Contacts of the helix formed by residues 296 - 318 (chain D) in PDB entry 1CX2
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 PRO 296 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D GLY 5.0 0.4 - - - +
295D VAL* 1.3 87.1 - - + +
297D GLY* 1.3 56.2 + - - +
299D MET* 3.7 11.0 - - + +
300D MET* 2.9 28.6 + - - +
407D PHE* 2.7 57.4 - - + +
409D TYR 4.2 2.5 - - - +
410D ASN* 3.6 30.1 - - + +
413D ILE* 4.7 4.5 - - + -
414D LEU* 4.3 8.2 - - + +
422D PHE* 4.0 13.8 - - + -
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Residues in contact with GLY 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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200D PHE* 3.8 38.1 - - - +
295D VAL* 2.9 5.9 + - - +
296D PRO* 1.3 74.9 - - - +
298D LEU* 1.3 69.0 - - - +
300D MET* 3.0 18.1 + - - +
301D TYR* 3.1 13.2 + - - +
407D PHE* 4.1 3.6 - - - -
422D PHE* 4.7 0.4 - - - -
426D PHE* 4.5 5.4 - - - -
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Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D PHE* 4.1 3.3 - - - +
203D GLN* 2.9 46.9 - - + +
204D HIS* 3.7 31.6 + - + +
207D HIS* 5.5 2.2 - - + -
291D VAL* 5.3 4.7 - - + +
292D PHE* 3.4 44.2 - - + +
294D LEU* 5.4 0.7 - - + -
295D VAL* 2.9 28.1 + - + +
297D GLY* 1.3 71.1 - - - +
299D MET* 1.3 54.2 + - - +
301D TYR* 2.7 32.5 + - - +
302D ALA* 3.1 11.4 + - - +
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Residues in contact with MET 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D MET* 4.5 0.2 - - + -
275D TYR* 3.3 26.0 - - + +
283D LEU* 5.5 3.1 - - + -
285D PHE* 3.5 34.3 - - + +
287D VAL* 3.3 36.6 - - + -
292D PHE* 3.4 9.7 + - - +
293D GLY* 3.4 24.7 - - - +
295D VAL 3.2 6.8 + - - +
296D PRO* 3.9 11.7 - - + +
298D LEU* 1.3 77.6 - - - +
300D MET* 1.3 57.6 + - - +
302D ALA* 3.9 4.0 - - - -
303D THR* 2.9 32.1 + - - +
414D LEU* 3.8 11.8 - - + +
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Residues in contact with MET 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D MET* 3.6 22.7 - - + +
200D PHE* 6.0 0.9 - - - -
296D PRO 2.9 15.5 + - - +
297D GLY 3.2 12.3 - - - +
298D LEU 2.8 0.4 + - - -
299D MET* 1.3 77.3 - - - +
301D TYR* 1.3 67.9 + - + +
303D THR* 3.3 7.6 + - - -
304D ILE* 3.1 40.6 + - + +
414D LEU* 3.9 13.7 - - + -
419D LEU* 3.8 15.8 - - + +
422D PHE* 3.8 28.7 - - + -
423D VAL* 3.5 37.0 - - + +
426D PHE* 4.2 13.5 - - - -
568D ILE* 5.3 0.2 - - + -
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Residues in contact with TYR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D MET* 2.9 39.8 + - - +
200D PHE* 3.7 19.7 - - + -
201D PHE* 3.0 59.6 - + - -
204D HIS* 3.8 21.8 - + + -
297D GLY 3.1 6.5 + - - +
298D LEU 2.7 14.2 + - - +
300D MET* 1.3 78.5 - - + +
302D ALA* 1.3 64.0 + - - +
303D THR 3.2 0.4 - - - -
304D ILE* 3.0 30.6 + - + +
305D TRP* 3.0 31.3 + - - -
564D ILE* 4.1 12.3 - - + +
567D LEU* 5.1 1.3 - - + -
568D ILE* 4.6 6.3 - - + -
580D PHE* 3.7 2.9 - - - -
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D HIS* 4.0 14.7 - - + -
232D HIS 5.9 0.7 - - - +
233D ILE* 5.7 4.2 - - + +
287D VAL* 3.3 41.7 - - + +
292D PHE* 4.7 6.1 - - + -
298D LEU 3.1 9.6 + - - +
299D MET* 4.1 6.3 - - - +
300D MET 3.4 0.2 - - - -
301D TYR* 1.3 76.6 - - - +
303D THR* 1.3 59.7 + - - +
304D ILE 3.0 0.2 + - - -
305D TRP* 3.3 3.2 + - - +
306D LEU* 2.8 32.9 + - - +
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Residues in contact with THR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D VAL 3.3 26.7 - - - +
262D TYR* 4.0 16.7 - - + -
263D PRO* 3.2 25.4 - - + +
299D MET* 2.9 23.6 + - - +
300D MET* 3.5 7.2 - - - -
301D TYR 3.2 0.4 - - - -
