
#######################################################
#                                                     #
#                        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    9 (   76),  selected    9 , name T0316TS658_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS658_1-D3.T0316_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    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    M     284      F     333          4.450
LGA    S     285      A     334          2.118
LGA    T     286      E     335          2.556
LGA    S     287      P     336          0.823
LGA    L     288      Q     337          0.675
LGA    E     289      R     338          1.780
LGA    A     290      A     339          3.177
LGA    -       -      I     340           -
LGA    S     291      T     341          2.345
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    Q     292      Y     372          3.198
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9   90    5.0      9    2.60    11.11      7.958     0.333

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.122957 * X  +   0.861425 * Y  +   0.492777 * Z  + -24.823927
  Y_new =   0.373865 * X  +   0.500169 * Y  +  -0.781061 * Z  +  -0.999181
  Z_new =  -0.919297 * X  +   0.088194 * Y  +  -0.383556 * Z  +  54.674881 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.915582   -0.226011  [ DEG:   167.0505    -12.9495 ]
  Theta =   1.166290    1.975302  [ DEG:    66.8235    113.1765 ]
  Phi   =   1.888536   -1.253057  [ DEG:   108.2051    -71.7949 ]
 
# 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: T0316TS658_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS658_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9   90   5.0    9   2.60   11.11   7.958
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS658_1-D3
PFRMAT TS
TARGET T0316
MODEL  1
PARENT 1aab 1aac 1aaf 1aaj 1aalA
ATOM   2548  H   MET   284      15.460   7.241  -2.927  1.00  1.00              
ATOM   2549  N   MET   284      15.492   6.293  -2.953  1.00 28.50              
ATOM   2550  CA  MET   284      15.748   5.627  -4.249  1.00 20.18              
ATOM   2551  CB  MET   284      14.702   4.526  -4.443  1.00  3.04              
ATOM   2552  C   MET   284      15.763   6.482  -5.528  1.00 17.05              
ATOM   2553  O   MET   284      15.408   5.943  -6.579  1.00  1.00              
ATOM   2554  CG  MET   284      13.294   5.050  -4.690  1.00  2.85              
ATOM   2555  SD  MET   284      12.089   3.720  -4.886  1.00 20.33              
ATOM   2556  CE  MET   284      11.923   3.171  -3.195  1.00 27.05              
ATOM   2557  H   SER   285      16.635   8.090  -4.778  1.00  1.00              
ATOM   2558  N   SER   285      16.259   7.715  -5.547  1.00  8.79              
ATOM   2559  CA  SER   285      16.452   8.400  -6.840  1.00  1.00              
ATOM   2560  CB  SER   285      17.018   9.805  -6.623  1.00  1.00              
ATOM   2561  C   SER   285      17.417   7.627  -7.741  1.00  1.00              
ATOM   2562  O   SER   285      18.428   7.103  -7.266  1.00  1.00              
ATOM   2563  OG  SER   285      17.291  10.428  -7.867  1.00  1.00              
ATOM   2564  H   THR   286      16.291   7.880  -9.337  1.00  1.00              
ATOM   2565  N   THR   286      17.129   7.585  -9.040  1.00  1.00              
ATOM   2566  CA  THR   286      17.996   6.890  -9.991  1.00  1.00              
ATOM   2567  CB  THR   286      17.206   5.870 -10.836  1.00  1.00              
ATOM   2568  C   THR   286      18.662   7.901 -10.925  1.00  1.00              
ATOM   2569  O   THR   286      19.422   7.508 -11.813  1.00  1.00              
ATOM   2570  CG2 THR   286      16.639   4.759  -9.964  1.00  1.00              
ATOM   2571  OG1 THR   286      16.130   6.554 -11.488  1.00  1.00              
ATOM   2572  H   SER   287      17.906   9.473  -9.998  1.00  1.00              
ATOM   2573  N   SER   287      18.559   9.192 -10.604  1.00  1.00              
