Contacts of the helix formed by residues 395 - 417 (chain B) in PDB entry 4RQO
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 6.0 0.2 - - - +
378A GLU* 3.4 19.1 - - - +
423A ILE* 4.0 20.9 - - + -
386B ASP 4.8 2.5 - - - +
387B PRO* 3.8 20.9 - - + -
393B GLN 3.8 0.2 - - - -
394B ILE* 1.3 85.5 - - + +
396B CYS* 1.3 65.8 + - - +
397B ILE 3.2 3.2 + - - -
398B GLU* 3.3 19.2 + - + +
399B ARG* 2.9 56.8 + - - +
501B SF4 4.8 2.0 - - - -
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Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 4.6 2.2 - - - +
292B GLY 4.7 2.7 - - - +
387B PRO* 3.9 13.5 - - - -
392B VAL* 3.8 17.0 - - + +
393B GLN 3.3 27.0 + - - +
395B PRO* 1.3 79.7 - - - +
397B ILE* 1.3 64.1 + - - +
399B ARG* 3.2 5.8 + - - +
400B ASN* 3.0 27.9 + - - -
501B SF4 2.0 55.6 - - - -
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A HIS* 3.9 17.7 - - + -
232B LEU* 3.9 28.0 - - + -
238B LEU* 4.1 9.0 - - + -
273B MSE 4.0 35.0 - - + +
276B ASN* 3.9 30.7 - - + +
277B GLU* 4.3 14.6 - - + +
392B VAL 4.5 2.5 - - - +
393B GLN* 2.8 36.5 + - + +
396B CYS* 1.3 72.7 - - - +
398B GLU* 1.3 63.7 + - - +
400B ASN* 3.2 10.6 + - - +
401B ALA* 3.5 10.7 + - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 4.3 2.1 - - - +
375A ILE* 3.7 23.0 - - + +
378A GLU* 2.4 31.0 - - - +
379A HIS* 3.0 21.0 + - - -
413A MSE 3.9 29.4 - - + -
421A HIS* 4.2 27.5 + - + +
273B MSE 6.1 0.2 - - - -
395B PRO* 3.4 21.1 - - + +
397B ILE* 1.3 78.4 - - - +
399B ARG* 1.3 62.0 + - - +
400B ASN 3.4 0.3 + - - -
401B ALA* 3.4 2.1 + - - +
402B MSE 2.9 36.7 + - - +
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 2.7 32.3 + - - +
379A HIS* 4.0 15.5 - - + +
381A LEU* 6.3 0.2 - - - +
423A ILE* 5.5 2.0 - - - +
343B CYS* 3.4 17.9 - - - +
347B VAL* 3.7 21.8 - - + +
383B MSE 3.4 34.9 - - - +
384B THR* 2.9 30.3 + - - +
386B ASP 5.5 0.2 - - - +
395B PRO* 2.9 39.0 + - + +
396B CYS* 3.6 6.1 - - - +
397B ILE 3.2 0.2 - - - -
398B GLU* 1.3 89.4 + - - +
400B ASN* 1.3 51.5 + - - +
402B MSE 3.6 0.9 - - - +
403B GLY* 2.6 30.3 + - - -
501B SF4 3.9 9.9 - - - -
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Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B ALA* 3.7 7.6 - - + +
276B ASN* 2.8 25.6 + - - +
292B GLY 2.8 23.2 + - - -
293B ALA* 3.0 31.5 - - - +
295B GLY* 3.1 12.1 + - - -
296B ILE* 3.3 21.2 - - + +
347B VAL* 4.1 5.5 - - - +
396B CYS 3.0 22.0 + - - -
397B ILE 3.2 4.2 + - - +
399B ARG* 1.3 72.9 - - - +
401B ALA* 1.3 61.0 + - - +
404B ALA* 2.8 29.6 + - - +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASN* 4.3 0.2 - - - -
413A MSE 3.9 20.9 - - + -
269B ASN* 3.4 29.1 - - - +
272B ALA* 3.6 12.4 - - - +
273B MSE 4.4 9.2 - - + -
397B ILE 3.5 7.7 + - - +
398B GLU 3.4 8.0 + - - +
400B ASN* 1.3 75.7 - - - +
402B MSE 1.3 64.9 + - - +
404B ALA* 3.0 14.8 + - - +
405B VAL* 3.1 16.3 + - - +
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Residues in contact with MSE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 4.2 14.1 - - + +
376A ALA* 6.4 0.2 - - - -
379A HIS* 3.4 33.4 - - + +
406A LYS* 3.8 40.8 - - + +
409A ASN* 3.6 30.7 - - + +
