Contacts of the helix formed by residues 256 - 283 (chain A) in PDB entry 3N4U
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 256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A HIS* 3.0 23.2 + - + -
255A LYS* 1.3 82.0 - - + +
257A ILE* 1.3 62.0 + - - +
258A PRO* 3.5 14.3 - - - +
259A THR* 2.4 44.7 + - - +
260A VAL 3.3 4.5 + - - -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A SER* 6.4 0.2 - - - -
249A LEU* 4.1 34.8 - - + -
250A ASN* 3.6 27.8 - - - +
254A HIS* 4.1 24.2 - - + +
255A LYS 3.9 0.8 - - - -
256A ASP* 1.3 74.5 - - - +
258A PRO* 1.3 72.9 - - + +
260A VAL* 2.9 16.4 + - - +
261A LEU* 2.9 32.9 + - + +
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Residues in contact with PRO 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP* 3.4 14.1 - - - +
257A ILE* 1.3 95.8 - - + +
259A THR* 1.3 56.1 + - - +
261A LEU* 3.4 13.0 + - + +
262A GLU* 3.1 31.4 + - - +
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Residues in contact with THR 259 (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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185A ILE* 4.5 25.0 - - + +
227A ASP* 4.3 3.8 - - - +
256A ASP* 2.4 37.3 + - - +
258A PRO* 1.3 76.0 - - - +
260A VAL* 1.3 66.5 + - - +
262A GLU* 3.3 9.6 + - - +
263A LYS* 3.0 49.4 + - + +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ASP* 3.5 17.3 - - - +
230A PHE* 4.4 10.5 - - + -
231A ILE* 3.9 14.6 - - + +
234A MET* 3.5 28.3 - - + -
249A LEU* 4.7 8.1 - - + -
254A HIS* 3.1 45.5 - - + +
256A ASP 3.7 1.3 - - - +
257A ILE* 2.9 10.8 + - - +
259A THR* 1.3 77.3 - - - +
261A LEU* 1.3 60.9 - - + +
263A LYS* 3.2 7.5 + - - +
264A TYR* 3.0 21.3 + - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A MET* 4.4 11.0 - - + -
242A MET* 3.6 34.3 - - + -
249A LEU* 5.4 0.4 - - + -
257A ILE* 2.9 35.6 + - + +
258A PRO* 3.6 13.2 - - + +
260A VAL* 1.3 76.3 - - + +
262A GLU* 1.3 62.3 + - - +
264A TYR* 3.4 8.7 + - + +
265A ARG* 3.1 22.0 + - - +
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN* 5.2 6.4 + - - -
185A ILE* 3.7 33.3 - - + +
186A TYR* 4.5 11.5 + - - +
258A PRO* 3.1 17.0 + - - +
259A THR* 3.5 12.4 + - - +
260A VAL 3.2 0.2 - - - -
261A LEU* 1.3 74.7 - - - +
263A LYS* 1.3 65.6 + - + +
265A ARG* 3.1 16.1 + - + +
266A MET* 3.0 21.1 + - - +
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Residues in contact with LYS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ILE* 3.4 26.1 + - + -
186A TYR* 4.1 26.9 - - + +
188A LYS 5.5 0.6 + - - -
189A TYR* 4.3 8.5 - - - +
225A ASP* 2.6 33.4 + - - +
227A ASP* 2.8 33.7 + - + +
228A ASN* 5.1 2.7 - - - +
231A ILE* 3.5 17.9 - - + -
259A THR* 3.0 30.4 + - + +
260A VAL 3.2 2.6 + - - +
262A GLU* 1.3 74.9 - - - +
264A TYR* 1.3 57.4 + - - +
266A MET* 3.3 7.9 + - + +
267A LYS* 2.9 32.7 + - + +
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Residues in contact with TYR 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ILE* 3.6 34.6 - - + +
234A MET* 3.7 40.7 + - + -
235A GLU* 3.1 41.6 - - + +
236A ASP* 4.3 6.9 + - - -
242A MET* 5.4 5.6 - - + -
260A VAL 3.0 9.5 + - - +
261A LEU* 3.7 11.0 - - + +
262A GLU 3.2 0.2 - - - -
263A LYS* 1.3 76.3 - - - +
265A ARG* 1.3 58.3 + - - +
