
#######################################################
#                                                     #
#                        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   62 (   62),  selected   62 , name T0356TS464_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_3-D2.T0356_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    K     123      C     150          1.347
LGA    R     124      W     151          1.681
LGA    L     125      -       -           -
LGA    R     126      -       -           -
LGA    G     127      P     152          3.320
LGA    A     128      E     153          3.628
LGA    P     129      D     154           #
LGA    C     130      A     155          2.219
LGA    Q     131      A     156          1.966
LGA    Q     132      P     157          5.456
LGA    K     133      L     158          4.911
LGA    I     134      -       -           -
LGA    V     135      -       -           -
LGA    S     136      -       -           -
LGA    G     177      -       -           -
LGA    I     178      -       -           -
LGA    Y     179      I     159           #
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    R     180      G     162           #
LGA    Q     181      L     163           -
LGA    V     219      T     164           -
LGA    A     220      -       -           -
LGA    L     221      -       -           -
LGA    G     222      -       -           -
LGA    A     223      -       -           -
LGA    D     224      -       -           -
LGA    P     225      -       -           -
LGA    A     226      -       -           -
LGA    Y     242      -       -           -
LGA    A     243      -       -           -
LGA    F     244      -       -           -
LGA    A     245      -       -           -
LGA    G     246      V     165           #
LGA    L     247      T     166          3.535
LGA    L     248      R     167           #
LGA    R     249      G     168          5.068
LGA    -       -      P     169           -
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
LGA    G     250      Q     174          1.833
LGA    T     251      N     175           -
LGA    K     252      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    T     253      L     239          5.378
LGA    E     254      S     240          0.395
LGA    V     255      E     241          3.252
LGA    V     256      Y     242          3.727
LGA    K     257      A     243          2.890
LGA    C     258      F     244          2.332
LGA    I     259      A     245          0.742
LGA    S     260      G     246          2.973
LGA    N     261      L     247          4.918
LGA    D     262      -       -           -
LGA    L     263      L     248          2.189
LGA    E     264      R     249          1.307
LGA    V     265      G     250          1.793
LGA    P     266      T     251          2.277
LGA    A     267      -       -           -
LGA    S     268      -       -           -
LGA    A     269      K     252          2.707
LGA    E     270      T     253          3.362
LGA    I     271      E     254          1.104
LGA    V     272      -       -           -
LGA    L     273      -       -           -
LGA    E     274      V     255          2.942
LGA    G     275      V     256          1.828
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    -       -      E     274           -
LGA    -       -      G     275           -
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   62  192    5.0     29    3.11     3.45      9.395     0.903

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.180666 * X  +  -0.010756 * Y  +  -0.983486 * Z  +  49.871716
  Y_new =   0.912268 * X  +  -0.371891 * Y  +   0.171650 * Z  +   3.925103
  Z_new =  -0.367596 * X  +  -0.928214 * Y  +  -0.057375 * Z  + 167.011108 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.632530    1.509062  [ DEG:   -93.5371     86.4629 ]
  Theta =   0.376423    2.765170  [ DEG:    21.5674    158.4326 ]
  Phi   =   1.375286   -1.766307  [ DEG:    78.7981   -101.2019 ]
 
# 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: T0356TS464_3-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_3-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   62  192   5.0   29   3.11    3.45   9.395
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_3-D2
