
#######################################################
#                                                     #
#                        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   27 (   27),  selected   27 , name T0318TS464_5_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS464_5_2-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      V       4           -
LGA    -       -      L       5           -
LGA    V      77      V       6          3.474
LGA    P      78      R       7          1.337
LGA    D      79      N       8           #
LGA    A      80      G       9           #
LGA    S      81      I      10          3.915
LGA    S      82      Q      11          5.154
LGA    -       -      A      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      D      15           -
LGA    -       -      G      16           -
LGA    -       -      L      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    -       -      V      23           -
LGA    -       -      G      24           -
LGA    -       -      K      25           -
LGA    -       -      K      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      K      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    -       -      T      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    -       -      W      52           -
LGA    -       -      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    -       -      H      73           -
LGA    -       -      L      74           -
LGA    -       -      I      75           -
LGA    -       -      T      76           -
LGA    -       -      V      77           -
LGA    -       -      P      78           -
LGA    -       -      D      79           -
LGA    -       -      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    -       -      T      88           -
LGA    -       -      N      89           -
LGA    -       -      A      90           -
LGA    -       -      H      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      K      98           -
LGA    -       -      P      99           -
LGA    -       -      I     100           -
LGA    -       -      N     101           -
LGA    -       -      Y     102           -
LGA    -       -      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    -       -      V     109           -
LGA    -       -      H     110           -
LGA    -       -      F     111           -
LGA    R      83      V     112          0.783
LGA    G      84      L     113          2.994
LGA    N      85      F     114          3.617
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    T      86      D     119          4.573
LGA    P      87      V     120          2.053
LGA    T      88      L     121          3.443
LGA    -       -      S     122           -
LGA    N      89      H     123          1.875
LGA    A      90      V     124          1.783
LGA    H      91      A     125          1.724
LGA    S      92      A     126          1.399
LGA    I      93      I     127          1.116
LGA    Y      94      A     128          1.354
LGA    K      95      R     129          1.405
LGA    E      96      T     130          0.547
LGA    L      97      F     131          0.741
LGA    K      98      C     132          1.888
LGA    -       -      K     133           -
LGA    P      99      F     134           #
LGA    I     100      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    D     153      I     141          4.420
LGA    K     154      R     142          3.386
LGA    L     155      E     143          1.964
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27  154    5.0     23    2.73     8.70     10.731     0.813

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.090244 * X  +  -0.988680 * Y  +  -0.119869 * Z  +  34.820271
  Y_new =   0.995892 * X  +   0.088686 * Y  +   0.018285 * Z  +  27.941338
  Z_new =  -0.007448 * X  +  -0.121027 * Y  +   0.992621 * Z  + -29.506924 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.121327    3.020265  [ DEG:    -6.9516    173.0484 ]
  Theta =   0.007448    3.134145  [ DEG:     0.4267    179.5733 ]
  Phi   =   1.480427   -1.661166  [ DEG:    84.8222    -95.1778 ]
 
# 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: T0318TS464_5_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS464_5_2-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  154   5.0   23   2.73    8.70  10.731
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM      1  CA  VAL    77      28.401  35.204  14.590  1.00  0.00
ATOM      2  CA  PRO    78      31.857  36.715  14.290  1.00  0.00
ATOM      3  CA  ASP    79      31.251  39.064  17.250  1.00  0.00
ATOM      4  CA  ALA    80      30.457  36.123  19.590  1.00  0.00
ATOM      5  CA  SER    81      33.601  34.383  18.344  1.00  0.00
ATOM      6  CA  SER    82      36.185  37.146  18.695  1.00  0.00
ATOM      7  CA  ARG    83      34.750  38.411  22.022  1.00  0.00
ATOM      8  CA  GLY    84      33.003  35.366  23.464  1.00  0.00
ATOM      9  CA  ASN    85      29.650  37.142  23.786  1.00  0.00
ATOM     10  CA  THR    86      26.021  36.039  24.023  1.00  0.00
ATOM     11  CA  PRO    87      24.064  36.498  20.786  1.00  0.00
ATOM     12  CA  THR    88      22.159  39.431  22.388  1.00  0.00
ATOM     13  CA  ASN    89      25.311  41.388  23.462  1.00  0.00
ATOM     14  CA  ALA    90      26.535  41.022  19.851  1.00  0.00
ATOM     15  CA  HIS    91      23.322  42.663  18.521  1.00  0.00
ATOM     16  CA  SER    92      23.159  45.521  21.015  1.00  0.00
ATOM     17  CA  ILE    93      26.847  46.355  20.405  1.00  0.00
ATOM     18  CA  TYR    94      26.076  46.664  16.683  1.00  0.00
ATOM     19  CA  LYS    95      23.203  49.046  17.388  1.00  0.00
ATOM     20  CA  GLU    96      25.321  51.400  19.534  1.00  0.00
ATOM     21  CA  LEU    97      27.777  51.511  16.626  1.00  0.00
ATOM     22  CA  LYS    98      25.156  52.811  14.208  1.00  0.00
ATOM     23  CA  PRO    99      24.822  55.758  16.555  1.00  0.00
ATOM     24  CA  ILE   100      28.512  56.538  16.056  1.00  0.00
ATOM     25  CA  ASP   153      30.888  58.221  13.576  1.00  0.00
ATOM     26  CA  LYS   154      33.711  55.648  13.809  1.00  0.00
ATOM     27  CA  LEU   155      32.730  53.449  10.888  1.00  0.00
TER
END
