UPPSALA UNIVERSITY

Ramachandran revisited

Latest update: 4 May, 2005.

This page contains some supplementary material to the Ways & Means article in Structure about Ramachandran plots.

Reference: GJ Kleywegt and TA Jones (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395 - 1400.


Generate Ramachandran plots of your own models with the STAN server !


QuickXS

Show me the distribution of phi and psi torsion angles for residues as a 2D plot in format


List of X-ray protein structures with more than 25% Ramachandran outliers

The following is a list of proteins with more than 25% outliers in the Ramachandran plot, sorted by the percentage of outliers. Clicking on a PDB identifier takes you to the entry's page at the PDB.

PDB identifier Resolution (Å) Year of deposition Nr of protein residues Nr of Ramachandran plot outliers Percentage Ramachandran plot outliers
2ABX 2.5 1986 138 100 72.464
1GMA 0.86 1988 24 15 62.500
1CYC 2.3 1976 89 45 50.562
3PGM 2.8 1982 214 99 46.262
1CTX 2.8 1982 64 27 42.188
2GN5 2.3 1986 78 32 41.026
2ATC 3.0 1982 430 174 40.465
1PYP 3.0 1983 263 106 40.304
4RCR 2.8 1991 706 282 39.943
1TRC 3.6 1990 122 48 39.344
155C 2.5 1976 119 46 38.655
2TAA 3.0 1982 435 166 38.161
4CAT 3.0 1983 657 248 37.747
5LDH 2.7 1980 292 108 36.986
1HDS 1.98 1979 520 183 35.192
4GPD 2.8 1988 1204 418 34.718
2GLS 3.5 1989 5148 1783 34.635
1GPD 2.9 1975 602 205 34.053
1CN1 3.2 1981 437 146 33.410
3PGK 2.5 1982 376 125 33.245
1TMF 3.5 1992 739 238 32.206
1HKG 3.5 1980 422 135 31.991
1TNV 5.0 1994 571 182 31.874
1MCW 3.5 1989 396 126 31.818
1PFC 3.125 1981 104 33 31.731
2SNS 1.5 1982 130 41 31.538
1RFB 3.0 1993 226 70 30.973
2PGK 3.0 1976 404 122 30.198
3SDP 2.1 1991 338 102 30.178
3GPD 3.5 1983 598 177 29.599
1RDD 2.8 1993 139 41 29.496
3LDH 3.0 1974 299 85 28.428
1SPI 2.8 1994 1192 331 27.768
2AAT 2.8 1989 364 100 27.473
1LLC 3.0 1988 283 77 27.208
3HVT 2.9 1994 890 239 26.854
1NRQ 3.5 1994 188 50 26.596
2RCR 3.1 1991 738 196 26.558
1GYL 3. 1995 645 171 26.512
1ACX 2.0 1982 88 23 26.136
1CNE 3.0 1995 238 62 26.050
1NRO 3.1 1994 198 51 25.758
1YST 3.0 1994 742 191 25.741
1AZU 2.7 1980 111 28 25.225
7ADH 3.2 1984 334 84 25.150


