
#######################################################
#                                                     #
#                        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   24 (  179),  selected   24 , name T0347TS319_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS319_4-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    D     134      S     175          3.297
LGA    P     135      D     176          3.596
LGA    F     136      S     177          2.326
LGA    R     137      F     178          3.292
LGA    -       -      D     179           -
LGA    S     138      D     180          1.857
LGA    L     139      A     181          2.170
LGA    A     140      L     182          2.087
LGA    G     141      A     183          0.923
LGA    A     142      E     184          0.675
LGA    L     143      A     185          1.331
LGA    R     144      M     186          1.615
LGA    M     145      K     187          1.066
LGA    A     146      L     188          0.562
LGA    G     147      A     189          0.895
LGA    G     148      K     190          0.983
LGA    Y     149      S     191          1.328
LGA    -       -      R     192           -
LGA    A     150      E     193          2.918
LGA    K     151      A     194          1.991
LGA    V     152      R     195          1.257
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    I     153      C     201          4.480
LGA    I     154      G     202           #
LGA    -       -      V     203           -
LGA    P     155      E     204          4.289
LGA    F     156      -       -           -
LGA    S     157      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   71    5.0     21    2.35     0.00     25.448     0.858

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.174885 * X  +   0.505499 * Y  +   0.844918 * Z  +   3.219933
  Y_new =   0.832684 * X  +   0.381996 * Y  +  -0.400894 * Z  +  65.895142
  Z_new =  -0.525407 * X  +   0.773660 * Y  +  -0.354115 * Z  +  38.586411 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.000047   -1.141546  [ DEG:   114.5943    -65.4057 ]
  Theta =   0.553194    2.588399  [ DEG:    31.6957    148.3044 ]
  Phi   =   1.363779   -1.777813  [ DEG:    78.1388   -101.8612 ]
 
# 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: T0347TS319_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS319_4-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   71   5.0   21   2.35    0.00  25.448
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS319_4-D2
PFRMAT TS
TARGET T0347
MODEL 4
PARENT N/A
ATOM    631  N   ASP   134       9.028  62.729  -7.905  1.00201.77       1SG 632
ATOM    632  CA  ASP   134       8.051  63.771  -7.741  1.00201.77       1SG 633
ATOM    633  CB  ASP   134       6.986  63.397  -6.705  1.00201.77       1SG 634
ATOM    634  CG  ASP   134       6.302  62.158  -7.268  1.00201.77       1SG 635
ATOM    635  OD1 ASP   134       6.289  62.002  -8.519  1.00201.77       1SG 636
ATOM    636  OD2 ASP   134       5.801  61.336  -6.457  1.00201.77       1SG 637
ATOM    637  C   ASP   134       8.838  64.918  -7.220  1.00201.77       1SG 638
ATOM    638  O   ASP   134       8.989  65.100  -6.018  1.00201.77       1SG 639
ATOM    639  N   PRO   135       9.221  65.749  -8.135  1.00250.93       1SG 640
ATOM    640  CA  PRO   135      10.291  66.692  -7.945  1.00250.93       1SG 641
