Contacts of the helix formed by residues 249 - 279 (chain K) in PDB entry 4DVQ
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 SER 249 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56K TRP* 3.7 17.5 + - - -
236K GLN 5.7 2.5 - - - -
237K LEU* 4.9 5.8 - - - -
240K MET* 5.7 2.9 - - - -
245K SER* 3.0 14.6 + - - -
248K ILE* 1.3 86.4 + - - +
250K PRO* 1.3 66.1 - - - +
251K LYS* 3.3 2.8 + - - +
252K VAL* 3.5 25.4 + - - +
253K TRP* 3.3 23.4 + - - -
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Residues in contact with PRO 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H TRP* 5.8 1.1 - - + -
245K SER 4.0 0.2 - - - -
246K ARG 3.5 22.9 - - - +
247K TRP* 3.4 16.4 - - - +
248K ILE 3.8 1.8 - - - +
249K SER* 1.3 86.1 - - - +
251K LYS* 1.3 64.9 + - + +
253K TRP* 3.5 9.6 + - + +
254K LYS* 3.0 27.8 + - - +
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Residues in contact with LYS 251 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249K SER* 3.3 1.2 - - - -
250K PRO* 1.3 79.5 - - + +
252K VAL* 1.3 56.0 + - + +
254K LYS* 3.1 11.2 + - + +
255K GLU* 2.7 38.5 + - - +
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Residues in contact with VAL 252 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K GLN* 5.7 2.2 - - - +
233K SER* 4.0 10.2 - - - +
236K GLN* 3.5 40.8 - - + +
237K LEU* 3.4 32.5 - - + -
249K SER* 3.5 29.3 + - - +
250K PRO 3.4 0.2 - - - -
251K LYS* 1.3 78.1 - - + +
253K TRP* 1.3 57.0 + - - +
255K GLU* 3.2 14.1 + - - +
256K HIS* 2.8 28.9 + - - +
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Residues in contact with TRP 253 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K GLU* 4.7 5.2 - - + -
115K PRO* 4.0 21.5 - - + -
118K ALA* 3.6 28.7 - - + -
237K LEU* 3.3 30.7 - - + +
242K ARG* 3.6 41.1 - - + -
245K SER* 3.0 40.2 + - - -
246K ARG* 3.7 12.2 - - + +
249K SER 3.3 22.0 + - - -
250K PRO* 3.6 9.2 - - + +
251K LYS 3.3 0.4 - - - -
252K VAL* 1.3 77.8 - - - +
254K LYS* 1.3 63.4 + - - +
256K HIS* 3.3 2.4 + - - +
257K PHE* 2.9 58.6 + + + +
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Residues in contact with LYS 254 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K PRO 3.0 12.6 + - - +
251K LYS* 3.3 12.1 - - + +
253K TRP* 1.3 78.3 - - - +
255K GLU* 1.3 63.5 + - + +
257K PHE* 3.9 4.8 - - - +
258K GLU* 3.1 47.1 + - - +
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Residues in contact with GLU 255 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K GLN* 5.9 0.7 + - - -
229K VAL* 3.9 30.0 - - + +
232K LYS* 5.1 12.0 + - - +
233K SER* 4.9 5.7 - - - -
236K GLN* 4.6 10.4 + - - +
251K LYS 2.7 18.9 + - - +
252K VAL* 3.4 18.4 + - - +
254K LYS* 1.3 74.8 - - + +
256K HIS* 1.3 61.3 + - - +
258K GLU* 3.3 10.5 + - - +
259K ALA* 3.0 28.2 + - - +
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Residues in contact with HIS 256 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K PRO* 3.5 33.9 + - + +
116K TRP* 3.7 3.6 - - - -
230K MET* 3.3 7.6 + - + -
233K SER* 2.5 35.7 + - - +
234K THR* 3.0 35.6 + - - -
237K LEU* 4.0 10.1 - - + -
252K VAL 2.8 16.5 + - - +
253K TRP* 3.5 4.7 - - - +
255K GLU* 1.3 77.1 - - - +
257K PHE* 1.3 64.4 + + + +
259K ALA* 3.3 5.7 + - - +
260K TRP* 3.1 66.9 + + - -
