
#######################################################
#                                                     #
#                        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   32 (   32),  selected   32 , name T0369TS464_1_2
# Molecule2: number of CA atoms  147 ( 1193),  selected  147 , name T0369.pdb
# PARAMETERS: T0369TS464_1_2.T0369.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      D       3           -
LGA    -       -      W       4           -
LGA    -       -      Q       5           -
LGA    -       -      Q       6           -
LGA    -       -      A       7           -
LGA    -       -      L       8           -
LGA    Q      27      D       9          3.461
LGA    -       -      R      10           -
LGA    -       -      H      11           -
LGA    -       -      V      12           -
LGA    P      28      G      13          2.174
LGA    E      29      V      14          3.507
LGA    D      30      G      15          2.675
LGA    -       -      V      16           -
LGA    -       -      R      17           -
LGA    -       -      T      18           -
LGA    W      31      T      19          3.670
LGA    D      32      -       -           -
LGA    K      33      -       -           -
LGA    R      34      -       -           -
LGA    P      35      -       -           -
LGA    I      36      -       -           -
LGA    S      37      -       -           -
LGA    Y     106      R      20          1.603
LGA    W     107      D      21           #
LGA    -       -      L      22           -
LGA    -       -      I      23           -
LGA    -       -      R      24           -
LGA    -       -      L      25           -
LGA    -       -      I      26           -
LGA    -       -      Q      27           -
LGA    -       -      P      28           -
LGA    -       -      E      29           -
LGA    -       -      D      30           -
LGA    -       -      W      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      R      34           -
LGA    -       -      P      35           -
LGA    -       -      I      36           -
LGA    -       -      S      37           -
LGA    -       -      G      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    -       -      S      41           -
LGA    -       -      V      42           -
LGA    -       -      Y      43           -
LGA    -       -      E      44           -
LGA    -       -      V      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      H      48           -
LGA    -       -      L      49           -
LGA    -       -      A      50           -
LGA    -       -      V      51           -
LGA    -       -      L      52           -
LGA    -       -      L      53           -
LGA    -       -      E      54           -
LGA    -       -      A      55           -
LGA    -       -      D      56           -
LGA    -       -      L      57           -
LGA    -       -      R      58           -
LGA    -       -      I      59           -
LGA    -       -      A      60           -
LGA    -       -      T      61           -
LGA    -       -      G      62           -
LGA    -       -      A      63           -
LGA    -       -      T      64           -
LGA    -       -      A      65           -
LGA    -       -      D      66           -
LGA    -       -      E      67           -
LGA    -       -      M      68           -
LGA    -       -      A      69           -
LGA    -       -      Q      70           -
LGA    -       -      F      71           -
LGA    -       -      Y      72           -
LGA    -       -      A      73           -
LGA    -       -      V      74           -
LGA    -       -      P      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      P      78           -
LGA    -       -      E      79           -
LGA    -       -      Q      80           -
LGA    -       -      L      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      R      84           -
LGA    -       -      L      85           -
LGA    -       -      D      86           -
LGA    -       -      Q      87           -
LGA    G     108      S      88          5.828
LGA    V     109      W      89          1.013
LGA    T     110      Q      90          5.401
LGA    -       -      Y      91           -
LGA    D     111      Y      92          1.459
LGA    -       -      Q      93           -
LGA    -       -      D      94           -
LGA    S     112      R      95          1.556
LGA    T     113      L      96          2.887
LGA    -       -      M      97           -
LGA    -       -      A      98           -
LGA    -       -      D      99           -
LGA    -       -      F     100           -
LGA    -       -      S     101           -
LGA    -       -      T     102           -
LGA    -       -      E     103           -
LGA    -       -      T     104           -
LGA    -       -      T     105           -
LGA    -       -      Y     106           -
