
#######################################################
#                                                     #
#                        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 (  113),  selected   23 , name T0347TS261_1_3-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS261_1_3-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      -       -           -
LGA    V      24      -       -           -
LGA    G      25      P       7          1.415
LGA    F      26      -       -           -
LGA    R      27      -       -           -
LGA    E      28      R       8          3.202
LGA    V      29      L       9          2.859
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    H      93      A      23          2.221
LGA    L      94      V      24          2.597
LGA    G      95      G      25          0.688
LGA    K      96      F      26          3.150
LGA    -       -      R      27           -
LGA    D      97      E      28          1.586
LGA    E      98      V      29          2.517
LGA    F      99      E      30          2.376
LGA    W     100      L      31          1.697
LGA    S     101      K      32          1.499
LGA    V     102      R      33          1.769
LGA    M     103      K      34          2.704
LGA    D     104      E      35          2.723
LGA    H     105      W      36          1.458
LGA    R     106      R      37          1.662
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    N     107      A      74          5.425
LGA    L     108      L      75          4.001
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   89    5.0     19    2.62    15.79     16.134     0.699

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.493263 * X  +   0.553502 * Y  +   0.671064 * Z  + -55.895996
  Y_new =   0.706185 * X  +   0.195655 * Y  +  -0.680457 * Z  +  36.575512
  Z_new =  -0.507931 * X  +   0.809540 * Y  +  -0.294366 * Z  +  -2.559835 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.919554   -1.222039  [ DEG:   109.9823    -70.0177 ]
  Theta =   0.532782    2.608811  [ DEG:    30.5261    149.4739 ]
  Phi   =   0.961084   -2.180508  [ DEG:    55.0661   -124.9339 ]
 
# 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: T0347TS261_1_3-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS261_1_3-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   89   5.0   19   2.62   15.79  16.134
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS261_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0347
PARENT 2gok_A
ATOM    786  N   ALA    23      16.714  24.170  -2.090  1.00  4.96
ATOM    787  CA  ALA    23      16.552  22.785  -2.526  1.00  4.96
ATOM    788  C   ALA    23      15.299  22.633  -3.375  1.00  4.96
ATOM    789  O   ALA    23      15.263  21.818  -4.291  1.00  4.96
ATOM    790  CB  ALA    23      16.444  21.828  -1.328  1.00  4.96
ATOM    791  N   VAL    24      14.266  23.405  -3.055  1.00  4.37
ATOM    792  CA  VAL    24      13.034  23.344  -3.827  1.00  4.37
ATOM    793  C   VAL    24      13.330  23.798  -5.261  1.00  4.37
ATOM    794  O   VAL    24      12.905  23.167  -6.233  1.00  4.37
ATOM    795  CB  VAL    24      11.972  24.252  -3.206  1.00  4.37
ATOM    796  N   GLY    25      14.065  24.895  -5.392  1.00  1.00
ATOM    797  CA  GLY    25      14.412  25.399  -6.715  1.00  1.00
ATOM    798  C   GLY    25      15.279  24.363  -7.432  1.00  1.00
