The amino acid sequence itself should be input into the bottom dialog box, which is labeled "Sequence:". The format for entering this sequence is to represent every amino acid with a single letter. At the bottom of this page a table is provided showing the conversions between three-letter and one-letter notation. For example, to evaluate the sequence, lysine-lysine-proline, you would enter into the "Sequence:" dialog box
KKP
and then click on the "Submit Sequence" button to both evaluate this and go to the page displaying the Paircoil program's analysis of your amino acid sequence. Note that an actual sequence (not the fictional one above) must be at least 28 amino acid residues long in order for the Paircoil program to meaningfully analyse the data.
In interpreting the entered sequence, the program ignores anything
which is not representative of a single amino acid. In particular, the
letters X, B, and Z are ignored, not replaced with one of the amino
acids they stand for. Also, whitespace such as returns and tabs, as
well as '*'s are ignored. The sequence below
K
K
P
is understood to be the same as the sequence above, KKP.
If at any time you wish to start over typing in your entry, click on the "Reset Form" button next to the "Submit Sequence" button.
A typical query might look something like this
Sequence Name: ctychrome c6 - brown alga (Petalonia fascia)
Probability Cutoff: 0.5
Sequence:
VDINNGESVFTANCSACHAGGNNVIMPEKTLKKDALEENEM
NNIKSITYQVTNGKNAMPAFGGRLSETDIEDVANFVISQSQKGW
After filling in the form with this data, clicking the "Submit
Sequence" button should return a page displaying the results of the
Paircoil program's analysis of this sequence.
The Paircoil program interface provides four formats for intrepreting data. Two are graphs of the residue-by-residue probability of that residue lying in a coiled coil. The x-axis contains the residue location (from the start, 1 being the first residue in the sequence), and the y-axis contains the probability of a coiled coil. The probability cutoff is shown as a dashed line. A gif version of the graph is shown by default. A postscript version of the same graph is available from the bottom of the page.
The two text formats for interpreting data, "Per-residue scores", and "Positions and Registers", are both available by following the links at the bottom of the page. The "Per-residue score" document has a table containing the sequence name, the type of every residue, this residue's position in the overall sequence, the register position in the heptad repeat which yielded a maximum probability for this residue forming part of a coiled coil, the probability as determined by the Paircoil program that this residue does lie in a coiled coil domain, and (in parentheses) the raw score which Paircoil assigns to every residue which is then scaled to give a probability.
"Positions and registers" contains a short summary of the overall score of the sequence. This document contains the sequence name, the probability cutoff, whether any domain in the sequence did meet this cutoff, and where the most likely coiled coil domain of the sequence was located, as well as how well this maximal point did score.
Warning! The data generated by using this program is not saved from session to session and the user is advised to save all relevant data after analyzing the sequence and before leaving the page. To ease the download of the results, a ZIP and a TAR archives containing all data files are provided. ZIP compatible programs are available mostly on PCs (pkunzip, winzip, etc.), while TAR is the standard UNIX archiving program. If you do not have either of these programs, you could download the data files you need by clicking on them and choosing the 'Save' command in your browser.
Bonnie Berger, David B. Wilson, Ethan Wolf, Theodore Tonchev, Mari Milla, and Peter S. Kim, "Predicting Coiled Coils by Use of Pairwise Residue Correlations", Proceedings of the National Academy of Science USA, vol 92, aug 1995, pp. 8259-8263.
The Paircoil program predicts the location of coiled-coil regions in amino acid sequences.
You can download the Paircoil program from this page. Instuctions for installing a copy of the program on your system are also available by sending mail to paircoil@csail.mit.edu.
Other questions can be sent to paircoil-help@csail.mit.edu.