The ConSurf Server colors amino acids in a 3D protein structure by evolutionary conservation -- entirely automatically. For details, please see the ConSurf Server. Beginning with ConSurf 3, the results of a ConSurf job can be saved in a specially annotated PDB file. The examples below were saved from ConSurf jobs. The parameters of each job can be viewed (after you display the result using one of the links below) by clicking ConSurf Job Information.

• 2VAA chain A: Major histocompatibility class I (mouse) complexed with an octapeptide from VSV nucleoprotein.
  Key points to appreciate about this intriguing pattern of conservation are noted in views saved from the ConSurf result as MolSlides.
  
  
  • 2VAA chain A: Insufficient data.
    150 sequence homologs were used for the above job, but in this job, only 50 were used. With only 50 sequences, conservation grades could not be calculated with confidence for all amino acids. A special yellow color indicates the amino acids for which the data were insufficient to calculate a reliable conservation grade. Detecting and marking amino acids with insufficient data is a new feature in ConSurf 3. After you display this result, you will see a link "Display #1" that enables you to hide the insufficient data color if you wish.
    
    
  • 2VAA chain A: Alternate color scheme.
    This illustrates how the default conservation color scheme used by ConSurf can be changed in a saved PDB file. (In this example, grades 4, 5, and 6 use the same color.) The default colors work best on a white background, but here, the default background has been changed to black, which works best for the alternate scheme. Instructions for changing the conservation color scheme are available by clicking the link "Changing the conservation color scheme" (at the bottom of the ConSurf or by clicking
  
  
• 1FLO chain A: Flp recombinase complexed with a DNA Holliday junction.
  Any combination of the four sequence-identical chains in this homotetramer can be colored according to the ConSurf results (see the checkboxes for each chain). This is a new feature in ConSurf 3. There are many amino acids with insufficient data here because only nine homologs were found in Uniprot. However, the data are sufficient to see conservation in the DNA-binding and catalytic regions with confidence.
  
  
• 1IGY chain B: Heavy chain of an intact IgG1 antibody.
  Illustrates a case in which ConSurf's automated gathering of homologous sequences leaves one or more entire domains with insufficient data for reliable assignment of conservation grades. Which domains have insufficient data varies with time, as the sequence databases grow. (When this example was run, in June 2006, the entire variable domain had insufficient data.) Whole domains with insufficient data is a common complication with multiple domain chains. To avoid this, it is recommended that you separate the single domain of interest from the PDB file (by text editing), and upload the single domain. (The absence of adequate data for the constant domains was not evident in ConSurf version 2, but could be detected when you inspected the multiple sequence alignment carefully.)
  
  Variable Domain of Heavy Chain: In order to guarantee that conservation grades are calculated for the variable domain of the antibody heavy chain, a separate run was performed by uploading a PDB file in which the constant domains (and corresponding SEQRES segment) were deleted for chain B (keeping only residues 2-114 in chain B). (The SEQRES must be changed since ConSurf uses it!) The striking patch of highly variable residues occurs at the antigen-binding face (complementarity-determining regions). The highly conserved residues appear to be those crucial for proper folding of this immunoglobulin domain.
  
  This is also a case in which the sequence contains "insertions" because the sequence is numbered according to a reference sequence. There are also many "gaps" in the sequence numbering for the same reason. In this case, these do not represent physical gaps in the polypeptide backbone. To see the inserted blocks, click on Clickable ConSurf-Colored Sequence 3D; they are marked with green asterisks. Such insertions were not handled correctly by ConSurf version 2.
  
  
• 1CBN: Seed protein crambin (single unnamed chain).
  This PDB file contains sequence microheterogeneity, which was not handled correctly by ConSurf 2, but is handled better by ConSurf 3.
  
  Sequence microheterogeneity can best be detected by a careful inspection of the contents of the PDB file. Typically, it is signified by the occurrence of residues with coordinates (ATOM records) that are not listed in the SEQRES records. Typically, in the coordinates, these have redundant sequence numbers with insertion letters. For example, in 1CBN, there is microheterogeneity at positions 22 and 25, noted in REMARK 4. This causes the number of residues in SEQRES to be less than the number with coordinates (shown in the ConSurf Job Information report). When this occurs, Protein Explorer asks you to confirm that the PDB file contains sequence microheterogeneity, as otherwise, this condition might signal an internal error in the ConSurf code.
  
  Sequence microheterogeneity typically shows up as "insertions" in Protein Explorer's ConSurf-Colored Sequence 3D, Seq3D, and Sequences listings, because Protein Explorer cannot presently distinguish true insertions (present in both SEQRES and coordinates) from sequence microheterogeneity.
  
  ConSurf calculates conservation grades for the residues in the SEQRES record, which do not include the "inserted" residues representing microheterogeneity. Therefore, the latter are not assigned conservation colors, and remain colored carbon gray.