Contacts of the helix formed by residues 275 - 299 (chain A) in PDB entry 4G1U
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 ASP 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ASN* 3.0 20.2 + - - -
273A GLY* 2.9 8.3 - - - +
274A ALA* 1.3 75.5 - - - +
276A HIS* 1.3 59.1 + - - +
277A ARG* 2.6 53.1 + - - +
278A TRP* 3.4 17.0 + - + +
279A LEU* 2.9 25.5 + - - +
100D PHE* 3.6 7.4 - - + -
104D GLU* 4.2 16.9 + - - +
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 4.1 14.2 + - + -
78A GLY* 4.3 6.0 - - - -
212A ALA* 3.5 27.8 - - + +
215A LEU* 3.1 52.4 - - + +
216A ASN* 3.1 23.8 + - - +
219A GLN* 4.1 16.4 - - + -
269A ARG* 5.6 1.8 + - - -
274A ALA 3.8 7.6 + - - -
275A ASP* 1.3 73.0 + - - +
277A ARG* 1.3 60.0 + - - +
278A TRP 3.2 0.2 - - - -
279A LEU* 3.5 28.4 - - + +
280A LEU* 2.9 37.0 + - + +
98D PHE* 5.4 5.0 - + - -
100D PHE* 5.0 0.4 - + - -
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Residues in contact with ARG 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 4.2 7.7 - - - +
212A ALA* 3.8 18.6 - - + +
213A ARG* 4.6 24.6 - - + +
216A ASN* 4.5 9.6 - - - +
275A ASP* 2.6 41.9 + - - +
276A HIS* 1.3 76.6 - - - +
278A TRP* 1.3 83.7 + - + +
281A PRO* 3.1 20.4 - - - +
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Residues in contact with TRP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.6 33.0 - - + +
8A ARG* 4.4 33.9 - - + -
11A LEU* 4.3 22.7 - - + +
272A ILE* 3.4 39.2 - - + +
275A ASP* 3.4 22.4 + - + +
277A ARG* 1.3 100.9 - - + +
279A LEU* 1.3 65.3 + - - +
280A LEU 3.6 0.2 - - - -
281A PRO* 3.6 3.6 - - + +
282A GLY* 3.4 15.6 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.9 15.0 - - + +
265A PRO* 3.9 12.8 - - + +
268A ILE* 3.5 22.8 - - + +
269A ARG* 3.6 48.0 - - + +
272A ILE* 5.2 0.2 - - - -
273A GLY 4.7 3.8 + - - +
274A ALA 4.2 8.5 - - - +
275A ASP 2.9 18.5 + - - +
276A HIS* 3.3 31.6 + - + +
278A TRP* 1.3 78.8 - - - +
280A LEU* 1.3 68.2 + - - +
282A GLY* 3.8 0.3 - - - -
283A ALA* 3.0 21.3 + - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.2 19.8 - - + +
74A THR* 4.2 20.0 - - + -
75A ILE* 4.0 26.0 - - + -
205A CYS 5.7 1.8 - - - +
208A GLY 3.1 33.0 - - - +
209A LEU* 3.6 15.5 - - + -
212A ALA* 3.4 19.5 - - + -
215A LEU* 5.2 4.5 - - + -
276A HIS* 2.9 28.6 + - + +
279A LEU* 1.3 75.5 - - - +
281A PRO* 1.4 68.5 - - + +
283A ALA* 3.1 2.9 + - - +
284A ALA* 2.9 21.9 + - - +
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Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.3 21.5 - - + -
209A LEU* 3.6 17.9 - - + -
277A ARG 3.1 27.8 - - - +
278A TRP* 3.6 8.1 - - + +
280A LEU* 1.4 94.3 - - + +
282A GLY* 1.3 65.2 + - - +
284A ALA* 3.2 10.8 + - + +
285A LEU* 3.1 30.2 + - + +
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.5 21.9 - - - +
14A LEU* 3.5 7.2 - - - +
268A ILE* 3.4 23.2 - - - +
272A ILE* 5.0 1.3 - - - -
278A TRP 3.4 9.1 + - - -
279A LEU 3.8 0.7 - - - -
280A LEU 3.3 0.8 - - - -
281A PRO* 1.3 85.4 - - - +
283A ALA* 1.3 60.1 + - - +
