Contacts of the helix formed by residues 240 - 267 (chain C) in PDB entry 5IYB
Residue contacts within the protein 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). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 240 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP* 4.8 18.2 - - - +
76C ASP* 3.5 24.4 + - - +
135C ARG* 5.6 8.1 - - - +
235C SER* 5.3 0.2 - - - -
239C LEU* 1.3 78.6 - - + +
241C PRO* 1.4 73.2 - - + +
242C GLU* 2.2 53.7 + - - +
243C THR* 3.0 29.5 + - - +
244C ILE* 3.1 9.7 + - - +
115K GLY 5.4 4.0 - - - -
116K ILE 3.0 13.9 + - - -
117K GLU* 3.1 33.1 + - - +
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Residues in contact with PRO 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.7 3.1 - - + -
15C THR 4.4 6.1 - - - +
16C ASP 3.7 15.7 - - - +
17C GLU 3.4 32.5 - - - +
18C ASN 3.9 6.1 - - - +
19C VAL* 3.6 32.0 - - + +
233C VAL* 4.7 3.7 - - + +
235C SER* 4.1 5.8 - - - +
239C LEU 3.5 3.7 - - - +
240C ARG* 1.4 86.1 - - + +
242C GLU* 1.3 65.1 - - - +
244C ILE* 3.1 24.5 + - + +
245C VAL* 3.2 16.1 + - - +
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 5.0 13.1 - - + +
19C VAL* 4.7 4.3 - - + +
240C ARG* 2.2 52.8 + - - +
241C PRO* 1.3 78.2 - - - +
243C THR* 1.3 66.2 + - - +
245C VAL* 3.4 3.7 + - - +
246C LEU* 3.0 30.4 + - - +
105K PHE* 4.0 13.5 - - + -
109K ILE* 3.8 41.7 - - + -
115K GLY 4.8 1.2 - - - +
116K ILE* 3.0 18.6 - - - +
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASP 6.0 1.3 - - - +
239C LEU* 3.7 27.3 - - + +
240C ARG* 3.0 39.3 + - - +
242C GLU* 1.3 81.5 + - - +
244C ILE* 1.3 64.2 + - - +
246C LEU* 4.1 8.3 - - + +
247C SER* 2.9 36.5 + - - +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 4.7 9.4 - - + +
42C VAL* 3.8 16.8 - - + +
178C PRO* 3.3 47.3 - - + +
179C THR* 5.0 4.7 - - + -
233C VAL* 5.0 8.7 - - + -
235C SER* 4.1 10.5 - - - -
239C LEU* 3.4 42.0 - - + +
240C ARG 3.1 8.6 + - - +
241C PRO* 3.1 13.7 + - + +
243C THR* 1.3 75.8 - - - +
245C VAL* 1.3 60.1 + - + +
247C SER* 3.3 3.5 + - - -
248C ALA* 2.9 27.4 + - - +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 4.5 5.6 - - + -
21C PHE* 4.5 15.0 - - + -
34C ILE* 5.6 0.2 - - + -
38C PHE* 3.5 38.1 - - + -
233C VAL* 4.4 16.4 - - + -
241C PRO 3.2 13.0 + - - +
242C GLU 3.8 5.6 - - - +
244C ILE* 1.3 76.1 - - + +
246C LEU* 1.3 64.6 + - - +
248C ALA* 3.3 1.9 + - - +
249C LEU* 3.0 39.1 + - + +
105K PHE* 3.9 24.9 - - + -
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLU 3.0 17.4 + - - +
243C THR* 4.1 8.3 - - + +
245C VAL* 1.3 76.2 - - - +
247C SER* 1.3 63.7 + - - +
249C LEU* 3.5 6.3 + - + +
250C SER* 3.2 30.4 + - - +
102K GLU* 3.5 38.4 - - + +
105K PHE* 4.5 9.8 - - + -
106K ARG* 3.6 35.4 - - + -
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 4.7 12.3 - - - -
43C PRO* 5.0 13.6 - - - +
239C LEU* 4.9 4.6 - - - +
243C THR* 2.9 31.5 + - - +
244C ILE* 3.7 4.9 - - - -
246C LEU* 1.3 76.9 - - - +
248C ALA* 1.3 57.2 + - - +
250C SER* 4.0 3.8 - - - -
251C GLY* 2.9 27.7 + - - -
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Residues in contact with ALA 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 5.9 0.2 - - + -
37C VAL* 3.4 29.6 - - + +
38C PHE* 3.7 18.2 - - + -
42C VAL* 3.5 18.9 - - + +
244C ILE 2.9 16.1 + - - +
245C VAL 3.5 5.4 - - - +
247C SER* 1.3 73.9 - - - +
249C LEU* 1.3 66.6 + - + +
251C GLY* 3.5 1.1 + - - -
252C LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ILE* 3.8 45.1 - - + -