410A ALA* 4.0 12.6 - - - -
413A MSE 4.3 7.4 - - + -
398B GLU* 2.9 38.5 + - - +
399B ARG 3.8 0.7 - - - +
401B ALA* 1.3 75.3 - - - +
403B GLY* 1.3 57.2 + - - +
405B VAL* 3.5 5.3 + - + +
406B LYS* 3.0 35.8 + - + +
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Residues in contact with GLY 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ILE* 3.8 14.8 - - - +
351B SER* 2.8 28.5 + - - -
380B HIS* 4.3 11.7 - - - -
399B ARG 2.6 23.2 + - - -
400B ASN 3.5 2.0 - - - -
401B ALA 3.1 0.6 - - - -
402B MSE 1.3 73.2 - - - +
404B ALA* 1.3 62.8 + - - +
406B LYS* 4.5 1.8 - - - +
407B ALA* 3.1 11.4 + - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LEU* 4.1 18.8 - - + -
272B ALA* 4.6 3.4 - - + -
296B ILE* 3.9 12.5 - - + +
299B ALA* 4.0 26.0 - - + -
300B VAL* 3.9 6.8 - - + +
400B ASN 2.8 16.0 + - - +
401B ALA 3.0 8.5 + - - +
403B GLY* 1.3 72.9 - - - +
405B VAL* 1.3 62.6 + - - +
407B ALA* 3.1 5.5 + - - +
408B VAL* 3.1 25.8 + - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A MSE 4.3 6.3 - - + +
405A VAL* 3.4 30.5 - - + -
406A LYS* 6.5 0.2 - - + -
409A ASN* 3.5 28.9 - - + +
265B MSE 3.7 26.0 - - + +
268B LEU* 4.0 26.0 - - + -
269B ASN* 4.1 3.4 - - - +
401B ALA 3.1 7.3 + - - +
402B MSE 3.7 10.3 - - + +
404B ALA* 1.3 73.6 - - - +
406B LYS* 1.3 65.2 + - + +
407B ALA 3.3 0.2 + - - -
408B VAL* 3.4 2.8 + - - +
409B ASN* 3.0 22.0 + - - +
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Residues in contact with LYS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A HIS* 3.0 36.3 + - - -
402A MSE 3.9 25.0 - - + +
406A LYS* 4.1 18.6 - - + +
351B SER* 3.9 5.4 - - - +
376B ALA* 4.8 4.6 - - - +
379B HIS* 2.7 39.2 + - + -
380B HIS* 3.1 34.6 + - + -
383B MSE 4.3 1.0 - - - +
402B MSE 3.0 26.6 + - + +
403B GLY 3.9 4.0 - - - +
405B VAL* 1.3 77.3 - - + +
407B ALA* 1.3 59.3 + - - +
409B ASN* 3.8 0.3 - - - +
410B ALA* 2.8 31.0 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B VAL* 4.3 6.1 - - + -
351B SER* 3.4 28.7 - - - +
354B ALA* 4.1 13.0 - - + -
355B ALA* 3.7 17.0 - - - +
358B LEU* 5.3 0.4 - - - -
376B ALA* 4.7 0.7 - - - -
403B GLY 3.1 19.1 + - - +
404B ALA* 3.1 6.4 + - - +
406B LYS* 1.3 76.9 - - - +
408B VAL* 1.3 64.2 + - - +
410B ALA* 4.4 0.7 - - - -
411B THR* 3.1 25.9 + - - -
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Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A MSE 4.0 16.8 - - + -
264B ILE* 5.0 0.7 - - + -
268B LEU* 3.8 22.4 - - + -
300B VAL* 4.3 12.8 - - + -
303B TYR* 4.2 36.1 - - + +
358B LEU* 4.2 15.9 - - + -
404B ALA 3.1 14.2 + - - +
405B VAL 3.9 5.6 - - - +
406B LYS 3.3 0.2 - - - -
407B ALA* 1.3 74.9 - - - +
409B ASN* 1.3 58.2 + - - +
411B THR* 3.1 6.8 + - - -
412B ARG* 3.0 41.3 + - - +
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Residues in contact with ASN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A MSE 3.1 24.4 - - - +
269A ASN* 3.0 40.3 + - - +
402A MSE 3.5 38.0 - - + +
405A VAL* 3.6 17.6 - - + +
405B VAL 3.0 17.4 + - - +
408B VAL* 1.3 73.7 - - - +
410B ALA* 1.3 60.6 + - - +
412B ARG* 3.1 7.7 + - - +
413B MSE 2.8 37.0 + - - +
