Contacts of the helix formed by residues 239 - 266 (chain C) in PDB entry 6A5T
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 LYS 239 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP* 4.3 18.8 - - + +
74C GLU* 2.6 40.4 + - + +
238C LEU* 1.3 76.3 - - - +
240C ALA* 1.3 56.0 + - - +
241C ASN* 3.0 17.6 - - - +
242C GLN* 2.3 61.7 + - - +
243C VAL* 3.0 3.3 + - - -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN 4.7 0.7 - - - +
14C ASP* 3.2 24.7 + - - +
15C ASP 3.9 13.0 - - - +
17C VAL* 3.5 30.7 - - + -
232C VAL* 4.7 7.5 - - + +
234C THR* 4.4 3.3 + - + +
238C LEU 3.8 2.0 + - - -
239C LYS* 1.3 69.5 - - - +
241C ASN* 1.3 59.0 + - - +
243C VAL* 2.9 37.0 + - + +
244C PHE* 3.0 7.4 + - - +
109K TRP* 5.5 0.2 - - + -
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Residues in contact with ASN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 5.1 1.0 - - - +
239C LYS* 2.9 26.0 - - - +
240C ALA* 1.3 74.2 - - - +
242C GLN* 1.3 69.1 + - - +
244C PHE* 3.3 2.1 + - - +
245C SER* 2.8 35.6 + - - +
105K PHE* 4.2 19.0 - - + -
106K ASN* 6.1 1.1 - - - +
109K TRP* 2.9 56.4 - - + +
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Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLU* 3.4 48.2 + - - +
238C LEU* 4.5 5.4 - - + +
239C LYS* 2.3 54.3 + - - +
241C ASN* 1.3 76.0 + - - +
243C VAL* 1.3 64.8 + - - +
245C SER* 4.3 6.1 - - - -
246C ARG* 2.8 52.6 + - + +
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C MET* 4.0 16.5 - - + +
40C VAL* 4.6 7.4 - - + +
172C PRO* 5.5 0.2 - - + -
173C CYS* 3.3 24.7 - - - -
232C VAL* 3.7 17.3 - - + -
234C THR* 3.4 31.6 - - + -
238C LEU* 4.5 17.2 - - + +
239C LYS 3.0 4.7 + - - +
240C ALA* 2.9 23.4 + - - +
242C GLN* 1.3 80.7 - - - +
244C PHE* 1.3 57.4 + - + +
246C ARG* 3.6 3.3 - - - +
247C GLY* 2.8 23.9 + - - -
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Residues in contact with PHE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 5.2 3.6 - - + -
19C LEU* 5.0 17.0 - - + -
21C LEU* 5.7 3.4 - - + -
32C LEU* 3.4 37.7 - - + -
36C MET* 4.6 11.7 - - - -
232C VAL* 5.8 3.8 - - + -
240C ALA 3.0 7.7 + - - +
241C ASN 4.0 4.7 - - - +
243C VAL* 1.3 83.5 - - + +
245C SER* 1.3 63.2 + - - +
246C ARG 3.1 0.2 + - - -
247C GLY* 3.2 2.1 + - - +
248C ILE* 3.0 55.1 + - + +
101K LEU* 4.0 21.5 - - + -
105K PHE* 3.2 56.8 - + + -
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ASN* 2.8 20.6 + - - +
242C GLN* 3.9 7.0 - - - -
244C PHE* 1.3 77.8 - - - +
246C ARG* 1.3 59.3 + - - +
248C ILE* 3.4 7.9 + - - +
249C LYS* 2.9 26.0 + - - +
102K ASP* 4.4 18.1 + - - +
105K PHE* 4.6 8.5 - - - -
106K ASN* 3.9 17.1 + - - -
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Residues in contact with ARG 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C VAL* 4.4 17.0 - - + -
41C PRO 4.7 1.2 + - - -
73C SER 3.9 3.4 + - - -
74C GLU 2.8 27.8 + - - -
75C ASP* 4.6 0.8 - - - +
76C VAL* 3.7 20.8 - - - +
77C GLU* 2.6 54.9 + - - +
238C LEU* 4.1 16.6 - - - +
242C GLN* 2.8 41.7 + - + +
243C VAL 3.7 2.0 - - - +
245C SER* 1.3 78.4 - - - +
247C GLY* 1.3 64.9 + - - +
248C ILE 3.1 1.1 - - - -
249C LYS* 3.7 7.3 - - + +
250C THR* 2.7 33.1 + - - +
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Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.8 10.1 - - - -
35C THR* 3.5 26.1 - - - +
36C MET* 5.0 4.5 - - - -
40C VAL* 4.1 7.0 - - - +
243C VAL 2.8 15.6 + - - -