38C PHE* 5.3 0.4 - - + -
245C VAL* 3.0 33.8 + - + +
246C LEU* 3.9 6.5 - - - +
248C ALA* 1.3 76.7 - - - +
250C SER* 1.3 58.8 + - - +
252C LEU* 3.5 6.8 + - + +
253C LYS* 2.9 27.9 + - - +
98K LEU* 4.8 16.6 - - + +
101K LEU* 4.6 13.9 - - + +
102K GLU* 4.3 35.4 - - + +
105K PHE* 4.9 10.3 - - + -
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Residues in contact with SER 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU* 3.2 18.8 + - - +
247C SER* 4.0 4.3 - - - -
249C LEU* 1.3 75.2 - - - +
251C GLY* 1.3 53.7 + - - +
253C LYS* 3.0 21.2 + - - +
254C LYS* 2.8 39.3 + - - +
102K GLU* 3.5 23.9 + - - +
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Residues in contact with GLY 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 6.0 3.6 - - - -
247C SER 2.9 19.1 + - - -
248C ALA* 4.0 0.9 - - - -
250C SER* 1.3 75.8 - - - +
252C LEU* 1.3 55.9 + - - +
254C LYS* 3.1 12.6 + - - +
255C LYS* 2.8 27.1 + - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 5.0 11.7 - - - +
34C ILE* 4.7 17.7 - - + -
37C VAL* 4.0 30.4 - - + +
41C GLU* 6.0 1.9 - - + +
248C ALA 3.0 18.6 + - - +
249C LEU* 3.6 7.0 - - - +
251C GLY* 1.3 71.7 - - - +
253C LYS* 1.3 60.8 + - - +
255C LYS* 3.2 22.4 + - + +
256C LEU* 3.0 47.3 + - + +
41K THR* 5.1 9.2 - - + +
42K LEU* 6.2 0.9 - - - -
45K ILE* 6.2 4.0 - - + -
98K LEU* 4.1 21.8 - - + -
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Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU 2.9 13.2 + - - +
250C SER* 3.0 22.8 + - - +
252C LEU* 1.3 75.1 - - - +
254C LYS* 1.3 61.3 + - + +
256C LEU* 4.1 5.4 - - - +
257C SER* 2.6 37.9 + - - +
95K ILE* 4.0 22.8 - - + +
98K LEU* 5.3 10.5 - - + +
99K SER* 3.2 28.0 - - - +
102K GLU* 3.2 28.5 + - - -
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASP* 5.0 11.5 + - - -
250C SER* 2.8 23.6 + - - +
251C GLY* 3.4 11.4 - - - +
253C LYS* 1.3 74.7 - - + +
255C LYS* 1.3 58.6 + - - +
257C SER* 3.7 6.8 - - - -
258C ASP* 3.0 29.3 + - - +
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Residues in contact with LYS 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 4.0 28.0 + - + +
171C LYS* 4.0 9.5 - - - +
251C GLY 2.8 12.7 + - - +
252C LEU* 3.2 28.7 + - + +
254C LYS* 1.3 78.4 - - - +
256C LEU* 1.3 60.9 + - + +
258C ASP* 3.4 8.3 + - - +
259C LEU* 3.2 18.9 + - - +
38K GLU* 2.9 35.6 + - - +
39K ASP* 5.1 1.6 - - - -
41K THR* 5.4 4.7 - - + -
42K LEU* 3.9 27.7 - - + +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 3.0 40.8 + - + +
253C LYS* 4.1 2.2 - - - +
255C LYS* 1.3 73.5 - - + +
257C SER* 1.3 56.6 + - - +
259C LEU* 3.0 12.2 + - + +
260C GLN* 2.8 31.9 + - - +
42K LEU* 4.8 18.6 - - + -
45K ILE* 5.5 6.3 - - + -
91K ILE* 4.3 14.6 - - + +
94K LEU* 3.6 38.1 - - + -
95K ILE* 3.9 26.5 - - + -
98K LEU* 4.1 13.9 - - + -
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Residues in contact with SER 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LYS* 2.6 30.1 + - - +
254C LYS* 3.7 7.6 - - - -
256C LEU* 1.3 76.4 - - - +
258C ASP* 1.3 57.1 + - - +
260C GLN* 3.2 5.9 + - - +
261C THR* 2.9 33.4 + - - +
95K ILE* 3.8 21.0 - - - +
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Residues in contact with ASP 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LYS 3.0 17.7 + - - +
255C LYS* 3.5 9.0 - - - +
256C LEU 3.1 0.2 - - - -
257C SER* 1.3 74.3 - - - +
259C LEU* 1.3 61.1 + - - +
261C THR* 3.0 12.8 + - - -
262C GLN* 2.9 49.7 + - - +