ATOM    799  O   GLY    25      15.070  24.058  -8.602  1.00  1.00
ATOM    800  N   PHE    26      16.234  23.799  -6.705  1.00  4.60
ATOM    801  CA  PHE    26      17.138  22.791  -7.251  1.00  4.60
ATOM    802  C   PHE    26      16.444  21.500  -7.681  1.00  4.60
ATOM    803  O   PHE    26      16.744  20.947  -8.741  1.00  4.60
ATOM    804  CB  PHE    26      18.213  22.401  -6.204  1.00  4.60
ATOM    805  N   ARG    27      15.518  21.023  -6.852  1.00  5.20
ATOM    806  CA  ARG    27      14.832  19.754  -7.103  1.00  5.20
ATOM    807  C   ARG    27      13.554  19.785  -7.919  1.00  5.20
ATOM    808  O   ARG    27      13.269  18.843  -8.664  1.00  5.20
ATOM    809  CB  ARG    27      14.503  19.052  -5.778  1.00  5.20
ATOM    810  N   GLU    28      12.770  20.845  -7.766  1.00  4.42
ATOM    811  CA  GLU    28      11.503  20.929  -8.478  1.00  4.42
ATOM    812  C   GLU    28      11.438  21.998  -9.561  1.00  4.42
ATOM    813  O   GLU    28      11.151  21.698 -10.723  1.00  4.42
ATOM    814  CB  GLU    28      10.338  21.173  -7.485  1.00  4.42
ATOM    815  N   VAL    29      11.708  23.240  -9.186  1.00  4.33
ATOM    816  CA  VAL    29      11.610  24.331 -10.140  1.00  4.33
ATOM    817  C   VAL    29      12.484  24.183 -11.379  1.00  4.33
ATOM    818  O   VAL    29      11.966  24.188 -12.503  1.00  4.33
ATOM    819  CB  VAL    29      11.893  25.693  -9.474  1.00  4.33
ATOM    820  N   HIS    93       3.271  47.795  -3.500  1.00  2.37
ATOM    821  CA  HIS    93       4.373  48.477  -2.821  1.00  2.37
ATOM    822  C   HIS    93       5.509  48.954  -3.725  1.00  2.37
ATOM    823  O   HIS    93       6.622  49.205  -3.260  1.00  2.37
ATOM    824  CB  HIS    93       4.939  47.564  -1.721  1.00  2.37
ATOM    825  N   LEU    94       5.235  49.074  -5.016  1.00  4.16
ATOM    826  CA  LEU    94       6.251  49.531  -5.952  1.00  4.16
ATOM    827  C   LEU    94       6.608  50.996  -5.666  1.00  4.16
ATOM    828  O   LEU    94       5.716  51.828  -5.502  1.00  4.16
ATOM    829  CB  LEU    94       5.727  49.404  -7.384  1.00  4.16
ATOM    830  N   GLY    95       7.902  51.307  -5.606  1.00  5.18
ATOM    831  CA  GLY    95       8.335  52.682  -5.365  1.00  5.18
ATOM    832  C   GLY    95       8.632  53.379  -6.692  1.00  5.18
ATOM    833  O   GLY    95       8.556  52.758  -7.754  1.00  5.18
ATOM    834  N   LYS    96       8.970  54.666  -6.627  1.00  4.51
ATOM    835  CA  LYS    96       9.257  55.449  -7.827  1.00  4.51
ATOM    836  C   LYS    96      10.386  54.878  -8.678  1.00  4.51
ATOM    837  O   LYS    96      10.299  54.867  -9.910  1.00  4.51
ATOM    838  CB  LYS    96       9.598  56.892  -7.448  1.00  4.51
ATOM    839  N   ASP    97      11.447  54.420  -8.021  1.00  4.54
ATOM    840  CA  ASP    97      12.592  53.846  -8.717  1.00  4.54
ATOM    841  C   ASP    97      12.132  52.621  -9.496  1.00  4.54
ATOM    842  O   ASP    97      12.538  52.406 -10.641  1.00  4.54
ATOM    843  CB  ASP    97      13.697  53.429  -7.721  1.00  4.54
ATOM    844  N   GLU    98      11.275  51.823  -8.862  1.00  5.12
ATOM    845  CA  GLU    98      10.760  50.628  -9.495  1.00  5.12
ATOM    846  C   GLU    98       9.935  50.948 -10.726  1.00  5.12
ATOM    847  O   GLU    98      10.092  50.298 -11.756  1.00  5.12
ATOM    848  CB  GLU    98       9.934  49.835  -8.468  1.00  5.12
