
#######################################################
#                                                     #
#                        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 T0330TS464_3_2
# Molecule2: number of CA atoms  225 ( 1744),  selected  225 , name T0330.pdb
# PARAMETERS: T0330TS464_3_2.T0330.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    S       2      -       -           -
LGA    R       3      -       -           -
LGA    T       4      -       -           -
LGA    L       5      -       -           -
LGA    V       6      -       -           -
LGA    L       7      -       -           -
LGA    F       8      -       -           -
LGA    G      12      S       2          4.992
LGA    -       -      R       3           -
LGA    T      13      T       4          1.956
LGA    L      14      L       5          3.099
LGA    L      15      V       6          3.164
LGA    K      16      L       7          1.020
LGA    V      17      F       8          1.782
LGA    E      18      D       9          1.704
LGA    S      19      I      10          1.616
LGA    M      20      D      11          3.805
LGA    -       -      G      12           -
LGA    -       -      T      13           -
LGA    -       -      L      14           -
LGA    N      21      L      15          0.649
LGA    R      22      K      16          1.617
LGA    E      36      V      17           -
LGA    -       -      E      18           -
LGA    -       -      S      19           -
LGA    -       -      M      20           -
LGA    -       -      N      21           -
LGA    -       -      R      22           -
LGA    -       -      R      23           -
LGA    -       -      V      24           -
LGA    -       -      L      25           -
LGA    -       -      A      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      I      30           -
LGA    -       -      E      31           -
LGA    -       -      V      32           -
LGA    -       -      Y      33           -
LGA    -       -      G      34           -
LGA    -       -      T      35           -
LGA    -       -      E      36           -
LGA    -       -      G      37           -
LGA    -       -      S      38           -
LGA    -       -      T      39           -
LGA    -       -      D      43           -
LGA    -       -      F      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      K      47           -
LGA    -       -      M      48           -
LGA    -       -      D      49           -
LGA    -       -      G      50           -
LGA    -       -      A      51           -
LGA    -       -      I      52           -
LGA    -       -      I      53           -
LGA    -       -      Y      54           -
LGA    -       -      E      55           -
LGA    -       -      V      56           -
LGA    -       -      L      57           -
LGA    -       -      S      58           -
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    -       -      L      62           -
LGA    -       -      E      63           -
LGA    -       -      R      64           -
LGA    -       -      A      65           -
LGA    -       -      E      66           -
LGA    -       -      I      67           -
LGA    -       -      A      68           -
LGA    -       -      D      69           -
LGA    -       -      K      70           -
LGA    -       -      F      71           -
LGA    -       -      D      72           -
LGA    -       -      K      73           -
LGA    -       -      A      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      T      77           -
LGA    -       -      Y      78           -
LGA    -       -      I      79           -
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      F      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      R      88           -
LGA    -       -      E      89           -
LGA    -       -      D      90           -
LGA    -       -      I      91           -
LGA    -       -      T      92           -
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      E      95           -
LGA    -       -      G      96           -
LGA    -       -      V      97           -
LGA    -       -      R      98           -
LGA    -       -      E      99           -
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    -       -      D     102           -
LGA    -       -      A     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      R     107           -
LGA    -       -      S     108           -
LGA    -       -      D     109           -
LGA    -       -      V     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      G     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      T     116           -
LGA    -       -      G     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      E     120           -
LGA    -       -      A     121           -
LGA    -       -      S     122           -
LGA    -       -      G     123           -
LGA    -       -      R     124           -
LGA    -       -      H     125           -
LGA    -       -      K     126           -
LGA    -       -      L     127           -
LGA    -       -      K     128           -
LGA    -       -      L     129           -
LGA    -       -      P     130           -
LGA    -       -      G     131           -
LGA    -       -      I     132           -
LGA    -       -      D     133           -
LGA    -       -      H     134           -
LGA    -       -      Y     135           -
LGA    -       -      F     136           -
LGA    -       -      P     137           -
LGA    -       -      F     138           -
LGA    -       -      G     139           -
LGA    -       -      A     140           -
LGA    -       -      F     141           -
LGA    -       -      A     142           -
LGA    -       -      D     143           -
LGA    -       -      D     144           -
LGA    -       -      A     145           -
LGA    -       -      L     146           -
LGA    -       -      D     147           -
LGA    -       -      R     148           -
LGA    -       -      N     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      P     152           -
LGA    -       -      H     153           -
