Sequence file: Difference between revisions
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CYSS 24 | CYSS 24 | ||
By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the trans position, | This sequence consists of 14 amino acid residues that are numbered consequtively 11-24. | ||
Residue names are case-sensitive. | |||
Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used. | |||
By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the ''trans'' position, ''ω'' = 180°. Optionally, OMEGA angles can be fixed in the ''cis'' position, ''ω'' = 0°, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above. | |||
== Equivalent forms == | == Equivalent forms == | ||
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TRP | TRP | ||
CYSS | CYSS | ||
Multiple residues can be written on a line: | Multiple residues can be written on a line: | ||
GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS | GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS | ||
== Multiple molecules == | |||
Multiple molecules must be separated by a stretch of "invisible" linker residues: | |||
GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 1 | |||
PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker | |||
GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2 | |||
The standard residue library provides the following linker residues: | |||
* '''PL''': Linker from a protein amino acid residue to a linker residue | |||
* '''LL''': Linker residue with a virtual bond length of 1 Å | |||
* '''LL2''': Linker residue with a virtual bond length of 2 Å | |||
* '''LL5''': Linker residue with a virtual bond length of 5 Å | |||
* '''LP''': Linker from a linker residue to a protein amino acid residue | |||
== Non-standard covalent links == | |||
A non-standard covalent link can be declared by a '''link''' statement. For instance, for a cyclic peptide: | |||
GLY 11 | |||
SER 12 | |||
ILE 13 | |||
PRO 14 | |||
CYSS 15 | |||
LEU 16 | |||
LEU 17 | |||
SER 18 | |||
cPRO 19 | |||
TRP 20 | |||
SER 21 | |||
GLU 22 | |||
TRP 23 | |||
CYSS 24 | |||
link N 11 C 24 | |||
The purpose of the '''link''' statement is to eliminate the steric repulsion between the two covalently bound atoms and the atoms directly bound to them. The '''link''' statement will ''not'' enforce the formation of a covalent bond between the two atoms. This must be made by explicit distance constraints. | |||
Latest revision as of 13:58, 29 January 2009
Basic format
GLY 11 SER 12 ILE 13 PRO 14 CYSS 15 LEU 16 LEU 17 SER 18 cPRO 19 TRP 20 SER 21 GLU 22 TRP 23 CYSS 24
This sequence consists of 14 amino acid residues that are numbered consequtively 11-24.
Residue names are case-sensitive.
Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.
By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the trans position, ω = 180°. Optionally, OMEGA angles can be fixed in the cis position, ω = 0°, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.
Equivalent forms
Residue numbers can be omitted if they are equal to the residue number of the previous residue plus 1. The first residue number can be omitted if it is equal to 1.
GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS
Multiple residues can be written on a line:
GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS
Multiple molecules
Multiple molecules must be separated by a stretch of "invisible" linker residues:
GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 1 PL 51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP # linker GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS # molecule 2
The standard residue library provides the following linker residues:
- PL: Linker from a protein amino acid residue to a linker residue
- LL: Linker residue with a virtual bond length of 1 Å
- LL2: Linker residue with a virtual bond length of 2 Å
- LL5: Linker residue with a virtual bond length of 5 Å
- LP: Linker from a linker residue to a protein amino acid residue
Non-standard covalent links
A non-standard covalent link can be declared by a link statement. For instance, for a cyclic peptide:
GLY 11 SER 12 ILE 13 PRO 14 CYSS 15 LEU 16 LEU 17 SER 18 cPRO 19 TRP 20 SER 21 GLU 22 TRP 23 CYSS 24 link N 11 C 24
The purpose of the link statement is to eliminate the steric repulsion between the two covalently bound atoms and the atoms directly bound to them. The link statement will not enforce the formation of a covalent bond between the two atoms. This must be made by explicit distance constraints.