
#######################################################
#                                                     #
#                        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    6 (   42),  selected    6 , name T0320TS074_3-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_3-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    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    T     222      K      39          0.690
LGA    S     223      Y      40          0.456
LGA    I     224      L      41          0.384
LGA    G     225      L      42          1.490
LGA    -       -      S      43           -
LGA    G     226      E      44          0.955
LGA    I     227      I      45          0.405
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      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    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      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    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      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)    6  214    5.0      6    0.83    16.67      2.767     0.646

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.928699 * X  +  -0.353807 * Y  +  -0.111077 * Z  +   4.563616
  Y_new =  -0.079884 * X  +  -0.483373 * Y  +   0.871762 * Z  +  32.294338
  Z_new =  -0.362127 * X  +  -0.800731 * Y  +  -0.477172 * Z  +  36.938011 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.108211    1.033382  [ DEG:  -120.7916     59.2084 ]
  Theta =   0.370549    2.771043  [ DEG:    21.2309    158.7691 ]
  Phi   =  -0.085806    3.055787  [ DEG:    -4.9163    175.0837 ]
 
# 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: T0320TS074_3-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_3-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  214   5.0    6   0.83   16.67   2.767
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_3-D1
PFRMAT TS
TARGET T0320
MODEL  3
PARENT N/A
ATOM      1  N   THR   222       5.038  20.531  35.972  1.00  1.00
ATOM      2  CA  THR   222       6.104  20.176  35.045  1.00  1.00
ATOM      3  C   THR   222       7.467  20.140  35.709  1.00  1.00
ATOM      4  O   THR   222       7.636  20.626  36.821  1.00  1.00
ATOM      5  CB  THR   222       6.170  21.172  33.871  1.00  1.00
ATOM      6  OG1 THR   222       6.466  22.481  34.371  1.00  1.00
ATOM      7  CG2 THR   222       4.842  21.204  33.126  1.00  1.00
ATOM      8  N   SER   223       8.437  19.562  35.012  1.00  1.00
ATOM      9  CA  SER   223       9.787  19.473  35.536  1.00  1.00
ATOM     10  C   SER   223      10.307  20.893  35.710  1.00  1.00
ATOM     11  O   SER   223      11.188  21.152  36.531  1.00  1.00
ATOM     12  HN  SER   223       8.326  19.156  34.105  1.00  1.00
ATOM     13  CB  SER   223      10.685  18.694  34.570  1.00  1.00
ATOM     14  OG  SER   223      10.779  19.356  33.316  1.00  1.00
ATOM     15  N   ILE   224       9.742  21.816  34.939  1.00  1.00
ATOM     16  CA  ILE   224      10.135  23.213  35.019  1.00  1.00
ATOM     17  C   ILE   224       9.756  23.831  36.361  1.00  1.00
ATOM     18  O   ILE   224      10.342  24.825  36.770  1.00  1.00
ATOM     19  HN  ILE   224       9.027  21.633  34.266  1.00  1.00
ATOM     20  CB  ILE   224       9.488  24.017  33.885  1.00  1.00
ATOM     21  CG1 ILE   224       7.957  24.034  33.922  1.00  1.00
ATOM     22  CG2 ILE   224      10.070  23.494  32.567  1.00  1.00
ATOM     23  CD1 ILE   224       7.339  25.015  32.954  1.00  1.00
ATOM     24  N   GLY   225       8.764  23.256  37.039  1.00  1.00
ATOM     25  CA  GLY   225       8.356  23.798  38.337  1.00  1.00
ATOM     26  C   GLY   225       9.474  23.586  39.356  1.00  1.00
ATOM     27  O   GLY   225       9.662  24.393  40.262  1.00  1.00
ATOM     28  HN  GLY   225       8.239  22.456  36.750  1.00  1.00
ATOM     29  N   GLY   226      10.209  22.487  39.210  1.00  1.00
ATOM     30  CA  GLY   226      11.304  22.193  40.131  1.00  1.00
ATOM     31  C   GLY   226      12.397  23.227  39.929  1.00  1.00
ATOM     32  O   GLY   226      12.982  23.725  40.890  1.00  1.00
ATOM     33  HN  GLY   226      10.085  21.800  38.494  1.00  1.00
ATOM     34  N   ILE   227      12.653  23.574  38.669  1.00  1.00
ATOM     35  CA  ILE   227      13.675  24.576  38.361  1.00  1.00
ATOM     36  C   ILE   227      13.270  25.954  38.864  1.00  1.00
ATOM     37  O   ILE   227      14.103  26.735  39.358  1.00  1.00
ATOM     38  HN  ILE   227      12.193  23.200  37.864  1.00  1.00
ATOM     39  CB  ILE   227      13.944  24.549  36.852  1.00  1.00
ATOM     40  CG1 ILE   227      14.551  23.245  36.370  1.00  1.00
ATOM     41  CG2 ILE   227      14.772  25.794  36.516  1.00  1.00
ATOM     42  CD1 ILE   227      14.592  23.130  34.841  1.00  1.00
TER
END
