Analysis of interatomic Contacts of Structural Units in PDB entry:
7YMD


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 7YMD entry

There are 3 chains in PDB entry 7YMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 114PRO 250
B
 PRO 11ILE 336
C
 ASP 7ILE 303
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
Back to top of page

There are 31 helices in PDB entry 7YMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
AA1
A
114 121Right-handed alpha
Helix 2
AA2
A
131 140Right-handed alpha
Helix 3
AA3
A
199 211Right-handed 310
Helix 4
AA4
A
219 227Right-handed alpha
Helix 5
AA5
B
13 27Right-handed alpha
Helix 6
AA6
B
34 49Right-handed alpha
Helix 7
AA7
B
56 77Right-handed alpha
Helix 8
AA8
B
91 97Right-handed alpha
Helix 9
AA9
B
151 168Right-handed alpha
Helix 10
AB1
B
181 195Right-handed alpha
Helix 11
AB2
B
215 219Right-handed 310
Helix 12
AB3
B
223 237Right-handed alpha
Helix 13
AB4
B
251 258Right-handed alpha
Helix 14
AB5
B
258 266Right-handed alpha
Helix 15
AB6
B
306 316Right-handed alpha
Helix 16
AB7
C
8 25Right-handed alpha
Helix 17
AB8
C
25 42Right-handed alpha
Helix 18
AB9
C
48 63Right-handed alpha
Helix 19
AC1
C
68 83Right-handed alpha
Helix 20
AC2
C
94 99Right-handed alpha
Helix 21
AC3
C
134 146Right-handed alpha
Helix 22
AC4
C
146 151Right-handed alpha
Helix 23
AC5
C
152 155Right-handed 310
Helix 24
AC6
C
177 195Right-handed alpha
Helix 25
AC7
C
201 209Right-handed alpha
Helix 26
AC8
C
210 212Right-handed 310
Helix 27
AC9
C
226 237Right-handed alpha
Helix 28
AD1
C
259 266Right-handed alpha
Helix 29
AD2
C
267 280Right-handed alpha
Helix 30
AD3
C
282 287Right-handed 310
Helix 31
AD4
C
289 298Right-handed alpha
Back to top of page

There are 5 sheets in PDB entry 7YMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5,

There are 3 strands in AA1 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
31 33first strand
Strand 2
B
131 136anti-parallel
Strand 3
B
81 86anti-parallel
Back to list of sheets
Back to top of page

There are 3 strands in AA2 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
206 208first strand
Strand 2
B
334 336parallel
Strand 3
B
281 282anti-parallel
Back to list of sheets
Back to top of page

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
B
240 242first strand
Strand 2
B
248 250anti-parallel
Back to list of sheets
Back to top of page

There are 3 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
46 47first strand
Strand 2
C
122 127anti-parallel
Strand 3
C
86 91anti-parallel
Back to list of sheets
Back to top of page

There are 3 strands in AA5 sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
C
199 200first strand
Strand 2
C
254 258anti-parallel
Strand 3
C
240 244anti-parallel
Back to list of sheets
Back to top of page
Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il