302D ALA* 1.3 80.2 - - - +
304D ILE* 1.3 59.6 + - - +
306D LEU* 4.0 6.2 - - + +
307D ARG* 2.8 48.8 + - + +
414D LEU* 4.5 1.8 - - - +
419D LEU* 4.5 6.1 - - + -
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Residues in contact with ILE 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D MET* 3.1 19.0 + - + +
301D TYR* 3.0 29.5 + - + +
302D ALA 3.0 0.6 - - - -
303D THR* 1.3 77.1 - - - +
305D TRP* 1.3 66.4 + - + +
307D ARG* 2.9 20.5 + - - +
308D GLU 2.9 9.4 + - - -
419D LEU* 3.2 30.1 - - + -
567D LEU* 3.8 44.0 - - + +
568D ILE* 4.4 10.8 - - + -
571D ASN* 3.9 8.1 - - + +
572D VAL* 4.0 20.0 - - + -
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Residues in contact with TRP 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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201D PHE* 4.2 19.2 - + - -
204D HIS* 3.0 40.3 + + - -
230D LEU* 5.1 0.7 - - + -
232D HIS* 5.4 2.7 - + - -
233D ILE* 3.3 34.5 - - + -
301D TYR* 3.0 27.8 + - - +
302D ALA 3.9 2.0 - - - +
304D ILE* 1.3 78.6 - - + +
306D LEU* 1.3 59.9 + - - +
308D GLU* 2.5 27.4 + - + +
309D HIS* 2.8 13.4 + - - +
336D LEU* 4.3 27.2 - - + +
339D GLU* 4.8 4.9 - - + -
340D THR* 3.4 31.0 - - + -
343D ILE* 4.3 11.7 - - + -
567D LEU* 3.6 43.7 - - + -
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ILE* 5.1 3.0 - - + +
252D LEU* 3.6 35.7 - - + -
253D LYS 3.0 24.7 - - - +
254D TYR* 3.8 3.6 - - + -
261D VAL* 3.6 26.9 - - + -
262D TYR 3.9 0.2 - - - -
263D PRO* 3.7 36.8 - - + -
264D PRO* 5.0 2.9 - - + -
287D VAL* 6.2 3.6 - - + -
302D ALA 2.8 21.2 + - - +
303D THR* 4.0 4.9 - - - +
305D TRP* 1.3 72.0 - - - +
307D ARG* 1.3 64.2 + - - +
309D HIS* 3.3 14.9 + - - +
310D GLN* 3.5 16.6 + - - +
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Residues in contact with ARG 307 (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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260D GLU* 3.2 37.6 + - - +
261D VAL* 3.3 49.0 + - + +
262D TYR* 4.8 1.0 - - - -
303D THR* 2.8 33.7 - - - +
304D ILE* 2.9 8.3 + - - +
306D LEU* 1.3 79.3 - - + +
308D GLU* 1.3 60.8 + - - +
309D HIS 3.2 0.2 + - - -
310D GLN* 3.4 6.6 + - - +
311D ARG* 3.0 20.1 + - - +
419D LEU* 3.7 24.7 - - - +
571D ASN* 3.1 40.8 + - + +
573D LYS 5.2 3.8 - - - +
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Residues in contact with GLU 308 (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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304D ILE 2.9 5.3 + - - -
305D TRP* 2.5 28.3 + - + +
307D ARG* 1.3 71.0 - - - +
309D HIS* 1.3 66.2 + - - +
311D ARG* 2.6 46.3 + - - -
312D VAL* 2.9 17.3 + - - +
336D LEU* 3.9 8.7 - - + -
339D GLU* 2.9 35.2 - - - +
567D LEU* 3.9 20.9 - - + +
570D ASN* 4.8 5.6 + - - +
571D ASN* 2.9 27.1 + - - +
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Residues in contact with HIS 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 2.5 39.8 + + - -
250D GLY 2.8 23.4 + - - -
252D LEU* 3.8 21.5 - - + -
305D TRP 2.8 8.9 + - - +
306D LEU 3.4 7.6 - - - +
308D GLU* 1.3 72.7 - - - +
310D GLN* 1.3 87.8 + - - +
312D VAL* 2.7 16.5 + - - +
313D CYS* 2.8 30.0 + - - -
329D PHE* 3.8 16.6 - + - -
332D SER* 3.2 23.6 - - - -
336D LEU* 4.0 15.2 - - + +
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Residues in contact with GLN 310 (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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251D LYS* 3.4 33.7 - - + +
252D LEU* 2.6 54.0 + - - +
254D TYR* 3.4 24.8 - - + -
306D LEU* 3.5 14.2 + - - +
307D ARG* 3.4 8.6 + - - +
309D HIS* 1.3 81.5 - - - +
311D ARG* 1.3 65.7 + - - +
313D CYS* 2.8 19.7 + - - +
314D ASP* 2.9 19.2 + - - +