ATOM    641  CD  PRO   135       8.265  66.202  -9.131  1.00250.93       1SG 642
ATOM    642  CB  PRO   135      10.120  67.749  -9.034  1.00250.93       1SG 643
ATOM    643  CG  PRO   135       8.626  67.674  -9.385  1.00250.93       1SG 644
ATOM    644  C   PRO   135      10.549  67.302  -6.613  1.00250.93       1SG 645
ATOM    645  O   PRO   135       9.925  68.299  -6.256  1.00250.93       1SG 646
ATOM    646  N   PHE   136      11.522  66.704  -5.896  1.00250.42       1SG 647
ATOM    647  CA  PHE   136      12.095  67.237  -4.703  1.00250.42       1SG 648
ATOM    648  CB  PHE   136      11.651  66.545  -3.401  1.00250.42       1SG 649
ATOM    649  CG  PHE   136      10.203  66.834  -3.199  1.00250.42       1SG 650
ATOM    650  CD1 PHE   136       9.800  68.087  -2.816  1.00250.42       1SG 651
ATOM    651  CD2 PHE   136       9.241  65.872  -3.404  1.00250.42       1SG 652
ATOM    652  CE1 PHE   136       8.468  68.371  -2.636  1.00250.42       1SG 653
ATOM    653  CE2 PHE   136       7.905  66.147  -3.225  1.00250.42       1SG 654
ATOM    654  CZ  PHE   136       7.514  67.404  -2.839  1.00250.42       1SG 655
ATOM    655  C   PHE   136      13.532  66.918  -4.888  1.00250.42       1SG 656
ATOM    656  O   PHE   136      14.116  66.136  -4.141  1.00250.42       1SG 657
ATOM    657  N   ARG   137      14.136  67.528  -5.917  1.00109.66       1SG 658
ATOM    658  CA  ARG   137      15.493  67.228  -6.219  1.00109.66       1SG 659
ATOM    659  CB  ARG   137      15.970  67.921  -7.506  1.00109.66       1SG 660
ATOM    660  CG  ARG   137      17.130  67.199  -8.192  1.00109.66       1SG 661
ATOM    661  CD  ARG   137      18.525  67.692  -7.809  1.00109.66       1SG 662
ATOM    662  NE  ARG   137      19.483  66.855  -8.580  1.00109.66       1SG 663
ATOM    663  CZ  ARG   137      19.860  65.641  -8.083  1.00109.66       1SG 664
ATOM    664  NH1 ARG   137      19.402  65.232  -6.865  1.00109.66       1SG 665
ATOM    665  NH2 ARG   137      20.691  64.838  -8.807  1.00109.66       1SG 666
ATOM    666  C   ARG   137      16.299  67.721  -5.067  1.00109.66       1SG 667
ATOM    667  O   ARG   137      17.242  67.062  -4.635  1.00109.66       1SG 668
ATOM    668  N   SER   138      15.924  68.898  -4.529  1.00 69.54       1SG 669
ATOM    669  CA  SER   138      16.644  69.478  -3.432  1.00 69.54       1SG 670
ATOM    670  CB  SER   138      16.070  70.831  -2.967  1.00 69.54       1SG 671
ATOM    671  OG  SER   138      16.830  71.340  -1.879  1.00 69.54       1SG 672
ATOM    672  C   SER   138      16.548  68.559  -2.262  1.00 69.54       1SG 673
ATOM    673  O   SER   138      17.533  68.318  -1.569  1.00 69.54       1SG 674
ATOM    674  N   LEU   139      15.341  68.018  -2.013  1.00 69.92       1SG 675
ATOM    675  CA  LEU   139      15.120  67.182  -0.871  1.00 69.92       1SG 676
ATOM    676  CB  LEU   139      13.640  66.815  -0.686  1.00 69.92       1SG 677
ATOM    677  CG  LEU   139      12.760  68.065  -0.499  1.00 69.92       1SG 678
ATOM    678  CD2 LEU   139      13.457  69.107   0.390  1.00 69.92       1SG 679
ATOM    679  CD1 LEU   139      11.341  67.707  -0.030  1.00 69.92       1SG 680
ATOM    680  C   LEU   139      15.910  65.920  -0.994  1.00 69.92       1SG 681
ATOM    681  O   LEU   139      16.502  65.464  -0.019  1.00 69.92       1SG 682
ATOM    682  N   ALA   140      15.948  65.322  -2.199  1.00 35.28       1SG 683
ATOM    683  CA  ALA   140      16.639  64.077  -2.376  1.00 35.28       1SG 684