37 * 37 Matrix of residue counts


      16      45      64      51      40      39      32      38      43      63
      35       4       0       0       0       0       0       0       0       0
       1       0       1       1       2       2       0       0       0       0
       0       0       0       0       1       0      16       1      10      23
      25      18      16      12      15      19      21       7       0       0
       0       0       0       0       0       0       0       0       0       0
       1       4       0       0       1       0       0       0       0       0
       0       0       0       1       0       1       7       5       2       7
       3       5       3       3       4       1       1       0       0       0
       0       0       0       0       0       0       1       3       3       1
       0       0       0       0       0       0       0       1       0       0
       0       1       5       2       1       3       3       4       4       3
       1       0       1       0       0       0       0       0       0       0
       0       0       0       1      11       2       0       0       0       0
       0       0       0       0       0       0       0       1       1       1
       2       0       1       2       8       2       5       0       1       0
       0       0       0       0       0       0       0       0       0       0
       3       9       0       0       0       0       0       0       0       0
       0       0       0       0       1       0       0       2       0       3
       2       5       8       1       0       0       1       0       0       0
       0       0       0       0       0       0       1       6      11       6
       1       0       0       0       0       0       0       1       0       0
       0       0       0       0       0       0       1       1       3       4
       2       0       0       0       1       0       1       0       0       0
       1       0       0       1       4       7       2       0       0       0
       0       0       0       0       0       0       0       0       0       0
       0       0       1       1       1       3       1       1       0       0
       0       1       0       1       0       0       0       0       2       2
       0       2       4       2       1       0       1       0       0       0
       0       0       0       0       0       0       0       2       0       2
       4       2       6       5       2       0       0       1       1       0
       1       0       1       0       0       0       1       1       1       2
       2       0       0       0       0       0       0       0       0       0
       0       1       0       1       0       0       0       1       7       5
       2       2       4       1       2       0       3       2       0       2
       1       1       2       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0       2       1
       0       0       4       2       5       5       7       6       7       9
       6       4       4       5       7       1       2       0       0       1
       0       0       0       0       0       3       0       0       0       0
       0       0       0       1       0       0       0       0       0       5
       4       5      13      22      12      16      22      30      49      52
      31      18       7       2       0       0       0       0       0       0
       0       0       6       1       0       0       0       1       1       0
       1       0       0       0       1       1       1       4      10      13
      38      34      49      72     160     709    1013     205      45       1
       2       0       1       0       1       0       0       0       4       7
       1       1       1       0       0       0       0       0       1       0
       1       0       0       0       1      10      22      42      67     101
     229    1035    6328    3530     357      18       6       2       0       0
       1       0       1       0       0       6       2       2       1       0
       2       0       1       2       0       0       1       0       0       0
       1       3       8      25      51      91     172     309    1589    4895
    1978     146      10       1       0       0       0       0       0       0
       0       1       7       5       1       0       1       0       0       1
       1       1       0       1       0       1       0       2       4      19
      46      97     125     199     387     966    1888     714      29       1
       1       0       0       0       0       0       0       0       1       2
       2       1       0       0       1       0       0       1       0       0
       0       1       0       0       2       7      23      78     145     180
     298     521     872     873     140       9       0       0       0       0
       0       0       0       0       0       1       0       2       3       1
       1       0       0       1       1       0       0       0       0       1
       0       1       9      25      93     127     251     438     625     517
     172      16       1       0       0       0       0       0       0       0
       0       0       2       4      11       6       3       0       0       0
       1       0       0       0       0       1       0       0       3      17
      38     117     167     379     456     374     124      12       4       0
       0       0       0       0       0       0       0       0       0       3
      24      31       6       0       0       0       0       0       0       0
       0       0       0       0       2       6      14      42     105     205
     282     247      96      20       3       1       0       0       0       0
       0       0       0       0       0       0      16      76      40       4
       0       0       0       0       0       0       0       0       0       0
       0       0       4      12      32      78     143     133      62      18
      11       1       2       0       0       0       0       0       0       0
       0       0       6      89     109      19       3       1       0       0
       0       0       0       0       0       1       0       0       1       4
      14      30      56      59      30      15      13       2       1       0
       0       0       0       0       0       0       0       0       2      31
     206     129      10       1       0       0       0       0       0       0
       0       0       0       0       0       1       1      13      18      30
      27      14      13      13       7       3       1       0       0       1
       0       0       0       1       0       7     111     263      74       2
       3       1       0       0       0       0       0       0       0       0
       0       0       0       5      12      28      25       7       9      13
      40      21       3       2       0       0       0       0       0       0
       0       1      10      84     103      17       0       3       0       0
       0       0       0       0       0       0       0       0       0       4
      12      27      41      47      15       5      39      65      32       1
       1       0       0       0       0       0       0       0       3      10
      33      29       4       1       0       0       0       1       0       0
       0       0       0       1       0       2       1      14      30      82
      59      16      15      53     106      43       1       1       0       2
       0       0       0       0       0       1       5       4       9       1
       1       0       1       0       0       0       0       0       0       1
       0       2       1       9      15      28      59      69      44      28
      57     104      46       4       0       0       0       2       0       0
       0       0       1       2       3       1       2       1       0       0
       1       0       0       0       0       0       0       0       1       1
       7      19      35      46      82      85      73     100     115      36
      10       2       1       0       0       1       0       0       1       0
       0       1       1       0       1       1       0       0       0       0
       0       2       0       0       1       1       3      13      27      58
     114     179     237     264     239     180      85      26       5       4
       1       1       0       0       0       0       0       0       0       0
       2       4       1       1       0       1       0       0       0       1
       0       0       3       3      15      27     101     219     360     458
     528     443     331     206     120      58      22       7       0       0
       0       1       0       0       0       0       1       1       0       2
       1       1       0       0       0       1       0       0       0       3
       4      27      69     202     397     798     940     762     632     499
     436     442     336     110      15       4       0       1       0       0
       0       0       0       1       2       0       1       2       0       0
       0       0       0       0       0       0       4      12      56     155
     293     617     883     852     717     565     559     668     801     587
     115       2       2       0       1       0       0       0       0       0
       0       1       1       2       0       0       0       0       0       1
       0       0       1      12      13      94     231     462     690     734
     567     480     384     457     685     856     434      36       2       0
       0       0       0       0       0       0       0       0       0       1
       2       0       0       0       0       0       0       0       0       4
      13      20     188     423     486     737     612     440     300     303
     401     594     549     150      14       1       0       0       0       0
       0       0       0       0       0       0       2       2       0       0
       1       0       0       0       0       1       2      20      57     189
     362     392     468     342     239     201     199     313     394     209
      21       3       0       0       0       0       0       0       0       0
       0       0       0       3       0       0       0       0       0       0
       0       1       1       5      57      32     100     162     169     160
     118      99      94     102     117     137      43       6       0       0
       0       0       0       0       0       0       0       0       1       4
       2       1       0       0       0       0       0       1       0       0
       2      32      16      45      64      51      40      39      32      38
      43      63      35       4       0       0       0       0       0       0
       0       0       1       0       1       1       2       2       0       0
       0       0       0       0       0       0       1       0      16
REMARK Total nr of residues  74893

