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The Contacts section lists all kinds of amino acid - amino acid contacts. This
section includes other kinds of contacts, between amino acids and other things.
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| Code | Type of data |
| cli | Residues with a atomic contact to ligand < 1.0 Ångström |
| cnu | Residue-nucleic acid spheres closer than 1.0 Ångström |
| iod | Residue distance to nearest (positive) ion |
| ion | Short residue-ion distances, grouped per ion |
| cys | Lists cysteine bridges |
| sbr | Lists salt bridges |
| sbh | Lists salt bridges assuming histidine is positive |
All contacts are listed between amino acids and anything that is neither protein
nor nucleic acid, nor sugar, nor water. All contacts are listed of
any atom in the amino acid any any atom in the ligand that have less than
1.0 Ångström distance
between their Van der Waals′ surfaces.
Be aware that the automatic detection of sugars is a weak-spot in our
software.
The output typically looks like:
1876 SO4 ( 168 )A O1 - 57 ARG ( 70 )A CG 3.461 1876 SO4 ( 168 )A O1 - 57 ARG ( 70 )A CD 3.712 1876 SO4 ( 168 )A S - 57 ARG ( 70 )A NE 3.866 1876 SO4 ( 168 )A O1 - 57 ARG ( 70 )A NE 2.874 1876 SO4 ( 168 )A O3 - 57 ARG ( 70 )A NE 3.539 1876 SO4 ( 168 )A S - 57 ARG ( 70 )A CZ 4.407 1876 SO4 ( 168 )A O1 - 57 ARG ( 70 )A CZ 3.655 1876 SO4 ( 168 )A O3 - 57 ARG ( 70 )A CZ 3.726 1876 SO4 ( 168 )A S - 57 ARG ( 70 )A NH2 3.944 1876 SO4 ( 168 )A O1 - 57 ARG ( 70 )A NH2 3.584 1876 SO4 ( 168 )A O3 - 57 ARG ( 70 )A NH2 3.001 1876 SO4 ( 168 )A S - 61 THR ( 74 )A CB 4.344 1876 SO4 ( 168 )A O2 - 61 THR ( 74 )A CB 3.364 1876 SO4 ( 168 )A S - 61 THR ( 74 )A OG1 3.842 1876 SO4 ( 168 )A O2 - 61 THR ( 74 )A OG1 2.650 1876 SO4 ( 168 )A S - 61 THR ( 74 )A CG2 4.137 1876 SO4 ( 168 )A O1 - 61 THR ( 74 )A CG2 4.089 1876 SO4 ( 168 )A O2 - 61 THR ( 74 )A CG2 3.663 1876 SO4 ( 168 )A O3 - 61 THR ( 74 )A CG2 3.816
At the WHAT IF servers help page
you find a detailed description of all columns.
In short the left half before the minus sign is reserved for atoms in the ligand(s), the right half for atoms in protein / nucleic acids. The number without brackets is the WHAT IF residue number. The number in brackets is the residue number according to the PDB. The chain identifier follows directly after the closing bracket (In this example the chain identifier of the ligand SO4 is A and the chain identifiers of the Arginine and the Threonine that contact this SO4 are both A too. This option knows its own whynot text: COMMENT: Contains no ligands.
All contacts are listed between amino acids and nucleic acids. A contact is
listed if the amino acid and the nucleic acid share a pair of atoms that has
less than 1.0 Ångström distance between their Van der Waals′
surfaces.
So, this option just lists pairs of residues, without detailed
atomic contact information.
The output typically looks like:
47 SER ( 9 )A - 41 DTHY( 20 )F 66 PRO ( 139 )A - 3 DCYT( 3 )B 68 ASP ( 141 )A - 4 DGUA( 4 )B 76 ARG ( 149 )A - 16 DADE( 18 )C 76 ARG ( 149 )A - 17 DGUA( 19 )C 82 SER ( 155 )A - 16 DADE( 18 )C
In which the left column holds the amino acid-, and the right column the the nucleic acid- in the contact pair. Numbers and brackets, etc., as described above and as here.
This option knows its own whynot text: COMMENT: Contains no nucleic acids.
All contacts are listed between (positive) ions and residues. The contacts are
sorted by the residue, so in the table all contacts made for one ion are listed
as one block.
The output typically looks like:
23 GLU ( 27 )A OE1 - 173 MG ( 183 )A MG 2.075 23 GLU ( 27 )A OE2 - 173 MG ( 183 )A MG 3.425 58 GLU ( 62 )A OE1 - 173 MG ( 183 )A MG 2.102 58 GLU ( 62 )A OE2 - 173 MG ( 183 )A MG 3.388 61 HIS ( 65 )A ND1 - 173 MG ( 183 )A MG 2.201
In which the left column holds the residue-, and the right column the the ion- in the contact pair. Numbers and brackets, etc., as described above and as here.
This option knows its own whynot texts: COMMENT: Contains no ions and COMMENT: No short contacts to metal ions.
All contacts are listed between (positive) ions and residues. The contacts are
sorted by the ion, so in the table all contacts made for one ion are listed
as one block.