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Residues in contact with PHE 257 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K PRO 3.6 20.9 - - - -
118K ALA* 3.5 22.2 - - + -
119K TYR* 3.3 25.0 - + + -
122K HIS* 3.8 44.0 - + + -
123K ARG* 5.2 4.9 - - - +
242K ARG* 4.6 9.6 - - - -
253K TRP* 2.9 48.2 + + + +
254K LYS* 4.0 5.4 - - - +
256K HIS* 1.3 83.9 - + - +
258K GLU* 1.3 58.1 + - - +
260K TRP 3.9 0.9 - - - -
261K ASP* 3.0 32.2 + - - +
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Residues in contact with GLU 258 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K LYS* 3.1 45.1 + - - +
255K GLU* 3.4 10.1 - - - +
257K PHE* 1.3 77.2 - - - +
259K ALA* 1.3 64.8 + - - +
260K TRP 3.3 0.2 - - - -
261K ASP* 3.1 14.8 + - + +
262K CYS* 3.1 22.0 + - - +
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Residues in contact with ALA 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226K ALA* 3.4 29.5 - - - +
229K VAL* 3.7 18.2 - - + -
230K MET* 3.8 10.8 - - + +
255K GLU 3.0 13.4 + - - +
256K HIS 3.3 9.4 + - - +
258K GLU* 1.3 76.3 - - - +
260K TRP* 1.3 57.5 + - - +
262K CYS* 3.2 6.3 + - - +
263K ILE* 3.0 31.7 + - - +
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Residues in contact with TRP 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K TRP* 3.4 33.0 - + - +
119K TYR* 3.3 38.6 - + + -
120K ARG* 3.4 33.2 - - - +
230K MET* 3.3 39.2 - - + +
256K HIS* 3.1 54.2 + + - +
259K ALA* 1.3 72.5 - - - +
261K ASP* 1.3 56.8 + - - +
263K ILE* 3.9 23.6 - - + -
264K PHE* 2.7 58.9 + + - +
309K MET* 5.9 1.1 - - + -
313K ALA* 4.9 8.7 - - + -
602K 1CA 4.9 3.6 - - - -
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Residues in contact with ASP 261 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K TYR* 3.0 19.1 + - - -
123K ARG* 2.9 34.3 + - - -
257K PHE 3.0 23.4 + - - +
258K GLU* 3.1 16.4 + - + +
260K TRP* 1.3 74.1 - - - +
262K CYS* 1.3 58.0 + - - +
264K PHE* 3.9 1.6 - - - +
265K GLN* 2.9 31.1 + - - +
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Residues in contact with CYS 262 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222K ASN* 4.0 26.0 - - - -
223K PHE* 4.7 2.0 - - - -
226K ALA* 3.7 21.5 - - + -
258K GLU 3.1 8.7 + - - +
259K ALA* 3.5 9.0 - - - +
260K TRP 3.1 0.2 - - - -
261K ASP* 1.3 80.7 - - - +
263K ILE* 1.3 60.1 + - - +
265K GLN* 3.5 10.0 + - - +
266K TYR* 3.1 22.5 + - - +
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Residues in contact with ILE 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223K PHE* 4.0 23.9 - - + -
226K ALA* 4.0 14.4 - - + +
227K LEU* 3.7 24.2 - - + -
230K MET* 3.8 28.3 - - + -
259K ALA 3.0 19.3 + - - +
260K TRP* 3.6 31.9 - - + +
262K CYS* 1.3 73.0 - - - +
264K PHE* 1.3 60.0 + - - +
266K TYR* 3.1 5.2 + - - +
267K GLY 2.8 24.8 + - - -
309K MET* 3.8 19.2 - - + +
313K ALA* 4.1 9.2 - - + -
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Residues in contact with PHE 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K TYR* 3.5 30.1 - + - +
120K ARG* 3.8 29.4 - - + -
125K HIS* 3.4 40.8 - + + +
260K TRP* 2.7 54.1 + + - +
261K ASP 4.0 1.3 - - - +
263K ILE* 1.3 72.2 - - - +
265K GLN* 1.3 54.6 + - - +
268K ASP* 2.5 42.1 + - + +
305K LYS 5.9 0.4 - - - -