Fortran subroutine

Use the subroutine as follows in your own program:

...
      integer coregn(37,37)
...
      call defcor (coregn)
...
      nongly = 0
      noutlr = 0
...
      do 330 i=1,nres
...
     c if not GLY then do:
            iphi = int ( (180.0+phi(i)) / 10.0 ) + 1
            ipsi = int ( (180.0+psi(i)) / 10.0 ) + 1
            if (iphi .ge. 1 .and. iphi .le. 37 .and.
     +          ipsi .ge. 1 .and. ipsi .le. 37) then
              nongly = nongly + 1
              if (coregn(iphi,ipsi) .ne. 1) then
                noutlr = noutlr + 1
              end if
            end if
...
330   continue
...
      call jvalut (' RAMA - Nr of non-Gly residues :',1,nongly)
      call jvalut (' RAMA - Nr of outliers (98%)   :',1,noutlr)
      if (nongly .gt. 0 .and. noutlr .gt. 0) then
        call fvalut (' RAMA - % Outliers             :',1,
     +      100.0*float(noutlr)/float(nongly))
      else
        call fvalut (' RAMA - % Outliers             :',1,0.0)
      end if



      subroutine defcor (coregn)
c
c ... this subroutine was auto-generated by
c     /home/gerard/pdb/phipsi/statjiffy.f
c
c ... COREGN will be set to 1 for all 10*10 degree squared
c     areas of the Ramachandran plot in which 98% of all
c     residues in ~400 <95% homologous <=2.0 A structures
c     are found
c
      implicit NONE
c
      integer m37
      parameter (m37=37*37)
c
      integer coregn (m37),i
c
code ...
c
      do i=1,m37
        coregn(i) = 0
      end do
c
      do i =    2,  11
        coregn (i) = 1
      end do
      do i =   40,  42
        coregn (i) = 1
      end do
      do i =   46,  47
        coregn (i) = 1
      end do
      coregn ( 414) = 1
      do i =  417, 422
        coregn (i) = 1
      end do
      do i =  451, 459
        coregn (i) = 1
      end do
      do i =  487, 496
        coregn (i) = 1
      end do
      do i =  524, 532
        coregn (i) = 1
      end do
      do i =  560, 569
        coregn (i) = 1
      end do
      do i =  597, 605
        coregn (i) = 1
      end do
      do i =  634, 641
        coregn (i) = 1
      end do
      do i =  670, 677
        coregn (i) = 1
      end do
      do i =  691, 692
        coregn (i) = 1
      end do
      do i =  708, 714
        coregn (i) = 1
      end do
      do i =  728, 729
        coregn (i) = 1
      end do
      do i =  745, 750
        coregn (i) = 1
      end do
      do i =  764, 766
        coregn (i) = 1
      end do
      do i =  782, 785
        coregn (i) = 1
      end do
      do i =  800, 802
        coregn (i) = 1
      end do
      do i =  819, 821
        coregn (i) = 1
      end do
      do i =  837, 839
        coregn (i) = 1
      end do
      do i =  856, 857
        coregn (i) = 1
      end do
      do i =  861, 862
        coregn (i) = 1
      end do
      do i =  874, 876
        coregn (i) = 1
      end do
      do i =  892, 894
        coregn (i) = 1
      end do
      do i =  897, 899
        coregn (i) = 1
      end do
      do i =  911, 912
        coregn (i) = 1
      end do
      do i =  929, 931
        coregn (i) = 1
      end do
      do i =  934, 936
        coregn (i) = 1
      end do
      do i =  966, 973
        coregn (i) = 1
      end do
      do i = 1002,1010
        coregn (i) = 1
      end do
      do i = 1039,1048
        coregn (i) = 1
      end do
      do i = 1076,1087
        coregn (i) = 1
      end do
      do i = 1112,1124
        coregn (i) = 1
      end do
      do i = 1149,1161
        coregn (i) = 1
      end do
      do i = 1186,1198
        coregn (i) = 1
      end do
      do i = 1222,1234
        coregn (i) = 1
      end do
      do i = 1258,1271
        coregn (i) = 1
      end do
      do i = 1295,1307
        coregn (i) = 1
      end do
      coregn (1332) = 1
      do i = 1334,1343
        coregn (i) = 1
      end do
c
      return
      end