267A LYS* 3.2 2.5 + - + -
268A GLU* 2.9 64.4 + - + +
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Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU 3.1 13.1 + - - +
262A GLU* 3.3 18.0 - - - +
264A TYR* 1.3 81.4 - - + +
266A MET* 1.3 62.0 + - - +
268A GLU* 3.6 27.1 + - - +
269A LYS* 3.7 16.6 - - + +
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.8 20.6 - - + -
176A PHE* 5.1 1.0 - - - -
180A ILE* 3.5 28.5 - - + -
186A TYR* 3.4 46.4 + - + +
262A GLU 3.0 6.8 + - - +
263A LYS* 3.6 12.8 - - + +
265A ARG* 1.3 75.2 - - - +
267A LYS* 1.3 94.5 + - + +
269A LYS* 3.3 11.9 + - - +
270A TYR* 2.9 41.6 + - - +
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 4.3 19.9 - - - -
228A ASN* 4.0 26.3 + - - +
231A ILE* 4.2 24.6 - - + +
263A LYS* 2.9 21.9 + - + +
264A TYR* 3.2 5.6 + - + +
266A MET* 1.3 99.8 - - + +
268A GLU* 1.3 57.7 + - - +
270A TYR* 3.7 18.2 - - + -
271A TRP* 2.6 37.6 + - - +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLU* 6.2 0.7 - - + -
264A TYR* 2.9 52.0 + - + +
265A ARG* 3.6 21.9 - - - +
266A MET 3.2 0.2 - - - -
267A LYS* 1.3 77.9 - - - +
269A LYS* 1.3 66.1 + - + +
271A TRP* 3.3 10.9 + - - +
272A SER* 3.3 14.9 + - - -
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 4.0 25.5 - - + -
180A ILE* 6.4 0.7 - - - -
265A ARG* 3.7 20.0 - - + +
266A MET* 3.3 8.0 + - - +
267A LYS 3.2 0.2 - - - -
268A GLU* 1.3 78.2 - - + +
270A TYR* 1.3 65.4 + - - +
272A SER* 3.2 22.3 + - - -
273A PHE* 3.5 14.0 - - + -
294A GLU* 6.5 0.4 - - - -
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Residues in contact with TYR 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.8 26.4 - + - -
149A LYS* 3.9 5.4 - - + +
150A ILE* 3.7 21.7 + - + -
153A ASP* 2.7 31.9 + - + +
176A PHE* 4.0 18.8 - + + -
177A TYR* 3.6 24.9 - + - -
180A ILE* 5.1 4.5 - - + -
266A MET* 2.9 28.1 + - - +
267A LYS* 3.4 30.1 - - + +
269A LYS* 1.3 77.4 - - - +
271A TRP* 1.3 63.6 + - - +
273A PHE* 3.0 14.6 + - - +
274A GLU* 3.1 30.7 + - + +
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Residues in contact with TRP 271 (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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235A GLU* 6.0 6.3 - - + -
267A LYS 2.6 19.8 + - - +
268A GLU* 3.7 7.2 - - - +
270A TYR* 1.3 72.6 - - - +
272A SER* 1.3 56.5 + - - +
274A GLU* 2.8 44.3 + - + +
275A LYS* 2.8 79.6 + - + +
278A TYR* 4.4 17.3 - + - -
287A TRP* 4.8 17.2 - + - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.3 12.5 + - - -
269A LYS* 3.2 12.4 + - - -
270A TYR 3.1 0.6 - - - -
271A TRP* 1.3 79.7 - - - +
273A PHE* 1.3 66.2 + - - +
275A LYS* 3.8 16.4 + - - +
276A ILE* 3.7 18.7 + - - +
290A GLU 6.2 0.2 - - - -
291A GLY* 3.8 13.0 - - - -
294A GLU* 4.6 25.6 + - - +
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 3.5 20.6 - - + +
172A LYS 5.0 0.2 - - - -
173A VAL* 4.3 15.3 - - + -
176A PHE* 3.6 51.8 - + + -
177A TYR* 3.5 23.3 - + - +
269A LYS* 3.5 15.0 - - + -
270A TYR* 3.0 7.4 + - + +
272A SER* 1.3 79.3 - - - +
274A GLU* 1.3 68.1 + - - +
276A ILE* 3.0 26.3 + - + +
277A ILE 3.8 0.5 + - - -
291A GLY 5.8 0.4 - - - -
294A GLU* 5.2 12.3 - - + -
295A ILE* 3.9 30.3 - - + -
298A ILE* 3.8 24.5 - - + -