244C PHE 3.2 2.9 + - - -
246C ARG* 1.3 75.8 - - - +
248C ILE* 1.3 62.8 + - - +
250C THR* 3.3 2.4 + - - -
251C LEU* 3.0 25.6 + - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.6 7.0 - - + -
244C PHE* 3.0 55.5 + - + +
245C SER* 3.5 8.1 - - - +
247C GLY* 1.3 77.2 - - - +
249C LYS* 1.3 64.0 + - - +
251C LEU* 3.2 5.1 + - - +
252C GLN* 2.9 30.3 + - - +
98K LEU* 3.7 38.5 - - + +
101K LEU* 4.5 3.6 - - + -
102K ASP* 3.8 32.8 - - + +
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 6.0 3.4 - - - +
245C SER 2.9 16.8 + - - +
246C ARG* 3.2 9.8 + - + +
248C ILE* 1.3 77.9 - - - +
250C THR* 1.3 64.6 + - - +
252C GLN* 3.2 22.1 + - - +
253C GLU* 2.9 60.1 + - + +
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Residues in contact with THR 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 4.6 4.9 - - + -
39C GLU* 3.5 41.9 + - + +
40C VAL* 4.7 1.0 - - - +
41C PRO* 4.7 8.6 - - + +
77C GLU* 5.0 2.4 + - - -
246C ARG* 2.7 24.3 + - - +
247C GLY* 3.6 5.9 - - - -
249C LYS* 1.3 76.6 - - - +
251C LEU* 1.3 59.8 + - + +
253C GLU* 3.0 13.3 + - + +
254C LYS* 2.8 30.8 + - + +
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 6.1 3.1 - - + -
31C SER* 4.3 14.8 - - - -
32C LEU* 4.9 8.3 - - + +
35C THR* 3.8 23.6 - - + +
39C GLU* 5.6 0.2 - - - +
247C GLY 3.0 16.6 + - - +
248C ILE* 3.9 4.7 - - - +
250C THR* 1.3 73.9 - - + +
252C GLN* 1.3 67.1 + - - +
254C LYS* 3.2 26.6 + - + +
255C LEU* 3.0 30.3 + - + +
41K THR* 4.7 11.2 - - + +
42K LEU* 5.6 2.5 - - + -
45K LEU* 4.2 24.0 - - + -
98K LEU* 4.4 20.4 - - + -
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Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 2.9 23.2 + - - +
249C LYS* 3.4 28.4 + - + +
251C LEU* 1.3 78.0 - - - +
253C GLU* 1.3 59.6 + - + +
255C LEU* 3.4 4.1 + - - +
256C ALA* 2.8 30.8 + - - +
95K ILE* 4.0 23.8 + - + +
98K LEU* 3.8 17.3 + - + +
99K LYS* 3.2 43.6 - - - +
102K ASP* 5.3 1.6 - - - +
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Residues in contact with GLU 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LYS* 2.9 54.4 + - - +
250C THR* 3.0 13.8 + - + +
252C GLN* 1.3 76.4 - - + +
254C LYS* 1.3 57.4 + - - +
256C ALA* 3.3 7.7 + - - +
257C ASN* 2.9 28.2 + - - +
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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
----------------------------------------------------------
39C GLU* 2.9 39.0 + - - -
165C LYS* 6.1 0.2 - - - +
250C THR* 2.8 18.1 + - + +
251C LEU* 3.2 23.8 + - + +
253C GLU* 1.3 77.6 - - - +
255C LEU* 1.3 63.2 + - - +
257C ASN* 3.0 12.2 + - + +
258C VAL* 3.0 23.5 + - + +
18K LYS* 5.9 1.1 - - - +
37K ARG 5.7 0.6 + - - -
38K GLU* 3.6 34.9 + - - +
41K THR* 5.2 4.7 - - + -
42K LEU* 4.4 22.7 - - + -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 3.0 22.8 + - + +
252C GLN* 4.0 2.7 - - - +
254C LYS* 1.3 75.8 - - - +
256C ALA* 1.3 58.3 + - - +
258C VAL* 3.2 7.9 + - + +
259C LEU* 2.9 28.9 + - - +
42K LEU* 4.2 25.8 - - + -
45K LEU* 4.6 9.2 - - + -
46K LEU* 4.4 15.9 - - + -
91K CYS* 4.2 25.1 - - + -
94K ILE* 3.8 36.8 - - + -
95K ILE* 4.3 18.1 - - + +
98K LEU* 5.4 2.0 - - + -
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLN 2.8 19.8 + - - +
253C GLU* 3.5 9.2 - - - +
254C LYS 3.1 0.2 - - - -
255C LEU* 1.3 77.0 - - - +
257C ASN* 1.3 61.6 + - - +
259C LEU* 3.3 8.0 + - - +
260C PHE* 2.9 24.9 + - - +
95K ILE* 4.6 10.5 - - + +