The output typically looks like:
187 CA ( 301 )A CA - 26 ALA ( 24 )A O 2.344 187 CA ( 301 )A CA - 29 GLU ( 27 )A O 2.430 187 CA ( 301 )A CA - 31 ARG ( 29 )A O 2.314 187 CA ( 301 )A CA - 34 SER ( 32 )A O 2.407 187 CA ( 301 )A CA - 39 GLU ( 37 )A OE1 2.426 187 CA ( 301 )A CA - 39 GLU ( 37 )A OE2 2.601 188 CA ( 302 )A CA - 66 ASP ( 64 )A OD1 2.274 188 CA ( 302 )A CA - 68 ASN ( 66 )A OD1 2.370 188 CA ( 302 )A CA - 70 ASP ( 68 )A OD1 2.429
In which the left column holds the ion-, and the right column the the residue- in the contact pair. Numbers and brackets, etc., as described above and as here.
This option knows its own whynot texts: COMMENT: Contains no ions and COMMENT: No short contacts to metal ions.
This Lists database lists for each PDB entry all its cysteine bridges in two directions (so each bridge is listed twice...). The output typically looks like:
3 CYS ( 3 )A - 40 CYS ( 40 )A
4 CYS ( 4 )A - 32 CYS ( 32 )A
16 CYS ( 16 )A - 26 CYS ( 26 )A
26 CYS ( 26 )A - 16 CYS ( 16 )A
32 CYS ( 32 )A - 4 CYS ( 4 )A
40 CYS ( 40 )A - 3 CYS ( 3 )A
Numbers and brackets, etc., as described above and as here.
This option knows its own whynot texts: COMMENT: Contains no cysteines and COMMENT: Contains no cysteine bridges.
Saltbridges are an important component of the protein stability. Proteins are loaded with charge-charge interactions, and if you consider also partial charges then all atom pairs also are a charge pair. We tend to talk about charge-charge intearactions only when dealing with full (or nearly full) charges like ions or the charged atoms in the side chains of, for example, Asp or Lys.
The files in this list contain all charge-charge pairs between oppositely charged protein atoms. So, interactions with ions are not listed here.
Saltbridge files typically look like:
... 30 GLU ( 29 )A OE1 - 62 LYS ( 61 )A NZ 7.018 37 ASP ( 36 )A OD2 - 33 LYS ( 32 )A NZ 8.333 37 ASP ( 36 )A OD1 - 41 ARG ( 40 )A NH2 7.244 37 ASP ( 36 )A OD1 - 62 LYS ( 61 )A NZ 2.821 * 44 ASP ( 43 )A OD2 - 22 LYS ( 21 )A NZ 9.816 44 ASP ( 43 )A OD2 - 78 LYS ( 77 )A NZ 2.661 52 GLU ( 51 )A OE2 - 78 LYS ( 77 )A NZ 7.272 52 GLU ( 51 )A OE1 - 95 LYS ( 94 )A NZ 7.725 57 ASN ( 56 )A O'' - 10 ARG ( 10 )A NE 2.832 ...
From left to right you find two residue-atom combinations, each existing of the sequential number of the residue in the PDB file, the residue type, in brackets the residue number and insertion code as found in the PDB file, the chain identifier of the chain in which this residue is found, and the atom involved in the saltbridge. The right-hand column holds the distance between the two atoms.
If you look at the saltbridge labelled with an asterix, you will realize that there is also a bridge between the OD2 of Asp and the NZ of Lys. In all these cases, however, only the atom pair with the shortest distance is listed. The N-terminus and the C-terminus are treated almost as if they are separate residues; so whereas you will normally see only one pair listed between a saltbridge forming residue pair, these can become multiple pairs if either one of them is a N- or C-terminal residue.
The last salt bridge in the table is between the O′′ (one of the two C-terminal oxygens) and Arginine 10. WHAT IF considers the N-terminus positive and the C-terminus negative; unless something is bound to them.
Saltbridges are an important component of the protein stability. Proteins are loaded with charge-charge interactions, and if you consider also partial charges then all atom pairs also are a charge pair. We tend to talk about charge-charge intearactions only when dealing with full (or nearly full) charges like ions or the charged atoms in the side chains of, for example, Asp or Lys.
There is a problem with Histidines because their sidechains can be positively charged, neutral, or even occasionally negatively charged. Perhaps we will one day make a list of saltbridge files in which we calculate the most likely protonation state of histidines, but for now, with the article deadline looming, we decided to make one list (see above) in which all histidines are considered neutral, and this list, in which all histidines are considered doubly protonated.
The files in this list contain all charge-charge pairs between oppositely charged protein atoms. So, interactions with ions are not listed here.
Saltbridge files typically look like:
... 44 ASP ( 43 )A OD2 - 22 LYS ( 21 )A NZ 9.816 44 ASP ( 43 )A OD1 - 42 HIS ( 41 )A NE2 4.938 44 ASP ( 43 )A OD2 - 78 LYS ( 77 )A NZ 2.661 44 ASP ( 43 )A OD2 - 111 HIS ( 110 )A NE2 6.906 52 GLU ( 51 )A OE1 - 47 HIS ( 46 )A ND1 4.349 52 GLU ( 51 )A OE2 - 78 LYS ( 77 )A NZ 7.272 ...
This table holds the same information as the saltbridge table in the previous (sbr) section.
Its is planned to make the cysteine bridges pages also list free cysteines and metal contacting cysteines. We also plan to make a saltbridges Lists in wich the charge of histidines is determined from its environment.
Unfortunately a day has only 24 hours...