
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0320TS464_5_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_5_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    S       4      E       8          2.112
LGA    K       5      M       9          1.815
LGA    A       6      C      10          1.756
LGA    A       7      Y      11          2.078
LGA    E       8      E      12          2.189
LGA    M       9      I      13          0.976
LGA    C      10      T      14          1.321
LGA    Y      11      N      15          1.883
LGA    E      12      S      16          1.280
LGA    I      13      Y      17          1.050
LGA    T      14      L      18          2.135
LGA    N      15      H      19          1.826
LGA    S      16      I      20          0.835
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    Y      17      I      27          3.446
LGA    L      18      A      28          4.752
LGA    -       -      S      29           -
LGA    H      19      T      30          0.970
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    I      20      A      33          2.634
LGA    D      21      I      34           #
LGA    Q      22      -       -           -
LGA    K      23      -       -           -
LGA    S      24      -       -           -
LGA    Q      25      -       -           -
LGA    I      26      -       -           -
LGA    I      27      -       -           -
LGA    A      28      -       -           -
LGA    S      29      -       -           -
LGA    T      30      -       -           -
LGA    Q      31      -       -           -
LGA    E      32      -       -           -
LGA    T     112      -       -           -
LGA    F     113      R      35          4.318
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    P     114      R      38          2.576
LGA    T     115      K      39          3.480
LGA    -       -      Y      40           -
LGA    L     116      L      41          3.367
LGA    E     117      L      42          4.273
LGA    N     118      S      43           -
LGA    F     119      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    V     120      S      50           #
LGA    L     121      P      51           #
LGA    E     122      -       -           -
LGA    T     123      -       -           -
LGA    S     124      L      52           #
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    E     125      S      59          3.909
LGA    R     126      Y      60          4.709
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    L     195      P     103           #
LGA    H     196      T     104          3.747
LGA    W     197      V     105          3.028
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    D     198      A     160           #
LGA    L     199      I     161          1.620
LGA    T     200      V     162          4.549
LGA    N     201      I     163           -
LGA    I     202      G     164           -
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    -       -      M     189           -
LGA    -       -      R     190           -
LGA    W     203      L     191           #
LGA    S     204      Q     192           -
LGA    F     205      P     193           -
LGA    L     206      L     194           -
LGA    L     207      L     195           -
LGA    -       -      H     196           -
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)   57  214    5.0     28    2.87     7.14      9.236     0.942

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.262837 * X  +   0.780981 * Y  +   0.566556 * Z  + -56.169025
  Y_new =   0.788627 * X  +  -0.512194 * Y  +   0.340184 * Z  +  29.983471
  Z_new =   0.555863 * X  +   0.357389 * Y  +  -0.750526 * Z  + -54.291000 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.697178   -0.444414  [ DEG:   154.5369    -25.4631 ]
  Theta =  -0.589401   -2.552191  [ DEG:   -33.7702   -146.2298 ]
  Phi   =   1.249090   -1.892502  [ DEG:    71.5676   -108.4324 ]
 
