
#######################################################
#                                                     #
#                        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   28 (   28),  selected   28 , name T0320TS464_4_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_4_2-D1.T0320_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    I      27      S      29          1.782
LGA    A      28      T      30          4.133
LGA    S      29      Q      31          2.722
LGA    -       -      E      32           -
LGA    T      30      A      33          2.669
LGA    Q      31      I      34          2.267
LGA    E      32      R      35          1.651
LGA    A      33      L      36          1.946
LGA    I      34      T      37          2.212
LGA    R      35      R      38          1.519
LGA    L      36      K      39          0.649
LGA    T      37      Y      40          0.749
LGA    R      38      L      41          1.359
LGA    K      39      L      42          1.809
LGA    Y      40      S      43          2.078
LGA    L      41      E      44          2.421
LGA    L      42      I      45          1.633
LGA    S      43      F      46          4.863
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    E      44      P      51           #
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    I      45      V     162          4.221
LGA    F      46      I     163          2.963
LGA    V      47      G     164          2.875
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    I     161      M     189          4.228
LGA    V     162      R     190          3.072
LGA    I     163      L     191          2.220
LGA    G     164      Q     192          1.142
LGA    I     165      P     193          3.219
LGA    -       -      L     194           -
LGA    R     166      L     195          1.517
LGA    H     167      H     196          2.671
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28  214    5.0     27    2.61     7.41      9.185     0.995

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.052456 * X  +   0.755728 * Y  +  -0.652781 * Z  + -65.422302
  Y_new =  -0.370808 * X  +  -0.592206 * Y  +  -0.715397 * Z  +  68.970306
  Z_new =  -0.927227 * X  +   0.279583 * Y  +   0.249165 * Z  +  71.165421 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.842864   -2.298728  [ DEG:    48.2926   -131.7074 ]
  Theta =   1.186939    1.954654  [ DEG:    68.0066    111.9934 ]
  Phi   =  -1.430264    1.711329  [ DEG:   -81.9481     98.0519 ]
 
# 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: T0320TS464_4_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_2-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28  214   5.0   27   2.61    7.41   9.185
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    27       1.930   9.943  22.672  1.00  0.00
ATOM      2  CA  ALA    28       3.341  12.091  25.448  1.00  0.00
ATOM      3  CA  SER    29       2.851  15.845  25.648  1.00  0.00
ATOM      4  CA  THR    30       6.222  17.613  25.874  1.00  0.00
ATOM      5  CA  GLN    31       4.815  21.038  26.836  1.00  0.00
ATOM      6  CA  GLU    32       3.454  19.277  29.909  1.00  0.00
ATOM      7  CA  ALA    33       6.862  17.995  31.159  1.00  0.00
ATOM      8  CA  ILE    34       8.352  21.470  30.798  1.00  0.00
ATOM      9  CA  ARG    35       5.856  23.203  33.156  1.00  0.00
ATOM     10  CA  LEU    36       6.096  20.438  35.787  1.00  0.00
ATOM     11  CA  THR    37       9.889  20.514  35.487  1.00  0.00
ATOM     12  CA  ARG    38       9.992  24.206  36.285  1.00  0.00
ATOM     13  CA  LYS    39       7.529  23.818  39.110  1.00  0.00
ATOM     14  CA  TYR    40       9.816  21.027  40.359  1.00  0.00
ATOM     15  CA  LEU    41      12.669  23.505  40.799  1.00  0.00
ATOM     16  CA  LEU    42      14.713  23.317  37.589  1.00  0.00
ATOM     17  CA  SER    43      16.276  26.758  36.973  1.00  0.00
ATOM     18  CA  GLU    44      16.516  26.053  33.217  1.00  0.00
ATOM     19  CA  ILE    45      15.106  23.350  30.985  1.00  0.00
ATOM     20  CA  PHE    46      16.687  22.680  27.583  1.00  0.00
ATOM     21  CA  VAL    47      14.718  20.281  25.427  1.00  0.00
ATOM     22  CA  ILE   161      19.984  23.671  38.232  1.00  0.00
ATOM     23  CA  VAL   162      19.923  22.618  34.585  1.00  0.00
ATOM     24  CA  ILE   163      17.410  20.029  33.380  1.00  0.00
ATOM     25  CA  GLY   164      18.013  18.420  29.990  1.00  0.00
ATOM     26  CA  ILE   165      14.833  17.059  28.510  1.00  0.00
ATOM     27  CA  ARG   166      15.267  14.287  25.945  1.00  0.00
ATOM     28  CA  HIS   167      11.914  13.528  24.271  1.00  0.00
TER
END
