
PFRMAT ABF1
TARGET T0004
AUTHOR 2125-9400-8806 Osvaldo Olmea, Florencio Pazos,
AUTHOR 2125-9400-8806 and Alfonso Valencia.
AUTHOR 2125-9400-8806     Protein Design Group. CNB-CSIC
AUTHOR 2125-9400-8806     Campus Universidad Autonoma.
AUTHOR 2125-9400-8806     Cantoblanco. M-28049 Madrid, Spain.
AUTHOR 2125-9400-8806     Tlf. +34.1.585.45.70  Fax. +34.1.585.45.06
AUTHOR 2125-9400-8806     email: valencia@samba.cnb.uam.es
REMARK 1.1 SECONDARY STRUCTURE PREDICTION BY PHD-SERVER EMBL-HEIDELBERG.
REMARK 1.1 INPUT ALIGMENT CONTAINS 23 SEQUENCES DOWN TO 30% SIMILARITY.
REMARK 1.1 SECONDARY STRUCTURE PREDICTION RELIABILITY IS ONLY GIVEN TO 
REMARK 1.1 FILL THE FORMAT BUT THEY ARE NOT USE IN OUR CONTACT PREDICTION METHOD.
REMARK 2.1 CONTACT BETWEEN SECONDARY STRUCTURE ELEMENTS.
REMARK 2.1 INITIAL INPUT FROM CONTACT PREDICTION (2.2) REFINED BY
REMARK 2.1 STATISTICAL CRITERIA ABOUT CONTACT DENSITY BETWEEN SECONDARY
REMARK 2.1 STRUCTURE ELEMENTS. THERE IS NO A SIMPLE DIRECT RELATION BETWEEN OUR
REMARK 2.1 RESIDUE-RESIDUE CONTACT PREDICTION AND THE PREDICTION OF CONTACT BETWEEN
REMARK 2.1 SECONDARY STRUCTURES.
REMARK 2.1 OUR METHOD DOES NOT PROVIDE INFORMATION ABOUT THE INTERACTION TYPE 
REMARK 2.1 (LESK CRITERIA) OR ABOUT THE MOST LIKELY CONTACTING RESIDUE. WE HAVE
REMARK 2.1 REFLECTED THESE FACTS WITH "?" SYMBOLS FOR THE INTERACTION TYPES AND
REMARK 2.1 WITH PROBABILITY "0" FOR THE MOST LIKELY CONTACTING RESIDUES.
REMARK 2.2 PREDICTION OF CONTACTS DONE COMBINING INFORMATION FROM CORRELATED
REMARK 2.2 MUTATIONS (GOBEL ET AL., 1994, OLMEA ET AL., 1996), SEQUENCE
REMARK 2.2 CONSERVATION, CONTACT DENSITY. A FEW RESIDUES ARE PREDICTED AND
REMARK 2.2 THE REST SET TO PROBABILITY "O". THE PROBABILITY 
REMARK 2.2 FOR THE PREDICTED CONTACTS IS TAKEN FOR THE AVERAGE IN A 
REMARK 2.2 TRAINING SET.
BEGDAT 1.1  1  1.0
SS 84
A C 0.9
E C 0.6
I E 0.3
E E 0.7
V E 0.5
G E 0.4
R E 0.6
V E 0.7
Y E 0.6
T E 0.6
G E 0.6
K E 0.7
V E 0.6
T E 0.8
R E 0.6
I E 0.5
V E 0.3
D C 0.1
F C 0.3
G E 0.1
A E 0.7
F E 0.9
V E 0.9
A E 0.9
I E 0.7
G E 0.1
G C 0.4
G C 0.6
K C 0.4
E E 0
G E 0.5
L E 0.8
V E 0.9
H E 0.9
I E 0.9
S E 0.8
Q E 0.5
I E 0.2
A C 0.2
D C 0.3
K C 0.4
R C 0.4
V C 0.3
E C 0.4
K C 0.6
V C 0.3
T C 0.2
D C 0
Y E 0.1
L E 0.4
Q E 0.3
M C 0.3
G C 0.8
Q C 0.4
E E 0.5
V E 0.9
P E 0.9
V E 0.9
K E 0.9
V E 0.9
L E 0.8
E E 0.7
V E 0.3
D C 0.4
R C 0.7
Q C 0.7
G C 0.2
R E 0.6
I E 0.9
R E 0.9
L E 0.9
S E 0.8
I E 0.6
K E 0.3
E C 0.3
A C 0.5
T C 0.7
E C 0.8
Q C 0.7
S C 0.5
Q C 0.7
P C 0.8
A C 0.8
A C 0.9
ENDDAT 1.1
BEGDAT 2.1  1   1.0  1
15
  1   2 ?? 0.00 0 0 0.00
  1   3 ?? 0.00 0 0 0.00
  1   4 ?? 0.00 0 0 0.00
  1   5 ?? 0.00 0 0 0.00
  1   6 ?? 0.00 0 0 0.00
  2   3 ?? 1.00 0 0 0.00
  2   4 ?? 0.75 0 0 0.00
  2   5 ?? 0.50 0 0 0.00
  2   6 ?? 0.00 0 0 0.00
  3   4 ?? 0.00 0 0 0.00
  3   5 ?? 0.19 0 0 0.00
  3   6 ?? 0.25 0 0 0.00
  4   5 ?? 0.00 0 0 0.00
  4   6 ?? 0.00 0 0 0.00
  5   6 ?? 0.25 0 0 0.00
ENDDAT 2.1
END