306K ALA* 6.1 3.6 - - - -
309K MET* 3.6 34.7 - - + +
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Residues in contact with GLN 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K ASP 2.9 19.4 + - - +
262K CYS* 3.6 10.5 + - - +
264K PHE* 1.3 76.1 - - - +
266K TYR* 1.3 61.9 + - - +
268K ASP* 4.0 5.4 - - - +
269K ASN* 3.0 32.3 + - - +
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Residues in contact with TYR 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K ILE* 3.7 13.3 - - + +
201K ASN* 4.1 3.7 + - - -
209K LEU* 3.4 29.1 - - + +
211K LEU* 5.3 0.9 - - - +
219K ALA* 4.0 34.1 - - + -
220K SER* 5.1 2.7 - - - -
223K PHE* 4.0 39.7 - + + -
262K CYS* 3.1 15.3 + - - +
263K ILE 3.4 7.2 - - - +
265K GLN* 1.3 82.6 - - - +
267K GLY* 1.3 62.9 + - - +
269K ASN* 3.3 9.2 + - + +
270K CYS* 3.2 38.3 + - - -
312K THR* 4.0 22.0 - - + -
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Residues in contact with GLY 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K PHE* 5.1 0.5 - - - -
263K ILE 2.8 14.7 + - - -
266K TYR* 1.3 76.5 - - - +
268K ASP* 1.3 59.5 + - - +
270K CYS* 3.2 8.1 + - - +
271K ILE* 2.9 34.1 + - - +
309K MET* 3.5 28.7 - - - +
312K THR* 4.5 6.7 + - - -
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Residues in contact with ASP 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264K PHE* 2.5 27.1 + - + +
265K GLN* 4.1 4.9 - - - +
267K GLY* 1.3 69.0 - - - -
269K ASN* 1.3 56.7 + - - +
271K ILE* 3.1 15.7 + - + +
272K GLN* 2.7 65.0 + - - +
305K LYS* 4.5 12.5 + - - +
309K MET* 4.4 1.4 - - + -
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Residues in contact with ASN 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496G LEU* 4.4 13.9 - - - +
265K GLN* 3.0 23.8 + - - +
266K TYR* 3.4 9.8 + - + +
268K ASP* 1.3 76.8 - - - +
270K CYS* 1.3 64.9 + - - +
272K GLN* 3.3 5.0 + - - +
273K LYS* 3.0 48.2 + - - +
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Residues in contact with CYS 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K ASN* 3.7 22.2 - - - -
205K PHE* 3.6 32.5 - - + -
209K LEU* 5.9 2.9 - - - -
266K TYR* 3.2 35.7 + - - -
267K GLY* 3.5 9.0 - - - +
268K ASP 3.2 0.2 - - - -
269K ASN* 1.3 84.5 - - - +
271K ILE* 1.3 62.3 + - - +
272K GLN 3.3 0.2 + - - -
273K LYS* 3.4 10.0 + - - +
274K ILE* 3.2 23.2 + - - +
312K THR* 4.8 1.1 - - - -
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Residues in contact with ILE 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K PHE* 4.6 1.1 - - + -
267K GLY 2.9 25.4 + - - +
268K ASP* 3.6 16.4 - - - +
270K CYS* 1.3 75.0 - - - +
272K GLN* 1.3 61.6 + - - +
274K ILE* 3.2 11.6 - - + +
275K TYR* 2.9 35.3 + - + +
290K VAL* 6.1 0.9 - - + -
294K LEU* 6.3 2.7 - - + -
301K LEU* 5.3 4.0 - - + -
304K ILE* 6.4 1.6 - - + -
305K LYS* 3.7 63.9 - - + +
308K SER* 3.7 23.3 - - - +
309K MET* 4.4 9.4 - - + -
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Residues in contact with GLN 272 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476G LEU* 6.1 0.6 - - - +
496G LEU* 3.9 22.4 - - + +
268K ASP* 2.7 51.5 + - - +
269K ASN* 3.7 6.7 - - - +
271K ILE* 1.3 74.9 - - - +
273K LYS* 1.3 63.4 + - - +
275K TYR* 3.9 17.3 - - - +
276K GLN* 3.2 25.1 + - - +
305K LYS* 4.5 16.0 + - - +
