Contacts of the helix formed by residues 281 - 305 (chain D) in PDB entry 1EQB
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 GLU 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C TYR* 3.0 35.5 + - + +
277D LYS* 3.7 13.9 + - - +
278D GLU* 3.1 18.9 + - + +
279D ALA 4.2 0.7 - - - +
280D MET* 1.3 81.3 - - - +
282D PRO* 1.3 70.9 - - - +
283D GLU* 3.3 25.5 - - + +
284D PHE* 2.9 26.3 + - - +
285D LYS* 3.5 4.2 + - - +
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Residues in contact with PRO 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D MET 4.1 3.8 - - - +
281D GLU* 1.3 85.3 - - + +
283D GLU* 1.3 78.9 + - - +
284D PHE 3.0 4.9 - - - -
285D LYS* 3.0 20.0 + - + +
286D THR* 3.3 16.4 + - - +
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D GLU* 3.3 28.8 - - + +
282D PRO* 1.3 95.6 - - - +
284D PHE* 1.3 57.5 + - - +
286D THR* 3.1 12.4 + - - +
287D TYR* 3.1 27.0 + - - +
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLY 3.9 14.8 - - - -
209D ALA* 3.9 8.5 - - + -
210D ALA* 4.6 5.8 - - + -
230D THR 4.0 8.5 - - - -
231D LEU* 4.0 22.9 - - + -
232D ALA* 4.8 4.3 - - + -
278D GLU* 3.6 16.8 - - + +
279D ALA* 3.0 44.9 - - + +
281D GLU* 2.9 16.9 + - + +
283D GLU* 1.3 80.3 - - - +
285D LYS* 1.3 62.0 + - + +
287D TYR* 3.4 15.2 + + - +
288D GLN* 3.0 52.6 + - + +
371D ARG* 5.1 9.2 - - - -
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Residues in contact with LYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ALA* 3.1 41.7 - - + +
211D GLY* 5.3 1.1 - - - -
212D VAL* 5.5 0.6 - - + +
281D GLU 3.5 4.1 + - - +
282D PRO* 3.0 14.9 + - + +
284D PHE* 1.3 78.1 - - - +
286D THR* 1.3 63.5 + - + +
288D GLN* 3.5 4.9 + - - +
289D GLN* 3.1 44.2 + - + +
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Residues in contact with THR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D PRO 3.3 9.6 + - - +
283D GLU* 3.1 19.6 + - - -
285D LYS* 1.3 77.2 - - + +
287D TYR* 1.3 63.9 + - - +
288D GLN 3.4 0.2 - - - -
289D GLN* 3.4 24.7 + - - +
290D GLN* 3.1 25.3 + - - +
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Residues in contact with TYR 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D ASN* 3.2 20.4 + - - -
230D THR* 4.5 4.9 - - - -
232D ALA* 5.1 1.1 - - + -
283D GLU 3.1 20.0 + - - +
284D PHE* 3.4 20.2 - + - +
285D LYS 3.2 0.2 - - - -
286D THR* 1.3 75.5 + - - +
288D GLN* 1.3 99.5 + - - +
290D GLN* 3.1 7.6 + - - +
291D VAL* 3.0 37.3 + - + +
367D PRO* 2.8 23.6 + - - +
370D THR* 3.8 8.7 - - + -
371D ARG* 3.3 49.8 - - + +
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Residues in contact with GLN 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D GLY 3.5 15.4 - - - +
207D LEU* 3.0 31.6 + - + +
210D ALA* 3.4 29.4 - - + -
212D VAL* 4.1 6.0 - - + +
230D THR* 3.2 15.3 + - - +
284D PHE* 3.0 39.9 + - + +
285D LYS 4.0 0.2 - - - +
286D THR 3.4 0.2 - - - -
287D TYR* 1.3 104.0 - - - +
289D GLN* 1.3 63.9 + - - +
291D VAL* 3.1 9.9 + - - +
292D ALA* 3.0 23.6 + - - +
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Residues in contact with GLN 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D VAL* 4.0 19.3 - - + +
285D LYS* 3.1 40.2 + - - +
286D THR* 3.4 28.6 + - - +
287D TYR 3.2 0.2 - - - -
288D GLN* 1.3 77.9 - - - +
290D GLN* 1.3 56.8 + - - +
