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Table 1 Defined labels for secondary structure vectors

From: TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

 

Vector type

Direction*

Strand

Helix

Inter-SSEs

x 2 -x 1 > 0, y 2 -y 1 > 0, z 2 -z 1 > 0

A

I

Q

x 2 -x 1 > 0, y 2 -y 1 > 0, z 2 -z 1 < 0

B

J

R

x 2 -x 1 > 0, y 2 -y 1 < 0, z 2 -z 1 > 0

C

K

S

x 2 -x 1 > 0, y 2 -y 1 < 0, z 2 -z 1 < 0

D

L

T

x 2 -x 1 < 0, y 2 -y 1 > 0, z 2 -z 1 > 0

E

M

U

x 2 -x 1 < 0, y 2 -y 1 > 0, z 2 -z 1 < 0

F

N

V

x 2 -x 1 < 0, y 2 -y 1 < 0, z 2 -z 1 > 0

G

O

W

x 2 -x 1 < 0, y 2 -y 1 < 0, z 2 -z 1 < 0

H

P

X

  1. * (x1, y1, z1) and (x2, y2, z2) denote start and end points of SSE vectors.
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Algorithms for Molecular Biology

ISSN: 1748-7188