International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, pp. 182-183

Section 3.6.7.5.3. Structural interactions

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.7.5.3. Structural interactions

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The data items in these categories are as follows:

(a) STRUCT_CONN_TYPE [Scheme scheme150]

(b) STRUCT_CONN [Scheme scheme151]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

The structural interactions that are described with data items in the STRUCT_CONN family of categories are the tertiary result of a structure determination, not the chemical connectivity of the components of the structure. In general, the interactions described using the STRUCT_CONN data items are noncovalent, such as hydrogen bonds, salt bridges and metal coordination.

It is useful to think of the structure interactions given in CHEM_COMP_BOND, CHEM_LINK and ENTITY_LINK as the covalent interactions that are known in advance of the structure determination because the chemistry of the components is well defined. Literature or calculated values for these interactions are often used as restraints during the refinement. In contrast, the structural interactions described in the STRUCT_CONN family of categories are not known in advance and are part of the results of the structure determination.

This distinction only holds approximately, as there are clearly bonds, such as disulfide links, that are covalent and usually restrained during the refinement but that are also a result of the folding of the protein revealed by the structure determination, and thus should be described using STRUCT_CONN data items.

In general, the STRUCT_CONN data items would not be used to list all the structure interactions. Instead, the author of the mmCIF would use the STRUCT_CONN data items to identify and annotate only the structural interactions worthy of discussion. The relationships between categories used to describe structural interactions are shown in Fig. 3.6.7.10[link].

[Figure 3.6.7.10]

Figure 3.6.7.10 | top | pdf |

The family of categories used to describe structural interactions such as hydrogen bonding, salt bridges and disulfide bridges. Boxes surround categories of related data items. Data items that serve as category keys are preceded by a bullet ([\bullet]). Lines show relationships between linked data items in different categories with arrows pointing at the parent data items.

Structural interactions such as hydrogen bonds, salt bridges and disulfide bridges can be described in the STRUCT_CONN category. The type of each interaction and the criteria used to identify the interaction can be specified in the STRUCT_CONN_TYPE category (Example 3.6.7.10[link]).

Example 3.6.7.10. A hypothetical salt bridge and hydrogen bond described with data items in the STRUCT_CONN_TYPE and STRUCT_CONN categories.

[Scheme scheme152]

The atoms participating in each interaction are arbitrarily labelled as `partner 1' and `partner 2'. Each is identified by the *_alt, *_asym, *_atom, *_comp and *_seq constituents of the corresponding atom-site label. The role of each partner in the interaction (e.g. donor, acceptor) may be specified, and any crystallographic symmetry operation needed to transform the atom from the position given in the ATOM_SITE list to the position where the interaction occurs can be given. The atoms participating in the interaction may also be identified using an alternative labelling scheme if the author has supplied one.

Unusual aspects of the interaction may be discussed in _struct_conn.details. The general type of an interaction can be indicated using _struct_conn.conn_type_id, which references one of the standard types described using data items in the STRUCT_CONN_TYPE category.

The specific types of structural connection that may be recorded are those allowed for _struct_conn_type.id, namely covalent and hydrogen bonds, ionic (salt-bridge) interactions, disulfide links, metal coordination, mismatched base pairs, covalent residue modifications and covalent modifications of nucleotide bases, sugars or phosphates. The criteria used to define each interaction may be described in detail using _struct_conn_type.criteria or a literature reference to the criteria can be given in _struct_conn_type.reference.








































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