LGA    -       -      I     154           -
LGA    -       -      A     155           -
LGA    -       -      L     156           -
LGA    -       -      E     157           -
LGA    -       -      R     158           -
LGA    -       -      A     159           -
LGA    -       -      R     160           -
LGA    -       -      R     161           -
LGA    -       -      M     162           -
LGA    -       -      T     163           -
LGA    -       -      G     164           -
LGA    -       -      A     165           -
LGA    -       -      N     166           -
LGA    -       -      Y     167           -
LGA    -       -      S     168           -
LGA    -       -      P     169           -
LGA    G      37      S     170          2.478
LGA    S      38      Q     171          3.212
LGA    T      39      I     172          3.488
LGA    G      40      V     173          4.218
LGA    S      41      I     174          3.284
LGA    H      42      I     175          3.465
LGA    -       -      G     176           -
LGA    -       -      D     177           -
LGA    -       -      T     178           -
LGA    -       -      E     179           -
LGA    -       -      H     180           -
LGA    F      44      D     181          2.482
LGA    S      45      I     182          3.434
LGA    -       -      R     183           -
LGA    -       -      C     184           -
LGA    G      46      A     185          1.259
LGA    -       -      R     186           -
LGA    -       -      E     187           -
LGA    -       -      L     188           -
LGA    -       -      D     189           -
LGA    K      47      A     190          1.128
LGA    M      48      R     191           #
LGA    D      49      S     192           -
LGA    G      50      I     193           -
LGA    -       -      A     194           -
LGA    -       -      V     195           -
LGA    -       -      A     196           -
LGA    -       -      T     197           -
LGA    -       -      G     198           -
LGA    -       -      N     199           -
LGA    -       -      F     200           -
LGA    -       -      T     201           -
LGA    -       -      M     202           -
LGA    -       -      E     203           -
LGA    -       -      E     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      R     207           -
LGA    -       -      H     208           -
LGA    -       -      K     209           -
LGA    -       -      P     210           -
LGA    -       -      G     211           -
LGA    -       -      T     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      K     215           -
LGA    -       -      N     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      T     220           -
LGA    -       -      D     221           -
LGA    -       -      E     222           -
LGA    -       -      V     223           -
LGA    -       -      L     224           -
LGA    -       -      A     225           -
LGA    -       -      S     226           -
LGA    -       -      I     227           -
LGA    -       -      L     228           -
LGA    -       -      T     229           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  225    5.0     21    2.81     9.52      6.157     0.722

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.317524 * X  +  -0.930303 * Y  +   0.183615 * Z  +  83.046799
  Y_new =   0.362993 * X  +  -0.298135 * Y  +  -0.882809 * Z  +  67.261360
  Z_new =   0.876022 * X  +  -0.213663 * Y  +   0.432359 * Z  + -27.040970 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.458980    2.682613  [ DEG:   -26.2976    153.7024 ]
  Theta =  -1.067551   -2.074042  [ DEG:   -61.1661   -118.8339 ]
  Phi   =   2.289479   -0.852114  [ DEG:   131.1775    -48.8225 ]
 
# 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: T0330TS464_3_2                                
REMARK     2: T0330.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2.T0330.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  225   5.0   21   2.81    9.52   6.157
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM      1  CA  SER     2      15.061  36.251  24.111  1.00  0.00
ATOM      2  CA  ARG     3      14.833  39.395  21.976  1.00  0.00
ATOM      3  CA  THR     4      17.423  41.997  22.997  1.00  0.00
ATOM      4  CA  LEU     5      20.896  42.708  24.347  1.00  0.00
ATOM      5  CA  VAL     6      21.115  46.072  26.107  1.00  0.00
ATOM      6  CA  LEU     7      23.941  48.087  27.609  1.00  0.00
ATOM      7  CA  PHE     8      23.202  50.558  30.403  1.00  0.00
ATOM      8  CA  GLY    12      21.744  53.403  34.989  1.00  0.00
ATOM      9  CA  THR    13      20.817  54.873  31.609  1.00  0.00
ATOM     10  CA  LEU    14      20.064  52.756  28.533  1.00  0.00
ATOM     11  CA  LEU    15      22.697  53.492  25.872  1.00  0.00
ATOM     12  CA  LYS    16      22.542  50.686  23.320  1.00  0.00
ATOM     13  CA  VAL    17      20.395  47.808  22.104  1.00  0.00
ATOM     14  CA  GLU    18      20.864  44.992  19.583  1.00  0.00
ATOM     15  CA  SER    19      18.195  42.601  18.320  1.00  0.00
ATOM     16  CA  MET    20      19.227  39.032  19.084  1.00  0.00
ATOM     17  CA  ASN    21      16.212  37.020  17.911  1.00  0.00
ATOM     18  CA  ARG    22      18.310  35.047  15.411  1.00  0.00
ATOM     19  CA  GLU    36      34.446  48.465  35.128  1.00  0.00
ATOM     20  CA  GLY    37      32.479  51.302  33.612  1.00  0.00
ATOM     21  CA  SER    38      29.536  52.143  31.312  1.00  0.00
ATOM     22  CA  THR    39      28.675  49.757  28.493  1.00  0.00
ATOM     23  CA  GLY    40      28.369  52.361  25.747  1.00  0.00
ATOM     24  CA  SER    41      27.819  50.102  22.764  1.00  0.00
ATOM     25  CA  HIS    42      26.560  46.575  22.143  1.00  0.00
ATOM     26  CA  PHE    44      30.544  42.523  21.528  1.00  0.00
ATOM     27  CA  SER    45      30.659  45.405  24.000  1.00  0.00
ATOM     28  CA  GLY    46      32.466  48.746  23.971  1.00  0.00
ATOM     29  CA  LYS    47      33.002  50.416  27.331  1.00  0.00
ATOM     30  CA  MET    48      34.084  53.566  29.096  1.00  0.00
ATOM     31  CA  ASP    49      36.634  51.364  30.809  1.00  0.00
ATOM     32  CA  GLY    50      38.603  51.539  27.525  1.00  0.00
TER
END