LGA    -       -      W     107           -
LGA    -       -      G     108           -
LGA    -       -      V     109           -
LGA    -       -      T     110           -
LGA    -       -      D     111           -
LGA    -       -      S     112           -
LGA    -       -      T     113           -
LGA    -       -      T     114           -
LGA    -       -      G     115           -
LGA    T     114      W     116          3.507
LGA    G     115      L     117          2.829
LGA    W     116      L     118          2.516
LGA    -       -      E     119           -
LGA    L     117      A     120          2.506
LGA    L     118      A     121          1.602
LGA    E     119      V     122          0.536
LGA    A     120      H     123          1.416
LGA    A     121      L     124          1.580
LGA    V     122      Y     125          0.910
LGA    H     123      H     126          1.722
LGA    L     124      H     127          2.568
LGA    Y     125      R     128          1.560
LGA    H     126      S     129          1.654
LGA    -       -      Q     130           -
LGA    -       -      L     131           -
LGA    -       -      L     132           -
LGA    -       -      D     133           -
LGA    -       -      Y     134           -
LGA    -       -      L     135           -
LGA    -       -      N     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      G     139           -
LGA    -       -      Y     140           -
LGA    -       -      D     141           -
LGA    -       -      I     142           -
LGA    -       -      K     143           -
LGA    -       -      L     144           -
LGA    -       -      D     145           -
LGA    -       -      L     146           -
LGA    -       -      F     147           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  147    5.0     25    2.72     4.00     12.022     0.886

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.329084 * X  +   0.318319 * Y  +   0.889031 * Z  + -54.473560
  Y_new =  -0.201359 * X  +   0.943472 * Y  +  -0.263276 * Z  +   4.041733
  Z_new =  -0.922582 * X  +  -0.092375 * Y  +   0.374578 * Z  +   4.788826 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.241786    2.899806  [ DEG:   -13.8533    166.1467 ]
  Theta =   1.174721    1.966872  [ DEG:    67.3065    112.6935 ]
  Phi   =  -0.549108    2.592485  [ DEG:   -31.4616    148.5384 ]
 
# 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: T0369TS464_1_2                                
REMARK     2: T0369.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0369TS464_1_2.T0369.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  147   5.0   25   2.72    4.00  12.022
REMARK  ---------------------------------------------------------- 
MOLECULE T0369TS464_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0369
PARENT N/A
ATOM      1  CA  GLN    27      15.358   5.826  -3.971  1.00  0.00
ATOM      2  CA  PRO    28      15.142   2.137  -3.135  1.00  0.00
ATOM      3  CA  GLU    29      11.947   0.981  -1.442  1.00  0.00
ATOM      4  CA  ASP    30      11.562  -2.426   0.167  1.00  0.00
ATOM      5  CA  TRP    31       8.433  -4.589   0.469  1.00  0.00
ATOM      6  CA  ASP    32       7.762  -3.213   3.952  1.00  0.00
ATOM      7  CA  LYS    33       7.606   0.203   2.262  1.00  0.00
ATOM      8  CA  ARG    34      10.803   1.594   3.778  1.00  0.00
ATOM      9  CA  PRO    35      12.820   4.039   1.663  1.00  0.00
ATOM     10  CA  ILE    36      16.606   4.354   1.383  1.00  0.00
ATOM     11  CA  SER    37      17.809   7.486  -0.444  1.00  0.00
ATOM     12  CA  TYR   106      11.489  -7.454  -4.161  1.00  0.00
ATOM     13  CA  TRP   107      13.165  -4.241  -5.218  1.00  0.00
ATOM     14  CA  GLY   108      12.150  -1.053  -7.036  1.00  0.00
ATOM     15  CA  VAL   109      14.976   1.257  -8.151  1.00  0.00
ATOM     16  CA  THR   110      13.514   4.800  -8.411  1.00  0.00
ATOM     17  CA  ASP   111      14.668   6.982 -11.466  1.00  0.00
ATOM     18  CA  SER   112      14.273  10.687 -10.859  1.00  0.00
ATOM     19  CA  THR   113      12.388  12.399  -8.078  1.00  0.00
ATOM     20  CA  THR   114       8.665  12.060  -8.822  1.00  0.00
ATOM     21  CA  GLY   115       6.518  13.277  -5.929  1.00  0.00
ATOM     22  CA  TRP   116       4.500  10.061  -6.143  1.00  0.00
ATOM     23  CA  LEU   117       7.333   7.478  -6.115  1.00  0.00
ATOM     24  CA  LEU   118       7.078   6.313  -2.496  1.00  0.00
ATOM     25  CA  GLU   119       3.322   5.913  -2.909  1.00  0.00
ATOM     26  CA  ALA   120       3.473   3.797  -6.038  1.00  0.00
ATOM     27  CA  ALA   121       6.482   1.788  -4.892  1.00  0.00
ATOM     28  CA  VAL   122       4.510   1.034  -1.771  1.00  0.00
ATOM     29  CA  HIS   123       1.468   0.068  -3.797  1.00  0.00
ATOM     30  CA  LEU   124       3.367  -2.208  -6.176  1.00  0.00
ATOM     31  CA  TYR   125       5.130  -4.038  -3.301  1.00  0.00
ATOM     32  CA  HIS   126       1.939  -4.308  -1.206  1.00  0.00
TER
END