Contours instead of boxes

To include the contours (if you really, really want to, despite the 10-degree resolution and the apparent left shift), generate your Ramachandran plot with MOLEMAN2, for instance:

MOLEMAN2> read 1cbs.pdb
MOLEMAN2> prot mc 1cbs.ps
Then remove the grey boxes from the PostScript file:

unix> grep -v LightBox 1cbs.ps > new.ps
Then open the file "new.ps" with your text editor, put your cursor after the bit that goes:

closepath gsave
gsave 1.0000 setgray fill grestore S
Then insert the PostScript code shown below (save it in a file first if you like; do not include the dashed lines):
-------------------------------------------------------------------
red 186.12 400 M 175 407.71 L 169.71 412.5 L 168.97 425 L
168.84 437.5 L 166.76 450 L 175 457.99 L 187.5 453.93 L
191.26 450 L 200 439.09 L 201.28 437.5 L 205.46 425 L
207.15 412.5 L 204.94 400 L 200 396.02 L 187.5 398.88 L 
186.12 400 L S 162.49 462.5 M 162.5 462.51 L 162.52 462.5 L 
162.5 462.48 L 162.49 462.5 L 
S 108.03 625 M 100.57 637.5 L 100 639.84 L 97.08 650 L 
94.22 662.5 L 100 667.9 L 110.44 662.5 L 112.5 660.22 L 
120.59 650 L 125 646.97 L 137.5 642.27 L 144.65 637.5 L 
150 626.9 L 151.08 625 L 150 624.28 L 137.5 617.84 L 
125 617.49 L 112.5 621.09 L 108.03 625 L S 172.04 637.5 M
172.89 650 L 175 656.45 L 187.5 658.57 L 193.07 650 L 
197.24 637.5 L 187.5 632.02 L 175 636.32 L 172.04 637.5 L S
green S 176.66 400 M 175 401.15 L 162.5 412.31 L 162.27 412.5 L 
155.66 425 L 152.49 437.5 L 150 442.44 L 143.44 450 L 
137.5 457.85 L 134.69 462.5 L 129.21 475 L 129 487.5 L 
137.5 491.42 L 150 488.97 L 151.77 487.5 L 162.5 480.62 L 
169.21 475 L 175 471.81 L 185.48 462.5 L 187.5 461.45 L 
198.46 450 L 200 448.07 L 208.48 437.5 L 211.35 425 L 
212.5 419.39 L 216.1 412.5 L 212.5 402.1 L 212.15 400 L 
200 390.21 L 187.5 391.18 L 176.66 400 L S 334.79 525 M
337.5 527.52 L 339.57 525 L 337.5 515.95 L 334.79 525 L 
S 122.8 600 M 112.5 604.09 L 100.16 612.5 L 100 612.61 L 
89.11 625 L 87.5 629.15 L 82.65 637.5 L 75 648.97 L 
74.46 650 L 64.89 662.5 L 65.67 675 L 75 682.84 L 
87.5 683.84 L 100 684.81 L 112.5 680.81 L 125 676.21 L 
129.46 675 L 137.5 671.01 L 150 670.61 L 153.94 675 L 
162.5 680.04 L 175 682.85 L 187.09 675 L 187.5 674.8 L 
197.6 662.5 L 200 658.76 L 205.7 650 L 209.52 637.5 L 
205.21 625 L 200 621.02 L 187.5 616.6 L 175 613.28 L 
173.31 612.5 L 162.5 604.66 L 153.01 600 L 150 598.77 L 
137.5 597.71 L 125 599.18 L 122.8 600 L S
yellow S 166.65 400 M 162.5 402.34 L 150 412.3 L 
149.67 412.5 L 139.46 425 L 137.5 428.57 L 126.82 437.5 L 
125 438.81 L 116.65 450 L 115.63 462.5 L 112.5 466.68 L 