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Residues in contact with LYS 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ARG* 6.2 0.2 - - - +
184G LEU* 5.1 5.6 - - - +
185G THR* 3.4 44.7 + - + +
496G LEU* 4.5 4.7 - - + -
207K GLU* 3.2 42.7 + - + +
209K LEU* 4.7 12.9 - - - +
269K ASN* 3.0 44.5 + - - +
270K CYS* 3.7 9.5 - - - +
272K GLN* 1.3 78.0 - - - +
274K ILE* 1.3 62.8 + - - +
276K GLN* 3.4 2.4 + - - +
277K GLU* 3.0 29.6 + - - +
----------------------------------------------------------
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Residues in contact with ILE 274 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ARG* 3.3 42.0 - - - +
205K PHE* 3.4 33.2 - - + +
270K CYS 3.2 11.2 + - - +
271K ILE* 3.2 17.9 - - + +
273K LYS* 1.3 77.8 - - - +
275K TYR* 1.3 67.6 + - - +
277K GLU* 3.2 2.6 + - - +
278K LEU* 2.9 35.6 + - + +
290K VAL* 4.2 10.1 - - + -
291K ALA* 4.0 21.8 - - + +
294K LEU* 3.7 16.4 - - + -
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Residues in contact with TYR 275 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476G LEU* 3.4 35.4 - - + -
271K ILE* 2.9 24.6 + - + +
272K GLN* 3.9 16.6 - - - +
274K ILE* 1.3 80.7 - - + +
276K GLN* 1.3 63.1 + - - +
278K LEU* 3.4 2.9 + - + +
279K ALA* 3.0 28.7 + - + +
294K LEU* 4.2 25.1 - - + -
301K LEU* 4.1 34.7 - - + +
305K LYS* 6.4 0.7 - - - -
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Residues in contact with GLN 276 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G THR* 3.7 6.4 - - + +
474G GLU 3.2 13.7 + - - +
475G THR* 3.8 2.1 - - - +
476G LEU* 3.1 48.5 + - + +
477G THR* 4.5 1.0 + - - -
496G LEU* 2.7 37.5 + - + +
497G LEU 3.6 0.2 - - - -
498G THR* 2.9 29.9 + - - +
272K GLN 3.2 15.7 + - - +
273K LYS 3.8 3.1 - - - +
275K TYR* 1.3 78.5 - - - +
277K GLU* 1.3 63.8 + - - +
279K ALA* 3.3 8.5 + - - +
280K PHE* 3.4 23.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 277 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ASN* 5.6 1.0 - - - +
181G ARG* 2.7 50.3 + - - +
183G SER* 3.2 38.1 + - - +
185G THR* 2.8 32.4 + - - +
498G THR* 4.2 5.8 - - + -
500G ARG* 3.1 26.5 + - - +
207K GLU* 3.8 12.5 - - - +
273K LYS* 3.0 18.1 + - - +
274K ILE 3.2 4.5 + - - +
276K GLN* 1.3 77.6 - - - +
278K LEU* 1.3 61.3 + - - +
280K PHE 3.3 2.4 + - - -
281K ASN 3.2 11.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 278 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G ARG* 3.4 29.8 - - - -
274K ILE* 2.9 18.5 + - + +
275K TYR* 4.1 3.8 - - + +
277K GLU* 1.3 76.8 - - - +
279K ALA* 1.3 59.3 + - - +
280K PHE 3.1 1.9 + - - -
281K ASN 3.4 15.2 + - - +
282K ARG* 3.9 14.0 + - - +
283K PRO* 3.4 27.4 - - + -
291K ALA* 3.7 36.3 - - + +
294K LEU* 3.8 28.0 - - + -
295K LEU* 4.5 13.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 279 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476G LEU* 4.0 29.3 - - + +
275K TYR* 3.0 23.8 + - + +
276K GLN 3.7 5.6 - - - +
277K GLU 3.2 0.8 - - - -
278K LEU* 1.3 76.0 - - - +
280K PHE* 1.3 64.7 + - + +
----------------------------------------------------------
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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).
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