292D ALA* 3.5 4.7 + - - +
293D LYS* 2.9 48.0 + - - +
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Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D THR 3.1 11.5 + - - +
287D TYR* 3.1 7.2 + - - +
289D GLN* 1.3 76.2 - - - +
291D VAL* 1.3 57.0 + - - +
293D LYS* 4.0 12.1 - - - +
294D ASN* 2.6 68.8 + - - +
370D THR* 3.4 19.5 - - + -
374D PHE 5.1 0.4 - - - +
375D LYS* 3.6 27.7 - - + +
376D GLU* 3.2 25.4 + - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LEU* 4.6 6.5 - - + -
230D THR* 5.5 0.2 - - + -
287D TYR* 3.0 35.8 + - + +
288D GLN* 3.2 17.7 - - - +
290D GLN* 1.3 77.3 - - - +
292D ALA* 1.3 64.2 + - - +
294D ASN 3.3 0.2 + - - -
295D ALA* 3.0 12.0 + - - +
317D HIS* 3.5 24.7 - - + -
366D THR* 2.7 33.3 + - - +
367D PRO* 3.9 13.5 - - + -
370D THR* 3.5 25.4 - - + -
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU* 5.2 3.4 - - + -
212D VAL* 4.3 20.2 - - + -
288D GLN 3.0 11.1 + - - +
289D GLN 4.0 3.1 - - - +
291D VAL* 1.3 78.9 - - - +
293D LYS* 1.3 63.7 + - - +
295D ALA* 3.1 12.0 + - - +
296D LYS* 3.1 24.8 + - - +
315D ASP 5.4 3.1 - - - +
316D ASN* 3.7 27.3 - - - +
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Residues in contact with LYS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D GLN* 2.9 36.5 + - - +
290D GLN* 3.2 16.2 + - - +
292D ALA* 1.3 76.9 - - - +
294D ASN* 1.3 60.7 + - - +
296D LYS* 3.3 13.5 + - + +
297D ALA* 3.2 19.8 + - - +
376D GLU* 3.2 35.5 - - + +
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Residues in contact with ASN 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D GLN* 2.6 29.1 + - - +
291D VAL 3.7 3.8 - - - +
293D LYS* 1.3 71.3 - - - +
295D ALA* 1.3 65.6 + - - +
297D ALA* 3.2 7.9 + - - +
298D MET* 3.1 26.9 + - - +
366D THR* 3.8 13.9 - - + -
369D ILE* 5.0 1.9 - - + +
370D THR* 3.0 24.7 + - - +
374D PHE* 3.2 25.3 + - - +
375D LYS 3.0 5.0 - - - -
376D GLU* 2.9 30.1 + - - +
379D ALA* 4.1 10.7 - - + +
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Residues in contact with ALA 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D VAL 3.0 11.2 + - - +
292D ALA 3.1 10.3 + - - +
294D ASN* 1.3 79.0 - - - +
296D LYS* 1.3 60.4 + - - +
298D MET* 3.4 4.0 + - - +
299D VAL* 3.2 26.2 + - - +
314D THR* 3.9 10.3 - - + -
316D ASN 3.3 21.8 - - - +
317D HIS 4.0 8.7 - - - +
319D PHE* 3.9 6.2 - - + -
366D THR* 3.4 20.3 - - + +
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Residues in contact with LYS 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D ALA* 3.1 22.0 + - - +
293D LYS* 3.6 13.5 - - + +
294D ASN 3.2 0.2 - - - -
295D ALA* 1.3 77.5 - - - +
297D ALA* 1.3 61.2 + - - +
299D VAL* 3.2 5.3 + - - +
300D GLU* 3.1 31.2 + - + +
314D THR* 2.7 42.0 + - + +
315D ASP* 3.9 15.8 + - - +
316D ASN 5.9 0.2 - - - +
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Residues in contact with ALA 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D LYS 3.2 10.8 + - - +
294D ASN* 3.2 9.8 + - - +
296D LYS* 1.3 80.5 - - - +
298D MET* 1.3 60.9 + - - +
299D VAL 3.6 0.2 + - - -
300D GLU* 3.6 15.0 + - - +
301D VAL* 3.5 24.3 + - - +
376D GLU* 4.2 20.9 - - + +
379D ALA* 4.5 2.7 - - + -
380D LYS* 3.8 30.4 - - + +
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Residues in contact with MET 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.1 14.1 - - + -