ATOM   2574  CA  SER   287      19.335  10.212 -11.311  1.00  1.14              
ATOM   2575  CB  SER   287      18.653  10.573 -12.630  1.00  1.00              
ATOM   2576  C   SER   287      19.536  11.490 -10.505  1.00  3.46              
ATOM   2577  O   SER   287      19.188  11.530  -9.324  1.00  1.00              
ATOM   2578  OG  SER   287      17.385  11.159 -12.380  1.00  1.00              
ATOM   2579  H   LEU   288      20.753  12.137 -11.891  1.00  1.00              
ATOM   2580  N   LEU   288      20.557  12.193 -10.968  1.00  8.44              
ATOM   2581  CA  LEU   288      21.367  13.088 -10.156  1.00  9.21              
ATOM   2582  CB  LEU   288      22.216  12.270  -9.178  1.00  3.53              
ATOM   2583  C   LEU   288      22.260  13.831 -11.137  1.00  6.26              
ATOM   2584  O   LEU   288      22.597  13.244 -12.168  1.00  1.00              
ATOM   2585  CG  LEU   288      22.940  11.064  -9.786  1.00  3.52              
ATOM   2586  CD1 LEU   288      24.387  11.411 -10.111  1.00 21.53              
ATOM   2587  CD2 LEU   288      22.857   9.868  -8.849  1.00 24.78              
ATOM   2588  H   GLU   289      22.919  15.052  -9.747  1.00  1.00              
ATOM   2589  N   GLU   289      22.997  14.818 -10.660  1.00  3.69              
ATOM   2590  CA  GLU   289      24.244  15.096 -11.356  1.00  1.31              
ATOM   2591  CB  GLU   289      24.344  16.581 -11.717  1.00  1.00              
ATOM   2592  C   GLU   289      25.452  14.681 -10.515  1.00  1.19              
ATOM   2593  O   GLU   289      25.455  14.868  -9.296  1.00  1.00              
ATOM   2594  CG  GLU   289      23.289  17.048 -12.711  1.00  1.00              
ATOM   2595  CD  GLU   289      23.364  18.535 -13.014  1.00  1.00              
ATOM   2596  OE1 GLU   289      24.220  19.225 -12.417  1.00  1.00              
ATOM   2597  OE2 GLU   289      22.652  18.991 -13.935  1.00  1.00              
ATOM   2598  H   ALA   290      26.453  14.080 -12.095  1.00  1.00              
ATOM   2599  N   ALA   290      26.521  14.233 -11.176  1.00  1.54              
ATOM   2600  CA  ALA   290      27.802  13.981 -10.512  1.00  1.19              
ATOM   2601  CB  ALA   290      28.470  12.741 -11.096  1.00  1.00              
ATOM   2602  C   ALA   290      28.700  15.196 -10.673  1.00  4.57              
ATOM   2603  O   ALA   290      28.666  15.846 -11.722  1.00  1.00              
ATOM   2604  H   SER   291      29.831  14.732  -9.137  1.00  1.00              
ATOM   2605  N   SER   291      29.615  15.415  -9.738  1.00  8.93              
ATOM   2606  CA  SER   291      30.615  16.427 -10.019  1.00  8.97              
ATOM   2607  CB  SER   291      31.213  16.959  -8.714  1.00  1.03              
ATOM   2608  C   SER   291      31.706  15.803 -10.876  1.00  7.58              
ATOM   2609  O   SER   291      32.881  16.109 -10.659  1.00  1.00              
ATOM   2610  OG  SER   291      30.236  17.675  -7.977  1.00  1.02              
ATOM   2611  H   GLN   292      30.454  15.106 -12.195  1.00  1.00              
ATOM   2612  N   GLN   292      31.284  15.524 -12.105  1.00  4.29              
ATOM   2613  CA  GLN   292      32.135  15.620 -13.280  1.00  1.00              
ATOM   2614  CB  GLN   292      32.668  14.239 -13.672  1.00  1.00              
ATOM   2615  C   GLN   292      31.377  16.232 -14.453  1.00  1.00              
ATOM   2616  O   GLN   292      31.922  17.148 -15.102  1.00  1.00              
ATOM   2617  OXT GLN   292      30.234  15.801 -14.710  1.00  1.00              
ATOM   2618  CG  GLN   292      33.604  13.620 -12.644  1.00  1.00              
ATOM   2619  CD  GLN   292      34.861  14.444 -12.430  1.00  1.00              
ATOM   2620  NE2 GLN   292      35.257  14.604 -11.172  1.00  1.00              
ATOM   2621 HE21 GLN   292      34.754  14.192 -10.489  1.00  1.00              
ATOM   2622 HE22 GLN   292      36.076  15.036 -10.995  1.00  1.00              
ATOM   2623  OE1 GLN   292      35.570  14.767 -13.388  1.00  1.00              
TER
END