109.4 475 L 110.94 487.5 L 112.5 490.93 L 116.79 500 L 
125 506.59 L 137.5 504.05 L 143.84 500 L 150 497.38 L 
161.9 487.5 L 162.5 487.12 L 175 478.13 L 177.85 475 L 
187.5 467.54 L 192.74 462.5 L 200 453.83 L 203.59 450 L 
210.88 437.5 L 212.5 429.74 L 216.51 425 L 221.09 412.5 L 
220.51 400 L 212.5 392.9 L 200 388.28 L 187.5 388.62 L 
175 394.83 L 166.65 400 L S 344.26 500 M 337.5 501.46 L 
330.22 512.5 L 325 522.9 L 323.41 525 L 325 530.77 L 
334.56 537.5 L 337.5 538.31 L 338.2 537.5 L 348.15 525 L 
350 519.82 L 353.22 512.5 L 351.46 500 L 350 495.86 L 
344.26 500 L S 160.22 562.5 M 160.77 575 L 151.38 587.5 L 
150 587.72 L 137.5 589.38 L 125 588.95 L 112.5 590.23 L 
100 596.99 L 96.33 600 L 87.5 612.26 L 87.38 612.5 L 
77.93 625 L 75 629.49 L 68.27 637.5 L 63.42 650 L 
62.5 651.33 L 56.52 662.5 L 54.26 675 L 62.5 687.16 L 
62.97 687.5 L 75 695.53 L 87.5 694.62 L 100 693.31 L 
112.5 691.05 L 123.38 687.5 L 125 687.14 L 137.5 686.33 L 
146.44 687.5 L 150 688.27 L 162.5 692.32 L 175 691.99 L 
180.01 687.5 L 187.5 683.19 L 194.52 675 L 200 667.06 L 
204.28 662.5 L 209.98 650 L 212.5 640.18 L 214.27 637.5 L 
214.05 625 L 212.5 623.31 L 200 614.71 L 192.55 612.5 L 
187.5 609.36 L 175 601.69 L 172.76 600 L 165.18 587.5 L 
163.94 575 L 164.35 562.5 L 162.5 559.43 L 160.22 562.5 L S
blue S 61.66 250 M 62.5 250.69 L 75 255.98 L 87.5 253.21 L 
95.45 250 L S 150.37 250 M 162.5 255.47 L 170.69 250 L 
S 184.08 387.5 M 175 389.36 L 162.5 393.49 L 150 397.84 L 
145.35 400 L 137.5 403.9 L 125.88 412.5 L 125 414.87 L 
121.79 425 L 112.5 435.6 L 110.89 437.5 L 105.41 450 L 
104.45 462.5 L 101.3 475 L 100.38 487.5 L 103.88 500 L 
107.54 512.5 L 112.5 517.46 L 125 518.04 L 131.14 512.5 L 
137.5 510.36 L 150 504.63 L 155 500 L 162.5 495.12 L 
170.36 487.5 L 175 484.29 L 183.47 475 L 187.5 471.88 L 
197.24 462.5 L 200 459.21 L 208.63 450 L 212.08 437.5 L 
212.5 435.47 L 221.36 425 L 223.59 412.5 L 225 400.9 L 
225.53 400 L 225 399.1 L 212.5 388.75 L 204.94 387.5 L 
200 385.24 L 187.5 385.92 L 184.08 387.5 L S 343.88 487.5 M
337.5 493.08 L 331.51 500 L 326.2 512.5 L 325 514.9 L 
317.36 525 L 318.99 537.5 L 325 546.95 L 337.5 546.94 L 
345.7 537.5 L 350 531.23 L 354.69 525 L 358.52 512.5 L 
358.63 500 L 360.87 487.5 L 350 480.43 L 343.88 487.5 L 
S 103.55 550 M 100 550.83 L 91.79 562.5 L 94.18 575 L 
96.5 587.5 L 87.5 592.61 L 82.25 600 L 78.61 612.5 L 
75 618.18 L 68.18 625 L 62.5 633.1 L 59.53 637.5 L 
55.67 650 L 52.23 662.5 L 50 670.92 L S 103.55 550 M
112.5 547.42 L 114.42 550 L 116.86 562.5 L 125 574.38 L 
125.98 575 L 137.5 580.08 L 144.98 575 L 146.91 562.5 L 
