Contacts of the helix formed by residues 259 - 292 (chain A) in PDB entry 3NA0
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 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A TRP* 3.4 37.2 - - - -
246A PRO* 3.0 45.5 + - - +
247A MET* 4.0 17.7 - - + -
250A LEU* 4.2 16.8 - - + +
255A PHE* 2.6 21.1 + - - +
258A PHE* 1.3 97.1 + - + +
260A THR* 1.3 53.7 + - - +
261A LYS 3.3 3.1 - - - -
262A THR* 3.0 10.8 + - - +
263A TRP* 2.8 31.5 + - - +
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Residues in contact with THR 260 (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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255A PHE 3.3 2.1 + - - -
256A ARG* 2.4 34.4 + - + +
257A LEU 3.9 8.3 + - - -
258A PHE 3.6 0.9 - - - -
259A ARG* 1.3 77.1 - - - +
261A LYS* 1.3 57.7 + - - +
263A TRP* 3.4 7.7 + - + +
264A LYS* 2.9 30.2 + - + +
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Residues in contact with LYS 261 (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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259A ARG 3.3 1.0 - - - -
260A THR* 1.3 79.4 - - - +
262A THR* 1.3 60.2 + - - +
264A LYS* 3.4 9.6 + - + +
265A ASP* 3.1 55.7 + - - +
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Residues in contact with THR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.2 33.7 - - - +
246A PRO* 3.9 24.4 - - + +
247A MET* 3.8 19.5 - - + -
259A ARG* 3.0 16.6 + - - -
261A LYS* 1.3 78.4 - - - +
263A TRP* 1.3 57.2 + - - +
265A ASP* 3.3 6.7 + - - +
266A HIS* 2.8 32.9 + - - +
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Residues in contact with TRP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.7 19.5 - - + -
128A ALA* 3.9 11.0 - - + -
129A TYR* 3.6 27.8 - - - -
132A TYR* 5.3 7.4 - + + -
133A TYR* 4.4 16.5 + + - -
247A MET* 3.2 44.6 - - + -
255A PHE* 3.9 18.8 - + + +
256A ARG* 4.9 16.3 - - + +
259A ARG 2.8 17.5 + - - +
260A THR* 3.6 8.5 - - + +
262A THR* 1.3 70.1 - - - +
264A LYS* 1.3 70.2 + - - +
266A HIS* 3.2 14.4 + + - +
267A VAL* 2.9 49.8 + - + +
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Residues in contact with LYS 264 (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 THR* 2.9 19.8 + - + +
261A LYS* 3.5 11.0 - - + +
262A THR 3.3 0.2 - - - -
263A TRP* 1.3 81.2 - - - +
265A ASP* 1.3 63.3 + - - +
267A VAL* 3.3 5.9 + - - +
268A ALA* 3.1 27.0 + - - +
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLN* 4.9 6.5 - - - +
243A THR* 4.0 17.4 - - + +
261A LYS* 3.1 50.8 + - - +
262A THR* 3.7 5.5 - - - +
264A LYS* 1.3 81.8 - - - +
266A HIS* 1.3 64.4 + - - +
268A ALA* 3.4 7.7 + - - +
269A ALA* 3.1 22.3 + - - +
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Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.8 20.9 - - + +
126A TRP* 3.6 12.0 - + - -
129A TYR* 5.0 1.6 - - + -
240A MET* 3.2 10.5 + - + -
243A THR* 2.8 36.7 + - - +
244A SER* 3.2 28.0 + - - -
247A MET* 4.7 1.3 - - - -
262A THR 2.8 22.0 + - - +
263A TRP* 3.5 21.8 - + - +
265A ASP* 1.3 75.1 - - - +
267A VAL* 1.3 62.8 + - - +
269A ALA* 3.3 5.7 + - - +
270A TRP* 3.0 56.9 + + - -
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.7 20.0 - - + -
133A TYR* 3.7 34.8 - - + +
263A TRP* 2.9 57.4 + - + +
264A LYS* 3.6 6.7 - - - +
266A HIS* 1.3 72.8 - - + +
268A ALA* 1.3 67.3 + - - +