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM     68  CA  THR   122      60.717  56.571  86.893  1.00  0.00
ATOM     69  CA  LYS   123      59.836  58.858  89.891  1.00  0.00
ATOM     70  CA  ARG   124      56.496  57.068  90.564  1.00  0.00
ATOM     71  CA  LEU   125      58.360  53.631  90.423  1.00  0.00
ATOM     72  CA  ARG   126      61.135  54.937  92.801  1.00  0.00
ATOM     73  CA  GLY   127      58.449  56.265  95.279  1.00  0.00
ATOM     74  CA  ALA   128      56.762  52.760  95.133  1.00  0.00
ATOM     75  CA  PRO   129      59.959  50.814  96.031  1.00  0.00
ATOM     76  CA  CYS   130      62.177  50.419  92.948  1.00  0.00
ATOM     77  CA  GLN   131      65.798  50.859  94.108  1.00  0.00
ATOM     78  CA  GLN   132      67.998  51.405  91.010  1.00  0.00
ATOM     79  CA  LYS   133      67.050  52.774  87.532  1.00  0.00
ATOM     80  CA  ILE   134      67.506  50.958  84.183  1.00  0.00
ATOM     81  CA  VAL   135      66.982  52.902  80.964  1.00  0.00
ATOM     82  CA  SER   136      65.509  51.490  77.771  1.00  0.00
ATOM     83  CA  GLY   177      71.489  58.555  98.445  1.00  0.00
ATOM     84  CA  ILE   178      74.297  60.314  96.542  1.00  0.00
ATOM     85  CA  TYR   179      74.406  63.014  93.741  1.00  0.00
ATOM     86  CA  ARG   180      76.306  63.003  90.476  1.00  0.00
ATOM     87  CA  GLN   181      77.810  66.529  90.714  1.00  0.00
ATOM     88  CA  VAL   219      64.272  50.938  68.470  1.00  0.00
ATOM     89  CA  ALA   220      66.548  52.151  65.697  1.00  0.00
ATOM     90  CA  LEU   221      67.502  55.539  67.064  1.00  0.00
ATOM     91  CA  GLY   222      66.209  53.904  70.456  1.00  0.00
ATOM     92  CA  ALA   223      64.803  57.359  71.298  1.00  0.00
ATOM     93  CA  ASP   224      64.023  57.998  74.983  1.00  0.00
ATOM     94  CA  PRO   225      60.308  58.729  74.485  1.00  0.00
ATOM     95  CA  ALA   226      57.699  59.865  71.972  1.00  0.00
ATOM     96  CA  TYR   242      87.467  69.588  75.898  1.00  0.00
ATOM     97  CA  ALA   243      86.313  67.545  78.918  1.00  0.00
ATOM     98  CA  PHE   244      82.703  67.433  77.666  1.00  0.00
ATOM     99  CA  ALA   245      83.738  66.520  74.147  1.00  0.00
ATOM    100  CA  GLY   246      85.979  63.597  75.112  1.00  0.00
ATOM    101  CA  LEU   247      83.461  62.473  77.740  1.00  0.00
ATOM    102  CA  LEU   248      80.685  62.298  75.112  1.00  0.00
ATOM    103  CA  ARG   249      82.815  60.754  72.349  1.00  0.00
ATOM    104  CA  GLY   250      82.494  63.953  70.253  1.00  0.00
ATOM    105  CA  THR   251      84.791  66.679  68.998  1.00  0.00
ATOM    106  CA  LYS   252      84.946  70.120  70.535  1.00  0.00
ATOM    107  CA  THR   253      83.367  71.463  67.342  1.00  0.00
ATOM    108  CA  GLU   254      80.313  69.295  68.088  1.00  0.00
ATOM    109  CA  VAL   255      80.105  70.859  71.571  1.00  0.00
ATOM    110  CA  VAL   256      80.512  74.098  69.527  1.00  0.00
ATOM    111  CA  LYS   257      77.774  73.652  66.976  1.00  0.00
ATOM    112  CA  CYS   258      75.549  71.920  69.580  1.00  0.00
ATOM    113  CA  ILE   259      76.210  74.614  72.156  1.00  0.00
ATOM    114  CA  SER   260      75.414  77.365  69.632  1.00  0.00
ATOM    115  CA  ASN   261      72.287  75.610  68.372  1.00  0.00
ATOM    116  CA  ASP   262      70.833  75.624  71.877  1.00  0.00
ATOM    117  CA  LEU   263      71.652  79.201  72.686  1.00  0.00
ATOM    118  CA  GLU   264      75.200  79.719  73.828  1.00  0.00
ATOM    119  CA  VAL   265      77.208  82.533  72.404  1.00  0.00
ATOM    120  CA  PRO   266      80.715  81.902  71.150  1.00  0.00
ATOM    121  CA  ALA   267      82.355  82.625  74.491  1.00  0.00
ATOM    122  CA  SER   268      80.000  80.541  76.584  1.00  0.00
ATOM    123  CA  ALA   269      80.249  77.758  73.992  1.00  0.00
ATOM    124  CA  GLU   270      84.048  77.866  74.145  1.00  0.00
ATOM    125  CA  ILE   271      84.035  77.976  77.927  1.00  0.00
ATOM    126  CA  VAL   272      82.001  74.728  77.998  1.00  0.00
ATOM    127  CA  LEU   273      84.318  73.052  75.492  1.00  0.00
ATOM    128  CA  GLU   274      87.248  74.087  77.646  1.00  0.00
ATOM    129  CA  GLY   275      85.677  72.527  80.762  1.00  0.00
TER
END