150 554.55 L 152.59 550 L 162.5 539.51 L 170.33 550 L 
174.87 562.5 L 175 564.13 L 176.04 575 L 175 578.88 L 
173.52 587.5 L 175 589.99 L 182.88 600 L 187.5 602.77 L 
200 609.26 L 204.74 612.5 L 212.5 616.05 L 220.73 625 L 
219.77 637.5 L 212.5 648.52 L 212.12 650 L 209.24 662.5 L 
200 672.34 L 198.16 675 L 187.5 687.45 L 187.41 687.5 L 
175 698.63 L 170.69 700 L S 497.14 675 M 500 680.99 L 
S 497.14 675 M 500 670.92 L S 52.78 687.5 M 61.66 700 L 
S 52.78 687.5 M 50 680.99 L S 95.45 700 M 100 699.46 L 
112.5 699.04 L 125 697.16 L 137.5 697.99 L 150 699.86 L 
150.37 700 L S
magenta S 50.23 250 M 62.5 260.14 L 69.06 262.5 L 75 267.5 L 
87.5 267.26 L 100 263.67 L 109.38 262.5 L 112.5 262.2 L 
125 259.18 L 137.5 261.46 L 142.5 262.5 L 150 264.52 L 
162.5 265.44 L 166.5 262.5 L 175 258.24 L 182.24 250 L 
S 118.14 387.5 M 114.66 400 L 112.5 405.64 L 107.16 412.5 L 
106.63 425 L 100 434.29 L 97.83 437.5 L 95 450 L 
94.02 462.5 L 87.5 473.32 L 86.54 475 L 87.5 478.87 L 
88.67 487.5 L 90.82 500 L 89.78 512.5 L 96.48 525 L 
91.81 537.5 L 87.5 542.32 L 79.82 550 L 77.28 562.5 L 
76.89 575 L 75 580 L 72.16 587.5 L 66.61 600 L 
64.69 612.5 L 62.5 614.69 L 57.54 625 L 51.57 637.5 L 
50.75 650 L 50 656.69 L S 118.14 387.5 M 125 383.07 L 
131.09 387.5 L 137.5 390.44 L 150 387.7 L 151.21 387.5 L 
162.5 382.5 L 175 380.81 L 187.5 378.53 L 200 378.3 L 
212.5 380.68 L 225 385.63 L 226.88 387.5 L 232.71 400 L 
226.72 412.5 L 225 414.92 L 224.27 425 L 217.26 437.5 L 
212.5 444.93 L 211.65 450 L 200 462.44 L 199.95 462.5 L 
187.5 474.49 L 186.84 475 L 177.55 487.5 L 175 492.26 L 
165.21 500 L 162.5 503.52 L 150 512.01 L 148.33 512.5 L 
137.5 522.72 L 134.55 525 L 125 530.99 L 117.88 537.5 L 
124.34 550 L 124.84 562.5 L 125 562.73 L 137.5 564.39 L 
138.09 562.5 L 141.78 550 L 150 539.51 L 151.9 537.5 L 
162.5 526.9 L 175 533.5 L 177.94 537.5 L 180.61 550 L 
182.44 562.5 L 183.8 575 L 184.22 587.5 L 187.5 593.18 L 
192.73 600 L 200 602.72 L 212.5 608.98 L 216.93 612.5 L 
224.73 625 L 223.07 637.5 L 219.33 650 L 212.5 660.99 L 
212.21 662.5 L 202.94 675 L 200 678.73 L 196.53 687.5 L 
187.5 695.91 L 182.24 700 L S 345.98 475 M 337.63 487.5 L 
337.5 487.61 L 326.78 500 L 325 505.37 L 319.23 512.5 L 
313.73 525 L 313.8 537.5 L 316.06 550 L 325 557.1 L 
337.5 557.43 L 343.28 550 L 350 538.54 L 350 537.5 L 
359.62 525 L 361.7 512.5 L 362.5 503.57 L 364.52 500 L 
370.52 487.5 L 369.63 475 L 362.5 466.28 L 350 470.74 L 
345.98 475 L S 497.67 662.5 M 490.34 675 L 493.97 687.5 L 
500 699.56 L S 497.67 662.5 M 500 656.69 L S 50.23 700 M
50 699.56 L S black
-------------------------------------------------------------------