270A TRP 3.6 0.9 + - - -
271A ASP* 3.0 35.2 + - - +
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Residues in contact with ALA 268 (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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264A LYS* 3.1 14.4 + - - +
265A ASP* 3.7 11.4 - - - +
266A HIS 3.3 0.2 - - - -
267A VAL* 1.3 76.7 - - - +
269A ALA* 1.3 63.1 + - - +
271A ASP* 3.3 11.4 + - - +
272A VAL* 3.2 26.5 + - - +
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Residues in contact with ALA 269 (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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236A ALA* 3.6 15.5 - - - +
239A GLN* 3.9 11.9 - - + -
240A MET* 3.6 30.3 - - - +
265A ASP 3.1 13.1 + - - +
266A HIS* 3.5 8.7 - - - +
267A VAL 3.2 0.2 - - - -
268A ALA* 1.3 73.4 - - - +
270A TRP* 1.3 66.4 + - - +
272A VAL* 3.2 8.1 + - - +
273A ILE* 3.1 25.8 + - - +
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Residues in contact with TRP 270 (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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126A TRP* 3.7 26.5 - + - +
129A TYR* 3.2 40.2 - + + -
130A HIS* 3.9 19.5 - + - -
140A LEU* 5.7 1.1 - - + -
240A MET* 3.4 37.5 - - + +
266A HIS* 3.0 54.2 + + - +
269A ALA* 1.3 74.6 - - - +
271A ASP* 1.3 55.5 + - - +
273A ILE* 3.1 26.9 + - + +
274A PHE* 2.8 62.4 + + - -
321A THR* 5.4 2.5 - - + -
322A GLU* 5.9 3.4 - - + -
325A ALA* 5.3 0.9 - - + -
602A 2DC 4.5 21.1 - - + -
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Residues in contact with ASP 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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129A TYR* 2.7 26.2 + - - -
133A TYR* 5.5 2.8 - - - -
135A ARG* 3.4 19.8 + - - +
267A VAL* 3.0 30.9 + - - +
268A ALA* 3.4 12.6 - - - +
269A ALA 3.2 0.4 - - - -
270A TRP* 1.3 70.9 - - - +
272A VAL* 1.3 61.3 + - + +
274A PHE* 3.8 2.3 - - - +
275A SER* 2.8 36.9 + - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.7 40.2 - - - +
233A PHE* 3.9 4.7 - - - +
236A ALA* 3.6 23.1 - - + -
268A ALA 3.2 16.2 + - - +
269A ALA* 3.5 7.0 - - - +
271A ASP* 1.3 72.7 - - + +
273A ILE* 1.3 70.0 + - - +
274A PHE 3.3 0.2 + - - -
275A SER* 3.8 3.9 - - - -
276A LYS* 3.1 49.0 + - + +
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Residues in contact with ILE 273 (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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233A PHE* 3.3 22.2 - - + -
236A ALA* 4.2 7.0 - - + +
237A ILE* 4.0 29.6 - - + -
240A MET* 3.9 36.1 - - + -
269A ALA 3.1 14.1 + - - +
270A TRP* 3.1 25.5 + - + +
272A VAL* 1.3 78.1 - - - +
274A PHE* 1.3 58.2 + - - +
277A ALA* 3.0 28.1 + - - +
321A THR* 3.7 22.4 - - + -
325A ALA* 4.2 19.1 - - + -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.6 27.1 - + - +
130A HIS* 3.3 35.7 - + - -
135A ARG* 3.7 32.5 - - + +
136A PRO* 3.9 25.8 - - + -
270A TRP* 2.8 43.9 + + - +
271A ASP 4.1 2.5 - - - +
273A ILE* 1.3 71.3 - - - +
275A SER* 1.3 66.2 + - - +
278A ASP* 2.9 43.6 + - - +
317A LYS* 6.5 0.2 - - + -
318A ALA* 5.6 2.0 - - - -
321A THR* 3.8 27.8 - - + -
322A GLU* 6.3 2.0 - - + -
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ARG* 5.5 2.8 + - - +
232A ARG* 6.2 1.3 - - - -
271A ASP* 2.8 30.8 + - - +