ATOM    684  CB  ALA   140      16.536  63.530  -3.810  1.00 35.28       1SG 685
ATOM    685  C   ALA   140      18.085  64.283  -2.069  1.00 35.28       1SG 686
ATOM    686  O   ALA   140      18.698  63.465  -1.386  1.00 35.28       1SG 687
ATOM    687  N   GLY   141      18.667  65.398  -2.544  1.00 14.97       1SG 688
ATOM    688  CA  GLY   141      20.059  65.632  -2.298  1.00 14.97       1SG 689
ATOM    689  C   GLY   141      20.242  65.733  -0.823  1.00 14.97       1SG 690
ATOM    690  O   GLY   141      21.232  65.256  -0.269  1.00 14.97       1SG 691
ATOM    691  N   ALA   142      19.277  66.379  -0.151  1.00 47.52       1SG 692
ATOM    692  CA  ALA   142      19.365  66.572   1.261  1.00 47.52       1SG 693
ATOM    693  CB  ALA   142      18.171  67.356   1.834  1.00 47.52       1SG 694
ATOM    694  C   ALA   142      19.375  65.235   1.923  1.00 47.52       1SG 695
ATOM    695  O   ALA   142      20.135  65.023   2.863  1.00 47.52       1SG 696
ATOM    696  N   LEU   143      18.528  64.291   1.466  1.00 96.17       1SG 697
ATOM    697  CA  LEU   143      18.498  63.017   2.125  1.00 96.17       1SG 698
ATOM    698  CB  LEU   143      17.418  62.049   1.609  1.00 96.17       1SG 699
ATOM    699  CG  LEU   143      15.992  62.410   2.054  1.00 96.17       1SG 700
ATOM    700  CD2 LEU   143      15.945  62.723   3.559  1.00 96.17       1SG 701
ATOM    701  CD1 LEU   143      14.995  61.314   1.646  1.00 96.17       1SG 702
ATOM    702  C   LEU   143      19.799  62.318   1.949  1.00 96.17       1SG 703
ATOM    703  O   LEU   143      20.395  61.861   2.917  1.00 96.17       1SG 704
ATOM    704  N   ARG   144      20.304  62.258   0.706  1.00129.14       1SG 705
ATOM    705  CA  ARG   144      21.499  61.505   0.488  1.00129.14       1SG 706
ATOM    706  CB  ARG   144      21.926  61.461  -0.988  1.00129.14       1SG 707
ATOM    707  CG  ARG   144      22.229  62.822  -1.611  1.00129.14       1SG 708
ATOM    708  CD  ARG   144      22.445  62.727  -3.121  1.00129.14       1SG 709
ATOM    709  NE  ARG   144      23.410  61.615  -3.352  1.00129.14       1SG 710
ATOM    710  CZ  ARG   144      24.752  61.841  -3.260  1.00129.14       1SG 711
ATOM    711  NH1 ARG   144      25.211  63.082  -2.933  1.00129.14       1SG 712
ATOM    712  NH2 ARG   144      25.633  60.821  -3.479  1.00129.14       1SG 713
ATOM    713  C   ARG   144      22.592  62.127   1.291  1.00129.14       1SG 714
ATOM    714  O   ARG   144      23.434  61.433   1.859  1.00129.14       1SG 715
ATOM    715  N   MET   145      22.598  63.468   1.367  1.00159.91       1SG 716
ATOM    716  CA  MET   145      23.602  64.171   2.104  1.00159.91       1SG 717
ATOM    717  CB  MET   145      23.372  65.692   2.065  1.00159.91       1SG 718
ATOM    718  CG  MET   145      24.293  66.502   2.978  1.00159.91       1SG 719
ATOM    719  SD  MET   145      23.819  66.548   4.736  1.00159.91       1SG 720
ATOM    720  CE  MET   145      22.505  67.786   4.531  1.00159.91       1SG 721
ATOM    721  C   MET   145      23.513  63.744   3.531  1.00159.91       1SG 722
ATOM    722  O   MET   145      24.522  63.451   4.167  1.00159.91       1SG 723
ATOM    723  N   ALA   146      22.279  63.686   4.056  1.00133.53       1SG 724
ATOM    724  CA  ALA   146      22.019  63.316   5.416  1.00133.53       1SG 725
ATOM    725  CB  ALA   146      20.532  63.418   5.799  1.00133.53       1SG 726