List of PDB and chain IDs

The following PDB entries and chains were used in the analysis:

 1cbn _
 8rxn A
 1igd _
 1arb _
 1cse IE
 2sn3 _
 5rxn _
 1cus _
 7rsa _
 135l _
 1fus _
 1ptx _
 1rro _
 1plc _
 1utg _
 4ptp _
 5p21 _
 1ppt _
 1thm _
 1eca _
 1hmt _
 1rcf _
 1rdg _
 1st3 _
 256b A
 2ctc _
 2ihl _
 3ebx _
 3sdh A
 1aba _
 2end _
 4gcr _
 2rn2 _
 1xnb _
 1xso A
 8abp _
 1aap A
 1bab BA
 1ccr _
 1cka A
 1ezm _
 1flp _
 1hpg A
 1isu A
 1lzr _
 1noa _
 1pmy _
 1poa _
 1sha A
 1wfb A
 2hbg _
 2mcm _
 2plt _
 2prk _
 2sga _
 3b5c _
 5cyt R
 6rxn _
 9rnt _
 2cba _
 3grs _
 5pal _
 1tca _
 1tgx A
 3ovo _
 1hfc _
 1erl _
 1ads _
 1bfg _
 1cdp _
 1csh _
 1hcb _
 1knt _
 1lid _
 1mrj _
 1nfp _
 1ppn _
 1ptf _
 1scs _
 1trz B
 2ayh _
 2dri _
 2er7 E
 2rhe _
 2sil _
 3gct A
 4bp2 _
 4icb _
 4xis _
 7pti _
 8tln E
 1htr PB
 2cpl _
 2rmc A
 1dts _
 1php _
 1pva A
 2wrp R
 3est _
 3psg _
 1cpc AB
 2hmz A
 3chy _
 2ccy A
 1osa _
 2trx A
 1alc _
 1bgc _
 1cll _
 1ctf _
 1etb 1
 1fkf _
 1fnc _
 1frd _
 1fxd _
 1gca _
 1gdm _
 1gmp A
 1gof _
 1hbq _
 1hml _
 1hrm _
 1knb _
 1l92 _
 1lsm _
 1mfa _
 1nsc A
 1ofv _
 1onc _
 1rop A
 1s01 _
 1sbp _
 1sgt _
 1tad C
 1ypc I
 2act _
 2alp _
 2bop A
 2csc _
 2cy3 _
 2mge _
 2mhr _
 3dfr _
 4dfr A
 5rub A
 8dfr _
 1ges A
 1myt _
 1mdc _
 1myg A
 1thv _
 2bbk H
 2cyr _
 3cla _
 1pda _
 1emy _
 1aaj _
 1amp _
 1apv E
 1ars _
 1bbh A
 1bgh _
 1btl _
 1caa _
 1cbs _
 1cig _
 1cmc A
 1ept ABC
 1fas _
 1fca _
 1fna _
 1frr A
 1gbs _
 1gd1 O
 1glq A
 1hcr A
 1hpi _
 1hrn B
 1hvi A
 1hyp _
 1ilk _
 1isc A
 1ivd _
 1kab _
 1len AB
 1lmb 3
 1lmn _
 1lst _
 1mng A
 1mrg _
 1nar _
 1npk _
 1olb A
 1omp _
 1pgs _
 1ppo _
 1rtm 1
 1shg _
 1srg A
 1ten _
 1tgs I
 1thg _
 1tml _
 1ton _
 1tph 1
 1ubi _
 1vfa BA
 1wap B
 1xnd _
 1ytb A
 2apr _
 2aza A
 2cdv _
 2exo _
 2fal _
 2fcr _
 2gst A
 2ohx A
 2pal _
 2por _
 2spc A
 2tgi _
 2zta A
 3cox _
 3sgb IE
 4fxn _
 7pcy _
 8fab BA
 8pti _
 9wga A
 1cel A
 1xya A
 1bit _
 1iae _
 2hts _
 5tim A
 1fdn _
 1hne E
 1tib _
 1hna _
 2ak3 B
 1aec _
 2cmd _
 1hsl A
 1ake A
 1aoz A
 1arp _
 1bmd A
 1bsr A
 1byb _
 1chm A
 1clc _
 1cth A
 1dfn A
 1ede _
 1fba A
 1fgv HL
 1gpb _
 1gpr _
 1hhl _
 1hrc _
 1hsb AB
 1lis _
 1loe C
 1mld A
 1nci A
 1nhk L
 1ntn _
 1opb A
 1pbe _
 1pbp _
 1pk4 _
 1raq _
 1rec _
 1rms _
 1rsy _
 1shf A
 1slt A
 1sxc A
 1ukz _
 1wtl A
 1yea _
 2chs A
 2cst A
 2fb4 HL
 2fx2 _
 2gbp _
 2mnr _
 2ran _
 3bcl _
 3hsc _
 3rp2 A
 3tgl _
 4enl _
 5azu A
 5fd1 _
 6fab LH
 7aat A
 7tim A
 1bam _
 1hle AB
 1lts ACD
 1ova B
 1yeb _
 2fbj HL
 1gar A
 1prn _
 2imn _
 1hds AB
 1abk _
 1acf _
 1afg A
 1ald _
 1alk A
 1apm E
 1bbp A
 1brs D
 1bsa A
 1cdg _
 1cew I
 1cfb _
 1cgt _
 1ddt _
 1drf _
 1dsb A
 1esl _
 1fdx _
 1fia B
 1frp A
 1gia _
 1gky _
 1gox _
 1gp1 A
 1hil BA
 1hip _
 1hoe _
 1hur A
 1huw _
 1hvd _
 1iag _
 1ids A
 1lct _
 1led _
 1lhs _
 1lki _
 1lld A
 1lob D
 1lte _
 1mee A
 1mjc _
 1mpp _
 1msc _
 1nba A
 1nbv H
 1nhp _
 1npc _
 1oyb _
 1pca _
 1pii _
 1poc _
 1poh _
 1ppa _
 1pso E
 1r69 _
 1rbp _
 1rei A
 1ris _
 1rtp 1
 1rva A
 1sac A
 1sem A
 1smr A
 1sph A
 1srd A
 1srp _
 1trb _
 1trk A
 1wht AB
 2blt A
 2cts _
 2dnj A
 2ebn _
 2hpd A
 2hpe A
 2i1b _
 2kau BCA
 2lhb _
 2mcg 1
 2mhb BA
 2nad A
 2paz _
 2pgd _
 2rsp B
 2scp A
 3blm _
 3cms _
 3il8 _
 3pga 3
 3rub LS
 4blm A
 7fab HL
 8acn _
 9ldt A