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Residues in contact with ARG 311 (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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307D ARG 3.0 13.3 + - - +
308D GLU* 2.6 56.3 + - - +
309D HIS 3.0 0.2 + - - -
310D GLN* 1.3 75.6 - - - +
312D VAL* 1.3 77.3 + - - +
314D ASP* 3.5 10.4 + - - +
315D ILE* 3.0 45.0 + - + +
339D GLU* 4.7 0.6 + - - -
558D ILE* 4.3 18.6 - - - +
570D ASN* 3.8 44.8 + - - +
571D ASN* 4.6 2.9 - - - +
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Residues in contact with VAL 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D GLU 2.9 17.1 + - - +
309D HIS 2.7 11.8 + - - +
311D ARG* 1.3 86.1 - - - +
313D CYS* 1.3 54.0 + - - +
314D ASP 2.7 1.0 + - - -
315D ILE* 2.6 35.0 + - - +
316D LEU* 2.8 36.1 + - + -
332D SER* 3.9 7.6 - - - +
335D ILE* 3.9 28.0 - - + -
336D LEU* 3.6 21.8 - - + -
339D GLU* 4.3 7.0 - - - +
558D ILE* 4.5 9.2 - - + -
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Residues in contact with CYS 313 (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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249D ASP 3.3 14.7 - - - +
250D GLY* 3.0 37.2 - - - -
251D LYS* 3.6 6.7 - - + +
309D HIS* 2.8 36.3 + - - -
310D GLN* 2.8 14.2 + - - +
312D VAL* 1.3 71.1 - - - +
314D ASP* 1.3 51.2 + - - +
316D LEU* 3.6 6.5 - - - +
317D LYS* 2.6 34.5 + - - +
328D LEU* 3.8 6.4 - - - +
332D SER* 3.3 15.9 + - - -
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Residues in contact with ASP 314 (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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249D ASP* 4.8 5.2 - - - +
251D LYS* 3.0 30.0 + - - -
310D GLN* 2.9 23.0 + - - +
311D ARG* 3.8 9.8 - - - +
312D VAL 2.7 4.6 + - - -
313D CYS* 1.3 72.8 - - - +
315D ILE* 1.3 61.2 + - + +
317D LYS* 3.1 16.6 + - - +
318D GLN* 3.0 29.3 + - - +
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Residues in contact with ILE 315 (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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311D ARG* 3.0 51.8 - - + +
312D VAL* 2.6 19.0 + - - +
314D ASP* 1.3 70.0 - - + +
316D LEU* 1.3 72.7 + - + +
318D GLN* 3.1 11.5 + - - -
319D GLU* 3.2 16.8 + - + +
554D VAL* 4.2 24.9 - - + -
558D ILE* 4.0 15.7 - - + -
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Residues in contact with LEU 316 (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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312D VAL* 2.8 20.5 + - + +
313D CYS* 3.7 4.9 - - - +
315D ILE* 1.3 81.3 - - + +
317D LYS* 1.3 55.4 + - - +
319D GLU* 2.8 11.1 + - + +
320D HIS* 2.8 38.8 + - - +
323D TRP* 3.9 15.7 - - + -
328D LEU* 3.3 19.5 - - + +
331D THR* 3.8 28.3 - - + -
332D SER* 3.7 26.0 - - - +
335D ILE* 4.0 19.3 - - + -
550D PHE 4.2 7.4 - - - +
551D GLY* 5.0 3.1 - - - -
554D VAL* 5.8 0.9 - - + -
555D GLY* 4.7 8.1 - - - +
558D ILE* 5.7 0.2 - - + -
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ASP* 3.9 25.8 - - + +
313D CYS 2.6 23.8 + - - +
314D ASP* 3.1 19.8 + - - +
316D LEU* 1.3 73.6 - - - +
318D GLN* 1.3 80.2 + - - +
319D GLU 3.4 0.7 - - - -
320D HIS 4.1 5.8 - - - +
321D PRO* 3.6 14.2 - - + +
328D LEU* 3.8 24.5 - - + -
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Residues in contact with GLN 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D ASP 3.0 13.6 + - - +
315D ILE* 3.1 6.3 + - - +
316D LEU 3.0 0.4 - - - -
317D LYS* 1.3 104.0 + - - +
319D GLU* 1.3 66.2 + - - +
320D HIS 3.5 0.2 - - - -
321D PRO* 3.8 23.4 - - - +
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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