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A MSE 3.9 2.6 - - - -
355B ALA* 4.3 0.4 - - + -
372B ALA* 3.5 27.2 - - - +
375B ILE* 3.8 19.1 - - + +
376B ALA* 3.7 20.2 - - + +
406B LYS 2.8 22.7 + - - +
407B ALA 3.7 4.0 - - - +
409B ASN* 1.3 72.9 - - - +
411B THR* 1.3 57.9 + - - +
413B MSE 3.3 4.4 + - - +
414B ALA* 2.9 29.6 + - - +
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Residues in contact with THR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PHE* 5.7 0.9 - - + -
355B ALA* 3.1 21.3 + - - -
358B LEU* 3.6 26.3 - - + +
359B THR* 3.2 25.3 + - - +
362B LEU* 4.0 18.8 - - + -
372B ALA* 4.4 1.5 - - - +
407B ALA 3.1 14.5 + - - -
408B VAL 3.1 9.6 - - - -
410B ALA* 1.3 77.7 - - - +
412B ARG* 1.3 57.1 + - + +
414B ALA* 3.1 4.3 + - - +
415B LEU* 3.1 34.2 + - + +
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PHE* 3.4 33.1 + - - +
261A GLN* 3.9 8.6 + - - +
263A ASP* 2.8 41.2 + - - -
265A MSE 3.8 13.1 - - - +
266A ASN* 3.1 25.8 + - - +
269A ASN* 4.1 13.9 - - - +
264B ILE* 4.6 4.9 - - - +
303B TYR* 3.3 25.5 + - - -
408B VAL* 3.0 33.5 + - + +
409B ASN* 3.1 15.5 + - - +
411B THR* 1.3 73.6 - - - +
413B MSE 1.3 58.8 + - - +
415B LEU* 4.6 3.8 - - - +
416B ILE* 2.8 45.9 + - + +
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Residues in contact with MSE 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN* 3.3 42.8 - - + +
273A MSE 4.1 23.1 - - - +
398A GLU* 4.0 24.7 - - + -
401A ALA* 4.0 17.3 - - + -
402A MSE 4.4 13.2 - - + -
371B ASN* 4.9 0.3 - - - +
375B ILE* 3.7 20.2 - - + -
409B ASN* 2.8 24.3 + - - +
410B ALA* 3.5 7.9 - - - +
412B ARG* 1.3 74.9 - - - +
414B ALA* 1.3 58.4 + - - +
416B ILE* 4.3 7.4 - - + -
417B GLY* 2.9 29.0 + - - +
421B HIS* 5.2 9.1 + - + +
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Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B THR* 4.8 2.2 - - + +
368B GLN* 3.2 33.5 + - + +
371B ASN* 3.6 22.7 - - - +
372B ALA* 3.9 12.8 - - + -
375B ILE* 5.1 0.9 - - + -
410B ALA 2.9 16.9 + - - +
411B THR 3.1 5.8 + - - +
413B MSE 1.3 78.3 - - - +
415B LEU* 1.3 58.6 + - - +
419B GLY* 3.0 26.1 + - - +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 3.5 55.6 - - + -
359B THR* 4.4 11.2 - - + +
362B LEU* 4.0 27.6 - - + +
363B GLY 5.0 1.8 - - - -
364B GLY* 4.1 24.5 - - - +
368B GLN* 3.9 19.1 + - - +
411B THR* 3.1 24.8 + - + +
412B ARG 4.1 0.7 - - - +
414B ALA* 1.3 77.7 - - - +
416B ILE* 1.3 66.6 + - - +
418B ASP* 3.0 17.3 + - - +
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 3.4 38.8 + - + -
245A LEU* 4.2 33.2 - - + -
259A PHE* 3.8 22.4 - - + -
260A GLU* 5.5 0.7 - - + -
266A ASN* 3.7 26.0 - - - +
269A ASN* 4.5 0.2 - - - +
273A MSE 4.4 14.1 - - + -
412B ARG* 2.8 31.3 + - + +
413B MSE 4.3 12.8 - - + +
415B LEU* 1.3 73.6 - - - +
417B GLY* 1.3 59.9 + - - +
418B ASP* 3.0 5.9 + - - +
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 3.4 12.4 + - - -
273A MSE 5.7 1.6 - - - -
413B MSE 2.9 20.9 + - - +
416B ILE* 1.3 79.3 - - - +
418B ASP* 1.3 55.2 + - - +
419B GLY 3.0 6.1 - - - -
420B GLN* 2.8 33.4 + - - +
421B HIS* 4.0 19.7 - - - -
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il