I see no reason why not. Just to make sure, I decided to test. I ran a search on all human proteins (using the UniProt flat file) for all possible dipeptide combinations of the 20 standard amino acids (selenocysteine is also present in humans but only in 22--or so, depending on how you count them--proteins, so I wouldn't expect all possible sec-containing dipeptides to be present.
As expected, each of the 400 possible dipeptides were indeed present in at least one human protein. In case anyone wants to repeat this, the "protocol" is as follows:
Download the human flat file from Expassy.
Extract the peptide sequences
perl -ne 'if(s/^\s+//){s/\s+//g;print}' human.flat > human.pep
Generate the list of possible dipeptides:
AA
AC
AD
AE
AF
AG
AH
AI
AK
AL
AM
AN
AP
AQ
AR
AS
AT
AV
AW
AY
CA
CC
CD
CE
CF
CG
CH
CI
CK
CL
CM
CN
CP
CQ
CR
CS
CT
CV
CW
CY
DA
DC
DD
DE
DF
DG
DH
DI
DK
DL
DM
DN
DP
DQ
DR
DS
DT
DV
DW
DY
EA
EC
ED
EE
EF
EG
EH
EI
EK
EL
EM
EN
EP
EQ
ER
ES
ET
EV
EW
EY
FA
FC
FD
FE
FF
FG
FH
FI
FK
FL
FM
FN
FP
FQ
FR
FS
FT
FV
FW
FY
GA
GC
GD
GE
GF
GG
GH
GI
GK
GL
GM
GN
GP
GQ
GR
GS
GT
GV
GW
GY
HA
HC
HD
HE
HF
HG
HH
HI
HK
HL
HM
HN
HP
HQ
HR
HS
HT
HV
HW
HY
IA
IC
ID
IE
IF
IG
IH
II
IK
IL
IM
IN
IP
IQ
IR
IS
IT
IV
IW
IY
KA
KC
KD
KE
KF
KG
KH
KI
KK
KL
KM
KN
KP
KQ
KR
KS
KT
KV
KW
KY
LA
LC
LD
LE
LF
LG
LH
LI
LK
LL
LM
LN
LP
LQ
LR
LS
LT
LV
LW
LY
MA
MC
MD
ME
MF
MG
MH
MI
MK
ML
MM
MN
MP
MQ
MR
MS
MT
MV
MW
MY
NA
NC
ND
NE
NF
NG
NH
NI
NK
NL
NM
NN
NP
NQ
NR
NS
NT
NV
NW
NY
PA
PC
PD
PE
PF
PG
PH
PI
PK
PL
PM
PN
PP
PQ
PR
PS
PT
PV
PW
PY
QA
QC
QD
QE
QF
QG
QH
QI
QK
QL
QM
QN
QP
QQ
QR
QS
QT
QV
QW
QY
RA
RC
RD
RE
RF
RG
RH
RI
RK
RL
RM
RN
RP
RQ
RR
RS
RT
RV
RW
RY
SA
SC
SD
SE
SF
SG
SH
SI
SK
SL
SM
SN
SP
SQ
SR
SS
ST
SV
SW
SY
TA
TC
TD
TE
TF
TG
TH
TI
TK
TL
TM
TN
TP
TQ
TR
TS
TT
TV
TW
TY
VA
VC
VD
VE
VF
VG
VH
VI
VK
VL
VM
VN
VP
VQ
VR
VS
VT
VV
VW
VY
WA
WC
WD
WE
WF
WG
WH
WI
WK
WL
WM
WN
WP
WQ
WR
WS
WT
WV
WW
WY
YA
YC
YD
YE
YF
YG
YH
YI
YK
YL
YM
YN
YP
YQ
YR
YS
YT
YV
YW
YY
Save that list as dip.txt.
Use that file to search the protein sequences:
perl -ne 'BEGIN{open(A,"human.pep"); while(<A>){chomp; $k.=$_}}; chomp; print "$_\n" if $k=~/$_/ ' dip.txt
The script above will print each dipeptide that was found in at least one protein. Since all were printed, all dipeptides exist in the human proteome.