285A LEU* 3.4 1.0 + - - -
286A GLY 3.0 17.5 + - - -
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 3.3 20.8 - - + +
71A VAL* 4.8 0.4 - - - +
74A THR* 3.8 22.2 - - - +
264A VAL* 4.0 9.3 - - + +
265A PRO* 4.6 6.5 - - + -
268A ILE* 3.8 13.5 - - + +
279A LEU* 3.0 14.4 + - + +
280A LEU 3.4 8.3 - - - +
282A GLY* 1.3 74.2 - - - +
284A ALA* 1.3 55.9 + - - +
286A GLY 2.9 1.2 + - - -
287A GLY 2.6 33.1 + - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A CYS* 3.5 33.8 - - - +
70A ALA* 4.1 4.4 - - - +
71A VAL* 3.5 28.7 - - + +
205A CYS* 5.4 0.9 - - + -
280A LEU 2.9 9.3 + - - +
281A PRO* 3.2 14.1 + - + +
283A ALA* 1.3 74.6 - - - +
285A LEU* 1.3 66.9 + - + +
288A ALA* 3.5 13.0 + - - +
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.7 32.8 - - + +
14A LEU* 4.0 16.1 - - + +
15A LEU* 3.8 34.5 - - + +
18A LEU* 4.6 10.1 - - + +
281A PRO* 3.1 20.3 + - + +
282A GLY 3.9 3.8 - - - +
283A ALA 3.1 0.6 - - - -
284A ALA* 1.3 82.5 - - + +
286A GLY* 1.3 59.9 + - - +
287A GLY 3.2 0.4 - - - -
288A ALA* 3.6 5.5 + - - +
289A CYS* 3.0 32.1 + - - -
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.3 11.0 - - - +
264A VAL* 3.2 17.0 - - - +
268A ILE* 4.0 6.7 - - - -
282A GLY 3.0 11.5 + - - -
283A ALA 2.9 5.6 + - - -
285A LEU* 1.3 74.9 - - - +
287A GLY* 1.3 61.3 + - - +
289A CYS* 3.5 7.2 - - - +
290A LEU* 2.9 29.8 + - - +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLY* 3.5 21.1 - - - -
70A ALA* 3.7 6.3 - - - -
260A ILE* 4.1 8.8 - - - +
264A VAL* 3.5 6.7 - - - +
283A ALA 2.6 20.4 + - - -
286A GLY* 1.3 71.7 - - - +
288A ALA* 1.3 59.1 + - - +
290A LEU* 4.0 1.1 - - - +
291A LEU* 2.9 34.3 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.7 25.7 - - + +
62A ALA 4.3 0.2 - - - -
63A VAL* 3.3 41.9 - - + +
66A GLY* 3.7 3.6 - - - -
67A CYS* 4.1 1.1 - - + +
284A ALA 3.5 17.3 + - - +
285A LEU* 3.8 3.6 - - - +
286A GLY 3.4 0.2 - - - -
287A GLY* 1.3 75.0 - - - +
289A CYS* 1.3 63.2 + - - +
292A LEU* 3.1 27.0 + - - +
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Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.7 27.8 - - + -
17A LEU* 3.8 24.0 - - + -
18A LEU* 3.8 20.2 - - - +
21A LEU* 3.8 13.3 - - + +
285A LEU 3.0 23.7 + - - +
286A GLY* 3.5 9.0 - - - +
288A ALA* 1.3 79.3 - - - +
290A LEU* 1.3 53.8 + - - +
292A LEU* 3.7 2.0 - - - +
293A THR* 2.8 37.5 + - - +
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ILE* 3.7 24.7 - - + -
263A VAL* 4.7 14.4 - - + -
264A VAL* 4.7 23.1 - - + +
267A LEU* 5.1 7.6 - - + -
286A GLY 2.9 17.1 + - - +
287A GLY* 3.3 3.6 + - - +
289A CYS* 1.3 75.3 - - + +
291A LEU* 1.3 65.7 + - - +
293A THR* 3.5 9.6 + - + -
294A ALA* 3.0 24.7 + - + +
316A LEU* 6.6 0.2 - - + -
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.6 17.7 - - + +
65A VAL* 3.5 22.7 - - + -
66A GLY* 3.3 30.5 - - - +
69A LEU* 5.1 0.9 - - + -
186A LEU* 5.0 4.0 - - + -
257A ILE* 4.1 16.8 - - + -
260A ILE* 4.1 22.1 - - + +
287A GLY 2.9 16.6 + - - +
290A LEU* 1.3 76.2 - - - +
292A LEU* 1.3 53.8 + - - +