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Residues in contact with GLU 274 (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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149A LYS* 4.0 20.8 + - - -
153A ASP* 4.1 17.9 - - - +
157A ILE* 5.3 0.7 - - - -
177A TYR* 4.9 1.0 + - - -
270A TYR* 3.1 27.2 + - + +
271A TRP* 2.8 40.2 - - + +
273A PHE* 1.3 75.1 - - - +
275A LYS* 1.3 55.0 + - - +
277A ILE* 2.8 41.0 + - + +
278A TYR* 3.4 27.9 + - + -
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A TRP* 2.8 73.6 + - + +
272A SER* 3.8 15.1 + - - +
273A PHE 3.2 0.2 - - - -
274A GLU* 1.3 73.3 - - - +
276A ILE* 1.3 54.9 + - - +
277A ILE 3.2 0.2 - - - -
278A TYR* 4.4 5.8 - - - -
279A GLY* 2.7 33.2 + - - -
287A TRP* 3.3 55.8 - - + +
290A GLU* 4.7 11.7 + - - -
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ILE* 4.6 10.5 - - + -
160A LEU* 4.6 2.0 - - + +
161A LEU* 3.7 31.9 - - + -
272A SER 3.7 10.5 + - - +
273A PHE* 3.0 24.1 + - + +
275A LYS* 1.3 76.5 - - - +
277A ILE* 1.3 59.6 + - + +
279A GLY* 4.7 0.9 - - - -
280A LYS* 2.9 30.0 + - - +
287A TRP 4.3 5.8 - - - +
288A TYR* 4.2 16.0 - - + +
291A GLY* 3.7 28.0 - - - +
292A LEU* 4.1 3.4 - - + +
295A ILE* 3.6 31.6 - - + -
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP* 4.5 9.9 - - - +
156A LYS* 3.9 34.8 - - + +
157A ILE* 3.1 36.8 - - + -
160A LEU* 3.3 27.7 - - + +
273A PHE 4.1 2.2 - - - +
274A GLU* 2.8 21.8 + - + +
276A ILE* 1.3 77.2 - - - +
278A TYR* 1.3 70.7 + - + +
280A LYS* 4.1 1.7 - - - +
281A GLU* 3.1 23.6 + - + +
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 3.5 27.7 + - + -
149A LYS* 5.1 6.6 + - - -
271A TRP* 4.4 16.3 - + - -
274A GLU* 3.4 43.7 + - + -
275A LYS* 4.4 2.7 - - - +
277A ILE* 1.3 83.1 - - + +
279A GLY* 1.3 56.2 + - - +
281A GLU* 4.2 5.8 - - + -
282A TYR* 2.6 65.7 + + + +
287A TRP* 3.7 24.7 - + + -
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS 2.7 25.1 + - - -
276A ILE 3.8 0.9 - - - -
277A ILE 3.2 0.2 - - - -
278A TYR* 1.3 74.1 - - - +
280A LYS* 1.3 56.1 + - - +
283A GLY* 2.9 24.4 + - - -
284A TYR* 3.0 27.7 + - - +
287A TRP* 3.9 11.6 - - - -
288A TYR* 4.3 7.5 - - - +
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A LEU* 3.4 50.4 + - + +
163A ARG* 6.0 2.0 - - - +
276A ILE 2.9 20.1 + - - +
277A ILE 4.2 2.5 - - - +
279A GLY* 1.3 71.6 - - - +
281A GLU* 1.3 66.7 + - - +
283A GLY* 3.7 6.3 + - - -
288A TYR* 3.5 38.4 - - + -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.2 24.2 - - + +
160A LEU* 6.2 0.2 - - - +
277A ILE* 3.1 19.4 + - + +
278A TYR* 3.5 6.5 - - + +
280A LYS* 1.3 79.7 - - - +
282A TYR* 1.3 83.5 + - + +
283A GLY* 3.1 0.6 + - - -
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.4 9.0 - - + -
31A GLY 5.8 0.9 - - - -
32A ASN* 3.0 41.1 + - - +
49A LYS* 6.2 1.8 - - - -
278A TYR* 2.6 50.1 + + + +
281A GLU* 1.3 91.7 - - + +
283A GLY* 1.3 61.5 + - - +
284A TYR* 3.5 50.2 - + + +
287A TRP* 4.2 5.8 - + - -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLY 2.9 10.4 + - - -
280A LYS* 3.7 5.6 + - - -
281A GLU 3.1 4.6 + - - -
282A TYR* 1.3 80.9 - - - +
284A TYR* 1.3 64.6 + - - +
285A MET* 3.7 3.5 + - - +
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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