TMhhcp
Transmembrane Helix-Helix Contact Predictor
 

HELP FOR USING TMhhcp

1. An example of the sequence

AQDMVSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVN
VENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGW
DIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNI
LVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF

2. An example of the topology of a transmembrane protein sequence

UUUUOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOHHHHHHHHHHHHHHHHHHHHIIIHHHHHHHHHHHHHHHHHHH
OOOOOOOOOOOOOOOHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHHOOUU

The format of the topology is given above. "H" denotes transmembrane segment, "O" denotes outside position, "I" denotes inside position and "U" denotes unknown topology. Please make sure that the topologies at each side of the transmembrane helix must be marked clearly. The topology for a sequence could be predicted using transmembrane protein topology prediction softwares such as TMHMM and HMMTOP.

3. Definitions of residue contacts

Two definitions of residue contacts were employed in this server.

DEF1: two residues within different helices are in contact if the minimal distance between side chain or backbone atoms was less than 5.5Å.

DEF2: C-beta atom (C-alpha atom for glycine) distance less than 8Å for two residues to be in contact.

4. Training and test data in TMhhcp

(1) Sequences and topologies for the training data

(2) Sequences and topologies for the test data

(3) Training data set for the first residue contact definition

(4) Training data set for the second residue contact definition

(5) Test data set for the first residue contact definition

(6) Test data set for the second residue contact definition

5. Output

The output of the server is a table listing the top L/5 predicted residue contacts of two helices for the protein. The column names "helix", "position", "residue", "score" in the table represent helix number, sequence position, residue type and the probability for two residues to contact, respectively.

6. Sourcecode of TMhhcp

(1) Sourcecode

(2) README of the sourcecode

(3) Unirf90 database


Copyright © 2011 Ziding Zhang's Lab, China Agricultural University
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