272A VAL* 3.3 4.9 + - - -
274A PHE* 1.3 74.6 - - - +
276A LYS* 1.3 63.5 + - - +
278A ASP* 3.3 5.1 + - - +
279A ILE* 3.0 38.5 + - - +
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Residues in contact with LYS 276 (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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229A GLU* 3.0 60.5 + - - +
232A ARG* 3.7 22.7 - - - +
233A PHE* 3.7 19.3 - - + -
272A VAL* 3.1 29.3 + - + +
275A SER* 1.3 78.3 - - - +
277A ALA* 1.3 65.2 + - - +
279A ILE* 3.8 16.4 - - + +
280A TYR* 2.9 43.5 + - + +
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Residues in contact with ALA 277 (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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233A PHE* 4.3 3.8 - - + -
273A ILE 3.0 20.2 + - - +
274A PHE 4.1 1.6 - - - +
276A LYS* 1.3 77.0 - - - +
278A ASP* 1.3 62.9 + - - +
280A TYR* 3.6 3.1 - - - +
281A THR* 2.9 31.3 + - - +
317A LYS* 5.2 0.2 - - - -
320A VAL* 5.2 0.2 - - - +
321A THR* 3.1 41.3 - - + +
324A LEU* 3.9 20.2 - - + -
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Residues in contact with ASP 278 (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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135A ARG* 5.4 4.3 + - - -
136A PRO* 6.0 1.0 - - - +
274A PHE* 2.9 36.4 + - - +
275A SER* 3.5 5.6 - - - +
277A ALA* 1.3 75.8 - - - +
279A ILE* 1.3 56.7 - - + +
281A THR* 3.3 1.2 + - - -
282A GLN* 2.8 39.0 + - - +
317A LYS* 3.1 39.2 - - - +
321A THR* 4.1 6.8 + - - -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A SER* 3.0 29.3 + - - +
276A LYS* 3.4 17.5 + - + +
278A ASP* 1.3 74.9 - - + +
280A TYR* 1.3 62.6 + - + +
282A GLN* 4.6 5.8 - - - +
283A ASN* 2.9 56.8 + - - +
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Residues in contact with TYR 280 (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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207A PHE* 3.8 29.3 - + - -
211A THR* 5.4 1.1 - - + -
215A PHE* 3.5 33.5 - + + -
219A GLN* 4.1 20.5 + - - -
227A ASN* 5.4 3.4 + - - -
229A GLU* 5.1 1.2 + - - +
230A ALA* 3.9 20.6 + - - +
233A PHE* 4.9 7.8 - + - +
276A LYS* 2.9 43.6 + - + +
277A ALA* 3.6 7.4 - - - +
279A ILE* 1.3 79.6 - - + +
281A THR* 1.3 56.8 + - - +
283A ASN* 3.9 5.5 - - - +
284A PHE* 3.0 30.0 + - - +
324A LEU* 4.5 7.4 - - + -
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Residues in contact with THR 281 (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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215A PHE* 4.3 0.4 - - - -
277A ALA 2.9 20.5 + - - -
278A ASP 3.8 1.1 - - - -
280A TYR* 1.3 71.7 - - - +
282A GLN* 1.3 58.4 + - - +
284A PHE* 3.3 3.5 + - - +
285A TYR* 3.0 27.0 + - - +
302A LEU* 4.1 31.8 - - + +
306A LEU* 5.6 0.2 - - + -
313A PHE* 4.0 19.7 - - + -
316A ILE* 5.1 0.4 - - + -
317A LYS* 3.7 35.5 - - + +
320A VAL* 3.6 21.7 - - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP* 2.8 27.2 + - - +
279A ILE* 3.9 5.6 - - - +
281A THR* 1.3 71.4 - - - +
283A ASN* 1.3 71.2 + - - +
285A TYR* 3.1 17.2 + - + +
286A TRP* 3.1 34.2 + - + +
313A PHE* 4.9 9.0 - - + -
317A LYS* 6.2 1.5 - - - +
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Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ILE* 2.9 44.3 + - - +
280A TYR* 3.9 6.4 - - - +
