Analysis of interatomic Contacts of Structural Units in PDB entry:
8YDM


Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 8YDM entry

There are 18 chains in PDB entry 8YDM (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ARG 4GLU 42
B
 PRO 10LEU 52
C
 SER 7GLY 413
D
 SER 5ASN 40
E
 ASP 4PRO 53
F
 PRO 3ASN 40
G
 ASP 5PRO 53
H
 PRO 3LEU 38
I
 ASP 4PRO 53
J
 SER 5ASN 40
K
 ASP 4PRO 53
L
 LYS 5GLY 310
M
 ASP 10VAL 304
N
 GLY 6LYS 61
O
 PRO 6ASN 40
P
 ASP 4PRO 53
Q
 SER 5ASN 40
R
 ASP 4PRO 53
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 68 helices in PDB entry 8YDM. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
7 31Right-handed alpha
Helix 2
AA2
B
19 47Right-handed alpha
Helix 3
AA3
C
10 50Right-handed alpha
Helix 4
AA4
C
55 65Right-handed alpha
Helix 5
AA5
C
80 98Right-handed alpha
Helix 6
AA6
C
111 123Right-handed alpha
Helix 7
AA7
C
123 128Right-handed alpha
Helix 8
AA8
C
130 134Right-handed 310
Helix 9
AA9
C
145 166Right-handed alpha
Helix 10
AB1
C
179 184Right-handed alpha
Helix 11
AB2
C
194 201Right-handed alpha
Helix 12
AB3
C
220 224Right-handed 310
Helix 13
AB4
C
225 229Right-handed 310
Helix 14
AB5
C
234 244Right-handed alpha
Helix 15
AB6
C
273 291Right-handed alpha
Helix 16
AB7
C
293 297Right-handed 310
Helix 17
AB8
C
319 341Right-handed alpha
Helix 18
AB9
C
342 344Right-handed 310
Helix 19
AC1
C
377 383Right-handed alpha
Helix 20
AC2
C
395 397Right-handed 310
Helix 21
AC3
C
400 407Right-handed alpha
Helix 22
AC4
C
408 412Right-handed 310
Helix 23
AC5
D
9 32Right-handed alpha
Helix 24
AC6
E
9 13Right-handed 310
Helix 25
AC7
E
17 47Right-handed alpha
Helix 26
AC8
F
6 32Right-handed alpha
Helix 27
AC9
F
36 40Right-handed 310
Helix 28
AD1
G
17 49Right-handed alpha
Helix 29
AD2
H
6 31Right-handed alpha
Helix 30
AD3
I
17 33Right-handed alpha
Helix 31
AD4
I
35 47Right-handed alpha
Helix 32
AD5
J
9 32Right-handed alpha
Helix 33
AD6
K
9 13Right-handed 310
Helix 34
AD7
K
17 49Right-handed alpha
Helix 35
AD8
L
32 40Right-handed alpha
Helix 36
AD9
L
67 87Right-handed alpha
Helix 37
AE1
L
95 103Right-handed alpha
Helix 38
AE2
L
109 113Right-handed 310
Helix 39
AE3
L
123 151Right-handed alpha
Helix 40
AE4
L
155 173Right-handed alpha
Helix 41
AE5
L
173 180Right-handed alpha
Helix 42
AE6
L
189 203Right-handed alpha
Helix 43
AE7
L
206 209Right-handed 310
Helix 44
AE8
L
210 238Right-handed alpha
Helix 45
AE9
L
247 257Right-handed alpha
Helix 46
AF1
L
262 288Right-handed alpha
Helix 47
AF2
L
296 303Right-handed 310
Helix 48
AF3
M
27 33Right-handed alpha
Helix 49
AF4
M
44 69Right-handed alpha
Helix 50
AF5
M
72 80Right-handed alpha
Helix 51
AF6
M
102 130Right-handed alpha
Helix 52
AF7
M
134 152Right-handed alpha
Helix 53
AF8
M
152 159Right-handed alpha
Helix 54
AF9
M
160 164Right-handed 310
Helix 55
AG1
M
168 183Right-handed alpha
Helix 56
AG2
M
185 188Right-handed 310
Helix 57
AG3
M
189 216Right-handed alpha
Helix 58
AG4
M
217 220Right-handed 310
Helix 59
AG5
M
223 230Right-handed alpha
Helix 60
AG6
M
231 247Right-handed alpha
Helix 61
AG7
M
251 277Right-handed alpha
Helix 62
AG8
M
284 293Right-handed alpha
Helix 63
AG9
N
16 42Right-handed alpha
Helix 64
AH1
O
7 32Right-handed alpha
Helix 65
AH2
P
17 49Right-handed alpha
Helix 66
AH3
Q
6 32Right-handed alpha
Helix 67
AH4
R
9 13Right-handed 310
Helix 68
AH5
R
17 47Right-handed alpha
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There are 7 sheets in PDB entry 8YDM. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7,

There are 2 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
175 176first strand
Strand 2
C
392 393anti-parallel
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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
205 206first strand
Strand 2
C
232 233anti-parallel
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There are 2 strands in AA3 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
247 249first strand
Strand 2
C
260 261anti-parallel
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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
364 366first strand
Strand 2
C
372 374anti-parallel
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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
M
19 20first strand
Strand 2
M
41 42anti-parallel
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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
M
24 25first strand
Strand 2
M
37 38anti-parallel
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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
N
46 47first strand
Strand 2
N
52 53anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il