76.438  1.00  0.00              
ATOM     39  C   LYS   450      53.624  59.664  75.316  1.00  0.00              
ATOM     40  O   LYS   450      54.821  59.459  75.530  1.00  0.00              
ATOM     41  N   MET   451      53.182  60.076  74.130  1.00  0.00              
ATOM     42  CA  MET   451      54.129  60.391  73.054  1.00  0.00              
ATOM     43  C   MET   451      53.699  61.597  72.230  1.00  0.00              
ATOM     44  O   MET   451      52.518  61.982  72.234  1.00  0.00              
ATOM     45  N   GLY   452      54.679  62.194  71.555  1.00  0.00              
ATOM     46  CA  GLY   452      54.452  63.154  70.498  1.00  0.00              
ATOM     47  C   GLY   452      54.677  62.457  69.161  1.00  0.00              
ATOM     48  O   GLY   452      55.606  61.648  69.017  1.00  0.00              
ATOM     49  N   LEU   453      53.828  62.772  68.193  1.00  0.00              
ATOM     50  CA  LEU   453      54.054  62.424  66.799  1.00  0.00              
ATOM     51  C   LEU   453      54.203  63.753  66.053  1.00  0.00              
ATOM     52  O   LEU   453      53.351  64.641  66.184  1.00  0.00              
ATOM     53  N   ASP   454      55.288  63.893  65.295  1.00  0.00              
ATOM     54  CA  ASP   454      55.446  65.020  64.378  1.00  0.00              
ATOM     55  C   ASP   454      55.505  64.480  62.970  1.00  0.00              
ATOM     56  O   ASP   454      56.048  63.391  62.739  1.00  0.00              
ATOM     57  N   ALA   455      54.958  65.246  62.034  1.00  0.00              
ATOM     58  CA  ALA   455      54.894  64.833  60.651  1.00  0.00              
ATOM     59  C   ALA   455      55.073  66.029  59.759  1.00  0.00              
ATOM     60  O   ALA   455      54.764  67.164  60.140  1.00  0.00              
ATOM     61  N   THR   456      55.589  65.751  58.568  1.00  0.00              
ATOM     62  CA  THR   456      55.621  66.704  57.482  1.00  0.00              
ATOM     63  C   THR   456      54.736  66.131  56.392  1.00  0.00              
ATOM     64  O   THR   456      54.815  64.950  56.088  1.00  0.00              
ATOM     65  N   ASN   457      53.881  66.969  55.820  1.00  0.00              
ATOM     66  CA  ASN   457      52.942  66.520  54.812  1.00  0.00              
ATOM     67  C   ASN   457      52.403  67.643  53.952  1.00  0.00              
ATOM     68  O   ASN   457      52.942  68.754  53.948  1.00  0.00              
ATOM     69  N   LYS   458      51.325  67.334  53.235  1.00  0.00              
ATOM     70  CA  LYS   458      50.725  68.234  52.245  1.00  0.00              
ATOM     71  C   LYS   458      49.274  68.542  52.603  1.00  0.00              
ATOM     72  O   LYS   458      48.667  67.847  53.422  1.00  0.00              
ATOM     73  N   TRP   459      48.716  69.563  51.954  1.00  0.00              
ATOM     74  CA  TRP   459      47.341  70.003  52.213  1.00  0.00              
ATOM     75  C   TRP   459      46.308  68.931  51.897  1.00  0.00              
ATOM     76  O   TRP   459      45.216  68.948  52.460  1.00  0.00              
ATOM     77  N   PRO   460      46.665  67.985  51.028  1.00  0.00              
ATOM     78  CA  PRO   460      45.767  66.889  50.676  1.00  0.00              
ATOM     79  C   PRO   460      45.854  65.700  51.646  1.00  0.00              
ATOM     80  O   PRO   460      45.262  64.655  51.402  1.00  0.00              
ATOM     81  N   GLY   461      46.600  65.863  52.738  1.00  0.00              
ATOM     82  CA  GLY   461      46.680  64.836  53.764  1.00  0.00              
ATOM     83  C   GLY   461      47.788  63.821  53.571  1.00  0.00              
ATOM     84  O   GLY   461      47.946  62.930  54.398  1.00  0.00              
ATOM     85  N   GLU   462      48.555  63.943  52.489  1.00  0.00              
ATOM     86  CA  GLU   462      49.727  63.083  52.281  1.00  0.00              
ATOM     87  C   GLU   462      50.747  63.276  53.407  1.00  0.00              
ATOM     88  O   GLU   462      51.129  64.394  53.710  1.00  0.00              
ATOM     89  N   THR   463      51.185  62.181  54.012  1.00  0.00              
ATOM     90  CA  THR   463      52.302  62.222  54.963  1.00  0.00              
ATOM     91  C   THR   463      53.612  61.912  54.219  1.00  0.00              
ATOM     92  O   THR   463      53.776  60.826  53.661  1.00  0.00              
ATOM     93  N   GLN   464      54.524  62.882  54.230  1.00  0.00              
ATOM     94  CA  GLN   464      55.832  62.779  53.570  1.00  0.00              
ATOM     95  C   GLN   464      56.861  62.085  54.475  1.00  0.00              
ATOM     96  O   GLN   464      57.651  61.248  54.030  1.00  0.00              
ATOM     97  N   ARG   465      56.840  62.440  55.754  1.00  0.00              
ATOM     98  CA  ARG   465      57.811  61.940  56.706  1.00  0.00              
ATOM     99  C   ARG   465      57.182  62.017  58.076  1.00  0.00              
ATOM    100  O   ARG   465      56.301  62.846  58.310  1.00  0.00              
ATOM    101  N   GLU   466      57.631  61.172  58.993  1.00  0.00              
ATOM    102  CA  GLU   466      57.170  61.302  60.373  1.00  0.00              
ATOM    103  C   GLU   466      58.183  60.826  61.396  1.00  0.00              
ATOM    104  O   GLU   466      59.114  60.073  61.082  1.00  0.00              
ATOM    105  N   TRP   467      57.989  61.291  62.621  1.00  0.00              
ATOM    106  CA  TRP   467      58.771  60.871  63.759  1.00  0.00              
ATOM    107  C   TRP   467      57.886  60.834  65.007  1.00  0.00              
ATOM    108  O   TRP   467      56.879  61.542  65.089  1.00  0.00              
END