awk definition of the core regions


# defcor.awk adapted from f77 subroutine defcor by Taylor/Kleywegt
# Charlie Bond 10i97
function defcor(coregn){
for ( i=1 ; i <=37 ; i++ )
{ for ( j=1 ; j <=37 ; j++ )  
  {  coregn[i,j] = 0 }}
for ( i = 2; i <=  11 ; i++ )
  { coregn[i,1] = 1 }
for ( i =   3;  i <=  5 ; i++ )
  { coregn[i,2] = 1 }
for ( i =   9;  i <=  10 ; i++ )
  { coregn[i,2] = 1 }
# 2005-05-04 - bug fixed in next line (11 should be 12; thanks are due to Peter Robinson)
coregn[7,12] = 1
for ( i =  10;  i <= 15 ; i++ )
  { coregn[i,12] = 1 }
for ( i =  7;  i <= 15 ; i++ )
  { coregn[i,13] = 1 }
for ( i =  6;  i <= 15 ; i++ )
  { coregn[i,14] = 1 }
for ( i =  6;  i <= 14 ; i++ )
  { coregn[i,15] = 1 }
for ( i =  5;  i <= 14 ; i++ )
  { coregn[i,16] = 1 }
for ( i =  5;  i <= 13 ; i++ )
  { coregn[i,17] = 1 }
for ( i =  5;  i <= 12 ; i++ )
  { coregn[i,18] = 1 }
for ( i =  4;  i <= 11 ; i++ )
  { coregn[i,19] = 1 }
for ( i =  25;  i <= 26 ; i++ )
  { coregn[i,19] = 1 }
for ( i =  5 ;  i <= 11 ; i++ )
  { coregn[i,20] = 1 }
for ( i =  25;  i <= 26 ; i++ )
  { coregn[i,20] = 1 }
for ( i =  5;  i <= 10 ; i++ )
  { coregn[i,21] = 1 }
for ( i =  24;  i <= 26 ; i++ )
  { coregn[i,21] = 1 }
for ( i =  5;  i <= 8 ; i++ )
  { coregn[i,22] = 1 }
for ( i =  23;  i <= 25 ; i++ )
  { coregn[i,22] = 1 }
for ( i =  5;  i <= 7 ; i++ )
  { coregn[i,23] = 1 }
for ( i =  23;  i <= 25 ; i++ )
  { coregn[i,23] = 1 }
for ( i =  5;  i <= 6 ; i++ )
  { coregn[i,24] = 1 }
for ( i =  10;  i <= 11 ; i++ )
  { coregn[i,24] = 1 }
for ( i =  23;  i <= 25 ; i++ )
  { coregn[i,24] = 1 }
for ( i =  4;  i <= 6 ; i++ )
  { coregn[i,25] = 1 }
for ( i =  9;  i <= 11 ; i++ )
  { coregn[i,25] = 1 }
for ( i =  23;  i <= 24 ; i++ )
  { coregn[i,25] = 1 }
for ( i =  4;  i <= 6 ; i++ )
  { coregn[i,26] = 1 }
for ( i =  9;  i <= 11; i++ )
  { coregn[i,26] = 1 }
for ( i =  4;  i <= 11 ; i++ )
  { coregn[i,27] = 1 }
for ( i = 3;  i <= 11 ; i++ )
  { coregn[i,28] = 1 }
for ( i = 3;  i <= 12 ; i++ )
  { coregn[i,29] = 1 }
for ( i = 3;  i <= 14 ; i++ )
  { coregn[i,30] = 1 }
for ( i = 2;  i <= 14 ; i++ )
  { coregn[i,31] = 1 }
for ( i = 2;  i <= 14 ; i++ )
  { coregn[i,32] = 1 }
for ( i = 2;  i <= 14 ; i++ )
  { coregn[i,33] = 1 }
for ( i = 1;  i <= 13 ; i++ )
  { coregn[i,34] = 1 }
for ( i = 1;  i <= 13 ; i++ )
  { coregn[i,35] = 1 }
for ( i = 1;  i <= 12 ; i++ )
  { coregn[i,36] = 1 }
coregn[37,37] = 1
for ( i = 2;  i <= 11 ; i++ )
  { coregn[i,37] = 1 }
return
}

Contoured PostScript Ramachandran plots for individual residue types

The following are links to PostScript files:

Colour-ramped, log-scaled PostScript Ramachandran plots for individual residue types

The following are links to PostScript files:

Contoured GIF Ramachandran plots for individual residue types

The following are links to GIF files:

Colour-ramped, log-scaled GIF Ramachandran plots for individual residue types

The following are links to GIF files:

Trends

The following two PostScript files were contributed by Morten Kjeldgaard:

Why definitions matter

Compare the Ramachandran plots for PDB entry 3LZ2 (just an example): In ProCheck's definition, 3LZ2 has 0% outliers (but note that it has only 76.8% of its residues in the most-favoured regions), whereas in the Kleywegt & Jones definition it has 13% outliers. WHAT IF deals with Ramachandran plots differently and assigns it a Z-score of -4.3 (which is poor).

The moral of this story: when you report validation results for your structure, quote the method/program used ! A statement in your paper that "there are no outliers in the Ramachandran plot" is completely meaningless if you don't tell the reader which definition you use !