ATOM    726  C   ALA   146      22.438  61.901   5.589  1.00133.53       1SG 727
ATOM    727  O   ALA   146      22.849  61.492   6.670  1.00133.53       1SG 728
ATOM    728  N   GLY   147      22.295  61.084   4.539  1.00 65.25       1SG 729
ATOM    729  CA  GLY   147      22.670  59.715   4.664  1.00 65.25       1SG 730
ATOM    730  C   GLY   147      24.132  59.670   4.962  1.00 65.25       1SG 731
ATOM    731  O   GLY   147      24.569  58.890   5.802  1.00 65.25       1SG 732
ATOM    732  N   GLY   148      24.942  60.481   4.256  1.00158.28       1SG 733
ATOM    733  CA  GLY   148      26.353  60.445   4.505  1.00158.28       1SG 734
ATOM    734  C   GLY   148      26.690  60.975   5.867  1.00158.28       1SG 735
ATOM    735  O   GLY   148      27.436  60.337   6.610  1.00158.28       1SG 736
ATOM    736  N   TYR   149      26.177  62.174   6.218  1.00 74.46       1SG 737
ATOM    737  CA  TYR   149      26.525  62.789   7.473  1.00 74.46       1SG 738
ATOM    738  CB  TYR   149      26.067  64.256   7.563  1.00 74.46       1SG 739
ATOM    739  CG  TYR   149      26.814  65.097   6.584  1.00 74.46       1SG 740
ATOM    740  CD1 TYR   149      26.499  65.057   5.244  1.00 74.46       1SG 741
ATOM    741  CD2 TYR   149      27.804  65.954   7.011  1.00 74.46       1SG 742
ATOM    742  CE1 TYR   149      27.184  65.839   4.343  1.00 74.46       1SG 743
ATOM    743  CE2 TYR   149      28.492  66.738   6.116  1.00 74.46       1SG 744
ATOM    744  CZ  TYR   149      28.176  66.684   4.780  1.00 74.46       1SG 745
ATOM    745  OH  TYR   149      28.874  67.485   3.853  1.00 74.46       1SG 746
ATOM    746  C   TYR   149      25.883  62.100   8.642  1.00 74.46       1SG 747
ATOM    747  O   TYR   149      26.553  61.676   9.584  1.00 74.46       1SG 748
ATOM    748  N   ALA   150      24.547  61.955   8.580  1.00 58.72       1SG 749
ATOM    749  CA  ALA   150      23.726  61.440   9.640  1.00 58.72       1SG 750
ATOM    750  CB  ALA   150      22.218  61.532   9.337  1.00 58.72       1SG 751
ATOM    751  C   ALA   150      24.025  60.002   9.916  1.00 58.72       1SG 752
ATOM    752  O   ALA   150      24.121  59.593  11.074  1.00 58.72       1SG 753
ATOM    753  N   LYS   151      24.217  59.199   8.856  1.00168.17       1SG 754
ATOM    754  CA  LYS   151      24.324  57.783   9.047  1.00168.17       1SG 755
ATOM    755  CB  LYS   151      24.466  56.960   7.756  1.00168.17       1SG 756
ATOM    756  CG  LYS   151      25.900  56.948   7.220  1.00168.17       1SG 757
ATOM    757  CD  LYS   151      26.190  55.817   6.233  1.00168.17       1SG 758
ATOM    758  CE  LYS   151      26.473  56.300   4.811  1.00168.17       1SG 759
ATOM    759  NZ  LYS   151      25.231  56.779   4.166  1.00168.17       1SG 760
ATOM    760  C   LYS   151      25.530  57.447   9.848  1.00168.17       1SG 761
ATOM    761  O   LYS   151      26.600  58.035   9.692  1.00168.17       1SG 762
ATOM    762  N   VAL   152      25.362  56.460  10.743  1.00 78.28       1SG 763
ATOM    763  CA  VAL   152      26.466  55.946  11.482  1.00 78.28       1SG 764
ATOM    764  CB  VAL   152      26.035  54.976  12.542  1.00 78.28       1SG 765
ATOM    765  CG1 VAL   152      27.286  54.403  13.227  1.00 78.28       1SG 766
ATOM    766  CG2 VAL   152      25.062  55.698  13.495  1.00 78.28       1SG 767
ATOM    767  C   VAL   152      27.246  55.195  10.459  1.00 78.28       1SG 768