18K LYS* 5.1 10.0 + - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LYS 3.2 9.5 + - - +
256C LEU* 3.0 15.1 + - + +
258C ASP* 1.3 80.5 - - - +
260C GLN* 1.3 57.6 + - - +
262C GLN* 3.8 3.8 - - + +
263C LEU* 2.9 29.5 + - - +
18K LYS* 4.5 19.3 - - + +
19K ILE* 4.7 13.5 - - + -
35K ILE* 4.2 32.8 - - + -
42K LEU* 3.6 39.5 - - + -
46K ILE* 4.6 3.8 - - + -
87K PHE* 4.7 4.7 - - + -
91K ILE* 4.1 23.8 - - + -
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Residues in contact with GLN 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LEU 2.8 16.5 + - - +
257C SER* 3.2 11.8 + - - +
259C LEU* 1.3 74.9 - - - +
261C THR* 1.3 59.8 + - + +
263C LEU* 3.3 32.1 + - - +
264C SER* 2.8 44.7 + - - +
88K THR* 3.6 24.5 - - - +
91K ILE* 3.6 22.7 - - + +
92K THR* 3.0 24.6 + - - -
95K ILE* 5.1 4.3 - - + +
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Residues in contact with THR 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C SER* 2.9 17.4 + - - +
258C ASP* 3.0 25.5 + - - -
260C GLN* 1.3 75.1 - - + +
262C GLN* 1.3 66.3 + - - +
264C SER* 3.6 7.3 + - - -
265C HIS* 3.1 22.5 + - - +
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Residues in contact with GLN 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ASP* 2.9 36.3 + - - +
259C LEU* 3.8 7.0 - - + +
261C THR* 1.3 78.6 + - - +
263C LEU* 1.3 62.4 + - - +
265C HIS* 3.2 14.7 + - - +
266C GLU* 3.1 33.2 + - - +
12K LEU* 5.7 1.1 - - - +
18K LYS* 3.3 42.6 + - + +
19K ILE* 4.6 6.7 - - + +
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 2.9 19.2 + - + +
260C GLN* 3.4 26.0 - - - +
262C GLN* 1.3 74.9 - - - +
264C SER* 1.3 64.7 + - - +
266C GLU* 3.3 21.5 + - + +
267C ILE* 3.5 17.0 + - + +
19K ILE* 4.1 20.4 - - + +
21K ILE* 4.0 27.1 - - + -
33K PHE* 4.4 6.5 - - + -
84K GLN* 5.1 1.8 - - + +
87K PHE* 3.5 30.3 - - + -
88K THR* 3.9 15.5 - - - +
91K ILE* 4.7 0.7 - - + -
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Residues in contact with SER 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLN* 2.8 34.1 + - - +
261C THR* 3.9 7.9 - - - -
263C LEU* 1.3 74.0 - - - +
265C HIS* 1.3 60.0 + - - +
267C ILE* 3.1 17.9 + - - +
268C GLN* 2.8 34.9 + - - +
88K THR* 6.1 0.3 - - - +
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Residues in contact with HIS 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C THR 3.1 18.4 + - - +
262C GLN* 3.2 16.6 + - - +
264C SER* 1.3 76.7 - - - +
266C GLU* 1.3 78.8 + - - +
268C GLN* 3.2 30.1 + - + +
269C SER* 4.0 10.8 + - - -
17K LYS* 6.1 0.9 - - - -
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Residues in contact with GLU 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C GLN* 3.1 21.3 + - - +
263C LEU* 3.3 14.4 - - + +
264C SER 3.2 0.4 - - - -
265C HIS* 1.3 91.2 - - - +
267C ILE* 1.3 60.1 + - + +
268C GLN 3.4 0.7 - - - -
269C SER* 4.4 5.1 + - - -
270C ASP 3.4 6.6 + - - +
272C LEU* 3.1 35.8 - - + +
17K LYS* 2.5 43.0 + - - +
18K LYS 5.8 0.2 + - - -
19K ILE* 3.4 25.7 + - + +
20K THR* 5.6 0.6 - - - -
21K ILE* 5.0 5.3 + - + -
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 3.6 20.2 - - + +
264C SER* 3.2 23.8 - - - +
266C GLU* 1.3 82.2 - - + +
268C GLN* 1.3 63.0 + - - +
269C SER 3.3 3.9 - - - +
270C ASP 3.6 11.5 - - - +
271C VAL* 3.9 20.3 - - - +
272C LEU* 4.7 7.0 - - + +
274C ILE* 3.6 40.6 - - + -
21K ILE* 5.4 4.5 - - + -
84K GLN* 5.7 0.9 - - + -
88K THR* 5.6 4.0 - - + +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il