# 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_5_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_2-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   57  214   5.0   28   2.87    7.14   9.236
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  SER     4       2.943  33.700  28.140  1.00  0.00
ATOM      2  CA  LYS     5       2.449  32.847  24.489  1.00  0.00
ATOM      3  CA  ALA     6       4.246  29.535  25.076  1.00  0.00
ATOM      4  CA  ALA     7       2.177  28.512  28.106  1.00  0.00
ATOM      5  CA  GLU     8      -1.194  28.818  26.439  1.00  0.00
ATOM      6  CA  MET     9      -0.001  27.411  23.098  1.00  0.00
ATOM      7  CA  CYS    10       1.349  24.351  24.947  1.00  0.00
ATOM      8  CA  TYR    11      -1.893  24.040  26.846  1.00  0.00
ATOM      9  CA  GLU    12      -3.899  24.353  23.589  1.00  0.00
ATOM     10  CA  ILE    13      -1.730  21.799  21.830  1.00  0.00
ATOM     11  CA  THR    14      -2.072  19.355  24.742  1.00  0.00
ATOM     12  CA  ASN    15      -5.822  19.891  25.045  1.00  0.00
ATOM     13  CA  SER    16      -6.296  18.794  21.443  1.00  0.00
ATOM     14  CA  TYR    17      -4.091  15.759  21.603  1.00  0.00
ATOM     15  CA  LEU    18      -0.428  16.529  21.206  1.00  0.00
ATOM     16  CA  HIS    19       2.049  14.977  23.536  1.00  0.00
ATOM     17  CA  ILE    20       4.696  17.120  25.174  1.00  0.00
ATOM     18  CA  ASP    21       7.232  16.630  22.397  1.00  0.00
ATOM     19  CA  GLN    22       4.859  17.284  19.532  1.00  0.00
ATOM     20  CA  LYS    23       3.477  20.281  21.436  1.00  0.00
ATOM     21  CA  SER    24       6.986  21.665  21.938  1.00  0.00
ATOM     22  CA  GLN    25       7.913  21.013  18.328  1.00  0.00
ATOM     23  CA  ILE    26       4.936  23.143  17.196  1.00  0.00
ATOM     24  CA  ILE    27       5.837  25.942  19.607  1.00  0.00
ATOM     25  CA  ALA    28       9.366  25.852  18.250  1.00  0.00
ATOM     26  CA  SER    29       6.592  26.407  15.907  1.00  0.00
ATOM     27  CA  THR    30       3.110  27.124  17.294  1.00  0.00
ATOM     28  CA  GLN    31       4.084  30.290  19.120  1.00  0.00
ATOM     29  CA  GLU    32       3.016  33.717  17.786  1.00  0.00
ATOM     30  CA  THR   112       1.370  18.334  28.879  1.00  0.00
ATOM     31  CA  PHE   113       1.221  21.980  29.948  1.00  0.00
ATOM     32  CA  PRO   114       4.524  23.436  31.137  1.00  0.00
ATOM     33  CA  THR   115       5.923  23.159  34.665  1.00  0.00
ATOM     34  CA  LEU   116       8.043  26.032  35.935  1.00  0.00
ATOM     35  CA  GLU   117      11.053  23.784  35.366  1.00  0.00
ATOM     36  CA  ASN   118      10.517  23.278  31.640  1.00  0.00
ATOM     37  CA  PHE   119       9.566  26.911  31.034  1.00  0.00
ATOM     38  CA  VAL   120      13.086  27.846  32.207  1.00  0.00
ATOM     39  CA  LEU   121      14.842  25.439  29.873  1.00  0.00
ATOM     40  CA  GLU   122      12.830  26.831  27.019  1.00  0.00
ATOM     41  CA  THR   123      13.890  30.373  27.921  1.00  0.00
ATOM     42  CA  SER   124      17.542  29.304  28.071  1.00  0.00
ATOM     43  CA  GLU   125      17.234  27.940  24.600  1.00  0.00
ATOM     44  CA  ARG   126      15.231  30.823  23.153  1.00  0.00
ATOM     45  CA  LEU   195      17.827  33.386  24.208  1.00  0.00
ATOM     46  CA  HIS   196      20.859  31.112  23.951  1.00  0.00
ATOM     47  CA  TRP   197      21.899  31.147  27.590  1.00  0.00
ATOM     48  CA  ASP   198      23.818  28.248  29.160  1.00  0.00
ATOM     49  CA  LEU   199      21.484  25.548  30.501  1.00  0.00
ATOM     50  CA  THR   200      20.305  26.625  33.934  1.00  0.00
ATOM     51  CA  ASN   201      20.821  30.376  33.622  1.00  0.00
ATOM     52  CA  ILE   202      17.174  31.367  34.040  1.00  0.00
ATOM     53  CA  TRP   203      16.605  28.877  36.869  1.00  0.00
ATOM     54  CA  SER   204      19.578  30.474  38.631  1.00  0.00
ATOM     55  CA  PHE   205      18.119  33.925  38.134  1.00  0.00
ATOM     56  CA  LEU   206      14.702  32.950  39.439  1.00  0.00
ATOM     57  CA  LEU   207      16.323  31.063  42.315  1.00  0.00
TER
END