282A GLN* 1.3 77.6 + - - +
284A PHE* 1.3 63.3 + - - +
286A TRP* 3.4 4.8 + - - +
287A GLU* 3.0 46.1 + - - +
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Residues in contact with PHE 284 (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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214A ILE 5.2 0.2 - - - -
215A PHE* 3.4 44.2 - + + -
217A GLU* 4.9 14.1 - - - -
280A TYR 3.0 19.5 + - - +
281A THR 3.4 5.2 - - - +
283A ASN* 1.3 76.5 - - - +
285A TYR* 1.3 62.0 + - - +
287A GLU* 3.6 9.7 + - - +
288A LEU* 3.1 31.3 + - + +
299A ARG* 5.0 2.7 - - + -
302A LEU* 3.4 25.4 - - + -
303A TYR* 3.7 47.3 - + + -
306A LEU* 3.8 13.5 - - + -
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Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A THR 3.0 13.6 + - - +
282A GLN* 3.1 10.9 + - + +
284A PHE* 1.3 76.6 - - - +
286A TRP* 1.3 98.0 - + - +
288A LEU* 3.4 16.1 - - + +
289A ARG* 3.4 55.7 + - - -
306A LEU* 4.3 22.9 - - + -
313A PHE* 3.6 41.3 - + + -
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Residues in contact with TRP 286 (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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282A GLN* 3.1 40.7 + - + +
283A ASN* 4.1 4.3 - - - +
285A TYR* 1.3 99.7 - + - +
287A GLU* 1.3 58.9 + - + +
288A LEU 3.1 1.8 - - - -
289A ARG* 3.0 44.2 + - + +
290A GLN* 3.0 29.9 + - + +
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Residues in contact with GLU 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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217A GLU* 4.0 17.3 - - - +
283A ASN* 3.0 37.1 + - - +
284A PHE* 4.0 8.1 - - - +
286A TRP* 1.3 72.1 - - + +
288A LEU* 1.3 60.0 + - - +
290A GLN* 3.6 22.4 - - - +
291A LYS* 3.1 57.6 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.1 24.2 + - + +
285A TYR* 3.4 11.9 - - - +
286A TRP 3.1 0.2 - - - -
287A GLU* 1.3 78.7 - - - +
289A ARG* 1.3 69.8 + - - +
291A LYS* 3.9 1.5 - - - -
292A GLY* 2.9 28.3 + - - -
293A SER 6.1 0.2 - - - +
299A ARG* 5.3 4.7 - - - +
303A TYR* 3.4 42.0 - - + +
306A LEU* 4.4 31.2 - - + -
307A GLY* 5.7 2.0 - - - +
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Residues in contact with ARG 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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285A TYR* 3.4 62.5 + - - -
286A TRP* 3.0 37.6 + - + +
288A LEU* 1.3 91.3 - - + +
290A GLN* 1.3 61.8 + - + +
291A LYS 3.5 0.2 - - - -
292A GLY* 3.9 7.6 + - - +
306A LEU* 5.5 6.5 + - - +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TRP* 3.0 36.9 + - + +
287A GLU* 3.6 22.5 - - + +
288A LEU 3.3 0.2 - - - -
289A ARG* 1.3 79.6 - - + +
291A LYS* 1.3 63.7 + - + +
292A GLY 3.5 0.2 - - - -
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 4.9 6.5 + - - -
287A GLU* 3.1 51.4 + - - +
288A LEU* 3.9 2.5 - - - +
290A GLN* 1.3 80.8 - - + +
292A GLY* 1.3 65.2 + - - +
293A SER* 2.8 17.4 + - - -
295A HIS* 5.1 7.9 + - - +
299A ARG* 5.8 5.8 - - - +
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU* 2.9 20.5 + - - -
289A ARG* 3.9 7.2 + - - -
290A GLN 3.5 2.0 - - - -
291A LYS* 1.3 75.1 - - - +
293A SER* 1.3 59.5 + - - -
----------------------------------------------------------
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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