ATOM    849  N   PHE    99       9.060  51.944 -10.623  1.00  6.45
ATOM    850  CA  PHE    99       8.216  52.343 -11.744  1.00  6.45
ATOM    851  C   PHE    99       9.050  52.739 -12.960  1.00  6.45
ATOM    852  O   PHE    99       8.734  52.369 -14.092  1.00  6.45
ATOM    853  CB  PHE    99       7.313  53.495 -11.336  1.00  6.45
ATOM    854  N   TRP   100      10.117  53.496 -12.720  1.00  3.02
ATOM    855  CA  TRP   100      11.006  53.937 -13.790  1.00  3.02
ATOM    856  C   TRP   100      11.756  52.758 -14.410  1.00  3.02
ATOM    857  O   TRP   100      11.987  52.732 -15.617  1.00  3.02
ATOM    858  CB  TRP   100      12.006  54.967 -13.250  1.00  3.02
ATOM    859  N   SER   101      12.129  51.783 -13.587  1.00  4.62
ATOM    860  CA  SER   101      12.844  50.614 -14.082  1.00  4.62
ATOM    861  C   SER   101      11.944  49.823 -15.028  1.00  4.62
ATOM    862  O   SER   101      12.392  49.337 -16.063  1.00  4.62
ATOM    863  CB  SER   101      13.285  49.733 -12.921  1.00  4.62
ATOM    864  N   VAL   102      10.669  49.705 -14.674  1.00  5.57
ATOM    865  CA  VAL   102       9.727  48.975 -15.510  1.00  5.57
ATOM    866  C   VAL   102       9.531  49.669 -16.858  1.00  5.57
ATOM    867  O   VAL   102       9.583  49.025 -17.902  1.00  5.57
ATOM    868  CB  VAL   102       8.377  48.821 -14.796  1.00  5.57
ATOM    869  N   MET   103       9.313  50.981 -16.834  1.00  6.50
ATOM    870  CA  MET   103       9.114  51.735 -18.067  1.00  6.50
ATOM    871  C   MET   103      10.360  51.665 -18.949  1.00  6.50
ATOM    872  O   MET   103      10.270  51.490 -20.164  1.00  6.50
ATOM    873  CB  MET   103       8.783  53.186 -17.744  1.00  6.50
ATOM    874  N   ASP   104      11.525  51.803 -18.330  1.00  2.99
ATOM    875  CA  ASP   104      12.785  51.762 -19.065  1.00  2.99
ATOM    876  C   ASP   104      12.999  50.409 -19.751  1.00  2.99
ATOM    877  O   ASP   104      13.497  50.348 -20.874  1.00  2.99
ATOM    878  CB  ASP   104      13.947  52.058 -18.108  1.00  2.99
ATOM    879  N   HIS   105      12.611  49.331 -19.072  1.00  3.56
ATOM    880  CA  HIS   105      12.771  47.984 -19.608  1.00  3.56
ATOM    881  C   HIS   105      11.666  47.610 -20.589  1.00  3.56
ATOM    882  O   HIS   105      11.823  46.681 -21.375  1.00  3.56
ATOM    883  CB  HIS   105      12.804  46.967 -18.459  1.00  3.56
ATOM    884  N   ARG   106      10.548  48.326 -20.528  1.00  5.11
ATOM    885  CA  ARG   106       9.432  48.021 -21.407  1.00  5.11
ATOM    886  C   ARG   106       8.545  46.952 -20.799  1.00  5.11
ATOM    887  O   ARG   106       7.722  46.349 -21.483  1.00  5.11
ATOM    888  CB  ARG   106       9.969  47.586 -22.781  1.00  5.11
ATOM    889  N   ASN   107       8.717  46.710 -19.503  1.00  4.78
ATOM    890  CA  ASN   107       7.928  45.709 -18.791  1.00  4.78
ATOM    891  C   ASN   107       6.553  46.290 -18.462  1.00  4.78
ATOM    892  O   ASN   107       6.453  47.392 -17.922  1.00  4.78
ATOM    893  CB  ASN   107       8.638  45.289 -17.478  1.00  4.78
ATOM    894  N   LEU   108       5.492  45.560 -18.796  1.00  6.09
ATOM    895  CA  LEU   108       4.141  46.032 -18.517  1.00  6.09
ATOM    896  C   LEU   108       3.809  45.876 -17.035  1.00  6.09
ATOM    897  O   LEU   108       4.156  44.877 -16.413  1.00  6.09
ATOM    898  CB  LEU   108       3.086  45.249 -19.328  1.00  6.09
TER
END