294D ASN 3.1 13.0 + - - +
295D ALA 3.8 2.2 - - - +
297D ALA* 1.3 74.1 - - - +
299D VAL* 1.3 65.4 + - - +
301D VAL* 3.4 3.5 + - - +
302D PHE* 3.1 31.0 + - + -
319D PHE* 3.8 16.6 - - + -
364D VAL* 4.4 9.9 - - + -
366D THR* 3.9 21.8 - - - -
369D ILE* 4.3 8.1 - - - -
379D ALA* 3.5 18.4 - - + +
382D LEU* 3.8 23.6 - - + -
383D ALA* 3.8 32.8 - - + +
386D MET* 3.9 16.4 - - - -
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Residues in contact with VAL 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D ALA 3.2 15.2 + - - +
296D LYS* 3.5 10.5 - - - +
298D MET* 1.3 74.0 - - - +
300D GLU* 1.3 70.6 + - + +
302D PHE* 3.2 8.3 + - - +
303D LEU* 3.0 37.0 + - + +
309D VAL* 4.4 10.1 - - + -
312D GLY 4.5 0.4 - - - +
313D GLY* 4.0 20.6 - - - -
314D THR* 3.7 16.6 - - + +
319D PHE* 3.4 33.0 - - + -
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Residues in contact with GLU 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D LYS* 3.1 20.9 + - - +
297D ALA* 3.7 15.5 - - - +
298D MET 3.3 0.2 - - - -
299D VAL* 1.3 79.1 - - + +
301D VAL* 1.3 65.1 + - + +
303D LEU* 3.0 10.4 + - - +
304D GLU* 2.9 39.7 + - + +
380D LYS* 3.9 21.3 + - - -
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ALA 3.5 15.2 + - - +
298D MET 3.4 6.2 + - - +
299D VAL 3.3 0.2 - - - -
300D GLU* 1.3 77.0 - - + +
302D PHE* 1.3 63.6 + - - +
304D GLU* 3.2 11.8 + - + +
305D ARG* 2.9 39.7 + - + +
380D LYS* 3.8 32.8 - - + +
383D ALA* 3.8 7.2 - - + +
384D GLY* 3.8 30.1 - - - +
387D CYS* 4.9 0.4 - - - -
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Residues in contact with PHE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D MET* 3.1 28.7 + - + +
299D VAL* 3.2 7.6 + - - +
301D VAL* 1.3 75.6 - - - +
303D LEU* 1.3 60.4 + - - +
305D ARG 3.4 5.5 + - - -
306D GLY 3.4 0.5 + - - -
307D TYR* 2.9 44.9 + - + +
309D VAL* 4.0 13.9 - - + -
319D PHE* 4.2 16.6 - + - -
321D VAL* 3.7 29.6 - - + -
362D ILE* 5.1 2.0 - - + -
364D VAL* 5.1 1.3 - - + -
383D ALA* 3.8 27.1 - - + -
386D MET* 4.0 35.4 - - + -
387D CYS* 4.0 18.2 - - - -
390D LEU* 4.3 17.3 - - + -
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Residues in contact with LEU 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D VAL* 3.0 25.7 + - + +
300D GLU* 3.0 9.7 + - - +
302D PHE* 1.3 71.2 - - - +
304D GLU* 1.3 62.0 + - + +
305D ARG 3.0 2.0 - - - -
306D GLY* 3.0 19.2 + - - -
307D TYR 3.3 20.0 - - - +
308D LYS* 5.0 0.4 - - - -
309D VAL* 3.8 24.0 - - + +
312D GLY* 3.8 22.4 - - - +
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D GLU* 2.9 32.9 + - - +
301D VAL* 3.2 12.9 + - + +
303D LEU* 1.3 76.5 - - + +
305D ARG* 1.3 62.4 + - + +
306D GLY 3.3 1.4 + - - -
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Residues in contact with ARG 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D VAL* 2.9 26.6 + - + +
302D PHE 3.8 4.9 - - - +
303D LEU 3.0 0.8 - - - -
304D GLU* 1.3 82.5 - - + +
306D GLY* 1.3 60.2 + - - +
307D TYR* 3.5 13.2 - - + -
326D LYS* 4.7 2.9 + - - -
384D GLY* 3.5 23.0 + - - -
387D CYS* 3.4 24.0 - - + +
388D ASP* 2.7 36.1 + - - +
391D ASP* 2.9 31.1 + - - +
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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