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Residues in contact with ASN 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLU 2.9 13.2 + - - +
254C LYS* 3.2 13.8 - - + +
256C ALA* 1.3 76.5 - - - +
258C VAL* 1.3 57.0 + - + +
260C PHE* 3.3 10.6 + - - +
261C GLU* 2.9 45.0 + - - +
18K LYS* 4.4 22.7 - - - +
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Residues in contact with VAL 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 20.3 + - + +
255C LEU* 3.2 11.4 + - + +
257C ASN* 1.3 75.7 - - + +
259C LEU* 1.3 67.9 + - - +
261C GLU* 2.9 17.0 + - - +
262C LEU* 3.0 25.6 + - + +
18K LYS* 5.1 13.0 - - + -
19K LEU* 4.1 19.5 - - + -
35K PHE* 4.5 11.0 - - + -
42K LEU* 4.0 26.0 - - + -
46K LEU* 4.8 9.9 - - + -
87K LEU* 5.8 1.3 - - + -
91K CYS* 4.8 8.5 - - - -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C LEU 2.9 16.0 + - - +
256C ALA* 3.7 6.3 - - - +
258C VAL* 1.3 77.3 - - - +
260C PHE* 1.3 63.5 + - - +
262C LEU* 3.3 6.9 + - + +
263C GLU* 3.0 46.8 + - - +
88K GLU* 3.7 42.4 - - + +
91K CYS* 4.1 20.4 - - + -
92K ALA* 5.5 4.3 - - + +
95K ILE* 5.1 11.2 - - + -
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Residues in contact with PHE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ALA 2.9 17.2 + - - +
257C ASN* 3.4 10.1 - - - +
259C LEU* 1.3 78.6 - - - +
261C GLU* 1.3 75.4 + - - +
263C GLU* 3.4 16.0 + - + +
264C ASN* 2.8 45.8 + - + +
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Residues in contact with GLU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ASN* 2.9 34.4 + - - +
258C VAL* 2.9 9.3 + - - +
260C PHE* 1.3 87.8 - - - +
262C LEU* 1.3 66.4 + - - +
264C ASN* 2.9 27.5 + - - +
265C SER* 3.0 14.4 + - - -
12K LEU* 5.9 0.2 - - - +
17K PRO* 5.2 3.3 - - - +
18K LYS* 3.4 40.0 + - + +
19K LEU* 4.4 21.4 + - + +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 3.0 29.2 + - + +
259C LEU* 3.6 11.9 - - - +
261C GLU* 1.3 77.1 - - - +
263C GLU* 1.3 62.6 + - - +
264C ASN 3.1 0.5 + - - -
265C SER* 3.2 7.8 + - - -
266C ARG* 3.0 19.1 + - - +
19K LEU* 3.8 25.6 - - + -
21K ILE* 4.4 13.6 - - + +
33K ILE* 5.5 1.8 - - + -
84K LYS* 5.1 15.5 - - + +
87K LEU* 3.6 41.5 - - + -
88K GLU* 4.8 18.6 - - + +
91K CYS* 4.7 5.4 - - - -
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 3.0 42.8 + - + +
260C PHE* 3.7 16.6 - - + +
262C LEU* 1.3 75.9 - - - +
264C ASN* 1.3 52.4 + - - +
266C ARG* 2.7 72.3 + - - +
88K GLU* 4.0 8.5 - - - +
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Residues in contact with ASN 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE* 2.8 36.0 + - + +
261C GLU* 2.9 26.5 + - - +
263C GLU* 1.3 73.2 - - - +
265C SER* 1.3 60.7 + - - +
266C ARG 2.7 16.8 - - - +
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Residues in contact with SER 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C GLU 3.0 10.6 + - - -
262C LEU 3.6 8.5 - - - -
264C ASN* 1.3 75.4 - - - +
266C ARG* 1.3 60.1 + - - +
19K LEU 5.9 1.8 - - - -
21K ILE* 4.1 24.9 - - - +
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Residues in contact with ARG 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C LEU 3.0 12.7 + - - +
263C GLU* 2.7 56.1 + - - +
264C ASN 2.7 18.0 - - - +
265C SER* 1.3 78.0 - - - +
84K LYS* 3.4 36.5 - - - +
88K GLU* 2.9 31.4 + - - -
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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