294A ALA* 2.9 7.1 + - + +
295A ASP* 2.7 34.6 + - + +
309A VAL* 3.6 28.3 - - + -
313A THR* 4.6 1.1 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 4.5 4.3 - - + -
21A LEU* 3.9 12.1 - - + -
22A ALA* 3.8 31.2 - - + +
25A SER* 4.3 5.8 - - - +
59A VAL* 3.7 26.7 - - + +
62A ALA* 3.6 27.3 - - + +
63A VAL* 3.9 20.9 - - + -
288A ALA 3.1 17.7 + - - +
289A CYS 3.7 2.5 - - - +
291A LEU* 1.3 77.7 - - - +
293A THR* 1.3 56.8 + - - +
295A ASP* 4.4 1.6 - - + +
296A THR* 2.8 49.0 + - - +
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Residues in contact with THR 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.5 25.1 - - + +
289A CYS 2.8 23.5 + - - -
290A LEU* 3.7 13.0 - - + +
291A LEU 3.3 0.2 - - - -
292A LEU* 1.3 76.9 - - - +
294A ALA* 1.3 57.9 + - - +
296A THR* 4.3 3.6 - - - -
297A LEU* 3.1 33.6 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ILE* 5.7 0.9 - - + -
290A LEU* 3.0 15.5 + - + +
291A LEU* 2.9 11.1 + - - +
293A THR* 1.3 77.0 - - - +
295A ASP* 1.3 60.0 + - - +
297A LEU* 3.9 4.7 - - - -
298A ALA* 3.1 24.3 + - - +
309A VAL* 4.1 17.7 - - + +
312A LEU* 3.6 16.3 - - + +
313A THR* 4.3 14.1 - - + +
316A LEU* 5.8 7.4 - - + -
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 2.7 41.0 + - - -
62A ALA* 4.4 12.1 - - + -
186A LEU* 3.1 40.3 - - - +
291A LEU* 2.7 18.6 + - + +
292A LEU* 4.1 2.9 - - + +
294A ALA* 1.3 71.0 - - - +
296A THR* 1.3 59.3 + - - +
297A LEU 3.1 1.1 - - - -
298A ALA* 2.8 26.5 + - - +
299A ARG* 3.2 9.2 + - - +
309A VAL* 3.3 19.7 - - + +
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 2.8 43.3 + - - +
28A MET* 4.3 22.0 - - + -
59A VAL* 5.0 0.9 - - - +
292A LEU* 2.8 28.4 + - - +
293A THR* 4.3 3.8 - - - -
295A ASP* 1.3 76.0 - - - +
297A LEU* 1.3 59.1 + - - +
298A ALA 3.5 0.3 + - - -
299A ARG* 3.7 20.7 + - - +
300A THR* 2.8 30.4 + - - +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A THR* 3.1 23.2 + - + +
294A ALA* 4.1 5.4 - - - +
295A ASP 3.1 0.6 - - - -
296A THR* 1.3 78.2 - - - +
298A ALA* 1.3 60.1 + - - +
300A THR* 3.9 4.0 - - + -
301A LEU* 2.9 64.1 + - + +
312A LEU* 4.1 16.3 - - + +
316A LEU* 5.2 11.7 - - + -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 5.3 1.1 - - - +
294A ALA 3.1 15.5 + - - +
295A ASP* 2.8 19.1 + - - +
297A LEU* 1.3 79.9 - - - +
299A ARG* 1.3 57.9 + - - +
300A THR 3.1 3.3 + - - -
301A LEU* 3.9 6.9 + - - +
302A VAL 4.8 0.3 + - - -
305A ALA 3.5 11.4 - - - +
307A MET* 3.5 37.7 - - + +
309A VAL* 4.5 10.8 - - + +
312A LEU* 3.8 13.7 - - + -
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 3.0 29.5 + - - -
28A MET* 2.9 34.4 + - - +
55A ARG* 3.7 22.8 - - - +
58A ARG* 3.3 46.8 - - - +
59A VAL* 5.1 6.1 - - - +
295A ASP 3.7 7.9 - - - +
296A THR* 3.7 17.7 + - - +
298A ALA* 1.3 77.3 - - - +
300A THR* 1.3 67.2 + - - +
302A VAL 4.2 5.2 - - - +
304A PRO* 5.6 1.6 - - - +
305A ALA 3.9 17.8 + - - +
306A GLU* 4.5 16.8 - - + +
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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