ATOM    768  O   VAL   152      26.673  54.553   9.580  1.00 78.28       1SG 769
ATOM    769  N   ILE   153      28.582  55.249  10.531  1.00150.51       1SG 770
ATOM    770  CA  ILE   153      29.296  54.600   9.479  1.00150.51       1SG 771
ATOM    771  CB  ILE   153      30.203  55.510   8.703  1.00150.51       1SG 772
ATOM    772  CG2 ILE   153      31.429  55.819   9.577  1.00150.51       1SG 773
ATOM    773  CG1 ILE   153      30.552  54.871   7.350  1.00150.51       1SG 774
ATOM    774  CD1 ILE   153      29.335  54.663   6.445  1.00150.51       1SG 775
ATOM    775  C   ILE   153      30.106  53.502  10.070  1.00150.51       1SG 776
ATOM    776  O   ILE   153      30.133  53.302  11.284  1.00150.51       1SG 777
ATOM    777  N   ILE   154      30.763  52.732   9.185  1.00119.52       1SG 778
ATOM    778  CA  ILE   154      31.522  51.590   9.581  1.00119.52       1SG 779
ATOM    779  CB  ILE   154      31.992  50.725   8.422  1.00119.52       1SG 780
ATOM    780  CG2 ILE   154      32.574  51.568   7.275  1.00119.52       1SG 781
ATOM    781  CG1 ILE   154      32.863  49.564   8.932  1.00119.52       1SG 782
ATOM    782  CD1 ILE   154      33.110  48.484   7.878  1.00119.52       1SG 783
ATOM    783  C   ILE   154      32.627  51.975  10.524  1.00119.52       1SG 784
ATOM    784  O   ILE   154      32.888  51.210  11.449  1.00119.52       1SG 785
ATOM    785  N   PRO   155      33.307  53.084  10.401  1.00 58.28       1SG 786
ATOM    786  CA  PRO   155      34.324  53.363  11.377  1.00 58.28       1SG 787
ATOM    787  CD  PRO   155      33.608  53.697   9.120  1.00 58.28       1SG 788
ATOM    788  CB  PRO   155      35.196  54.463  10.780  1.00 58.28       1SG 789
ATOM    789  CG  PRO   155      35.017  54.288   9.264  1.00 58.28       1SG 790
ATOM    790  C   PRO   155      33.678  53.758  12.666  1.00 58.28       1SG 791
ATOM    791  O   PRO   155      32.562  54.273  12.635  1.00 58.28       1SG 792
ATOM    792  N   PHE   156      34.346  53.510  13.810  1.00 92.59       1SG 793
ATOM    793  CA  PHE   156      33.781  53.912  15.065  1.00 92.59       1SG 794
ATOM    794  CB  PHE   156      33.014  52.775  15.774  1.00 92.59       1SG 795
ATOM    795  CG  PHE   156      32.505  53.283  17.080  1.00 92.59       1SG 796
ATOM    796  CD1 PHE   156      31.492  54.213  17.134  1.00 92.59       1SG 797
ATOM    797  CD2 PHE   156      33.065  52.845  18.259  1.00 92.59       1SG 798
ATOM    798  CE1 PHE   156      31.039  54.681  18.343  1.00 92.59       1SG 799
ATOM    799  CE2 PHE   156      32.613  53.304  19.472  1.00 92.59       1SG 800
ATOM    800  CZ  PHE   156      31.597  54.224  19.514  1.00 92.59       1SG 801
ATOM    801  C   PHE   156      34.893  54.427  15.933  1.00 92.59       1SG 802
ATOM    802  O   PHE   156      36.059  54.090  15.733  1.00 92.59       1SG 803
ATOM    803  N   SER   157      34.561  55.297  16.911  1.00 47.74       1SG 804
ATOM    804  CA  SER   157      35.558  55.867  17.779  1.00 47.74       1SG 805
ATOM    805  CB  SER   157      35.001  56.979  18.688  1.00 47.74       1SG 806
ATOM    806  OG  SER   157      36.024  57.501  19.527  1.00 47.74       1SG 807
ATOM    807  C   SER   157      36.120  54.780  18.689  1.00 47.74       1SG 808
ATOM    808  O   SER   157      37.002  55.111  19.526  1.00 47.74       1SG 809
ATOM    809  OXT SER   157      35.681  53.606  18.563  1.00 47.74       1SG 810
TER
END
