Contacts of the helix formed by residues 407 - 437 (chain F) in PDB entry 2FRV
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 THR 407 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TRP* 4.7 9.6 - - + -
271F TRP* 4.1 20.2 - - + -
274F ILE 2.6 22.6 + - - -
275F GLY* 3.5 9.2 - - - -
406F SER* 1.3 69.4 - - - +
408F LEU* 1.3 65.1 + - - +
410F ARG* 3.2 21.1 + - - +
411F THR* 2.8 30.0 + - - +
522F ARG 3.6 28.9 - - - +
523F THR* 3.5 10.5 + - - -
526F SER* 3.7 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TRP* 5.1 9.6 - - + -
265F ALA* 4.0 40.2 - - + +
268F TYR* 3.7 27.4 - - + +
269F LYS* 4.1 7.2 - - + -
271F TRP* 3.1 27.0 + - + +
272F ALA* 3.6 21.3 - - + +
397F LEU* 4.9 12.1 - - + -
399F VAL* 6.5 0.7 - - + -
403F ALA 5.1 0.2 - - - +
407F THR* 1.3 80.1 - - - +
409F GLY* 1.3 55.6 + - - +
411F THR* 3.0 15.6 + - + -
412F ALA* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F LEU* 3.7 3.5 - - - +
403F ALA 3.8 7.9 + - - -
404F LEU* 3.5 34.0 - - - +
406F SER* 2.9 12.1 + - - -
408F LEU* 1.3 74.6 - - - +
410F ARG* 1.3 59.8 + - - +
412F ALA* 4.2 3.8 - - - +
413F ALA* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 410 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F GLY 2.7 23.2 + - - -
277F THR* 3.2 22.4 + - - -
368F GLU* 3.1 21.6 + - - +
371F PRO* 4.9 0.8 - - + +
372F LEU* 4.2 20.8 + - + +
404F LEU 4.2 0.4 + - - -
406F SER* 3.0 16.9 + - - +
407F THR* 3.2 34.9 + - - +
408F LEU 3.2 0.2 - - - -
409F GLY* 1.3 77.7 - - - +
411F THR* 1.3 58.9 + - - +
413F ALA* 4.1 2.8 - - - +
414F ARG* 3.7 27.1 + - - +
505F ALA* 4.4 2.0 - - - +
523F THR 4.7 0.6 + - - -
526F SER* 3.3 38.3 + - - +
527F TYR* 3.3 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112F PHE* 5.0 8.7 - - + -
116F HIS* 3.5 35.4 - - + +
120F TRP* 5.1 4.8 - - + +
257F TYR* 4.8 1.4 + - - -
261F LEU* 3.6 24.3 - - + +
265F ALA* 6.4 0.7 - - + -
407F THR* 2.8 19.2 + - - +
408F LEU* 3.0 17.1 + - + +
410F ARG* 1.3 76.3 - - - +
412F ALA* 1.3 64.8 + - - +
414F ARG* 3.6 18.1 + - - +
415F GLY 3.7 3.8 + - - -
526F SER* 3.7 5.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 412 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F LEU* 4.2 16.9 - - + +
262F LEU* 5.4 2.9 - - + -
265F ALA* 6.1 3.6 - - + -
393F VAL* 4.1 27.4 - - + +
397F LEU* 5.2 7.4 - - + -
404F LEU* 5.4 4.5 - - + -
408F LEU* 2.9 16.3 + - + +
409F GLY* 4.2 5.6 - - - +
411F THR* 1.3 75.3 - - - +
413F ALA* 1.3 53.9 + - - +
415F GLY* 2.7 24.6 + - - -
416F ILE* 3.0 16.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F PRO* 3.6 5.5 - - - +
372F LEU* 3.6 37.9 - - + +
375F VAL* 3.7 11.6 - - + +
404F LEU* 5.5 2.4 - - + +
409F GLY 2.9 19.5 + - - +
410F ARG 4.1 2.2 - - - +
412F ALA* 1.3 76.1 - - - +
414F ARG* 1.3 56.5 + - - +
416F ILE* 3.7 13.8 - - + +
417F GLN* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108F HIS* 3.5 25.6 + - + -
111F HIS* 3.5 32.8 - - - -
112F PHE* 5.5 0.7 - - - +
116F HIS* 5.2 0.4 + - - -
257F TYR* 3.8 12.7 + - - +
371F PRO* 3.6 38.4 - - + +
410F ARG* 3.7 18.3 + - - +
411F THR* 3.6 15.6 + - - +
412F ALA 3.2 0.8 - - - -
413F ALA* 1.3 78.0 - - - +
415F GLY* 1.3 58.1 + - - +
417F GLN* 4.5 0.4 - - - -
418F CYS* 3.0 29.8 + - - +
462F PRO 5.5 0.4 + - - -
463F ARG* 5.7 0.8 - - - +
526F SER* 2.6 35.9 + - - +
527F TYR* 3.8 5.3 + - - +
528F ASP* 3.4 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F TYR* 3.7 10.4 + - - -
258F ILE* 3.2 24.2 - - - +
261F LEU* 3.6 22.7 - - - -
411F THR 3.7 2.4 + - - -
412F ALA 2.7 10.5 + - - -
414F ARG* 1.3 80.5 - - - +
416F ILE* 1.3 60.6 + - - +
418F CYS* 3.5 2.9 + - - +
419F LEU* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 416 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258F ILE* 5.4 0.2 - - - -
375F VAL* 4.0 21.8 - - + -
386F THR* 4.7 9.4 - - + +
389F ALA* 3.8 26.7 - - + +
390F VAL* 3.9 28.5 - - + -
393F VAL* 4.1 28.5 - - + -
404F LEU* 5.3 6.5 - - + -
412F ALA* 3.0 19.4 + - + +
413F ALA* 3.7 14.8 - - - +
415F GLY* 1.3 75.4 - - - +
417F GLN* 1.3 65.7 + - - +
419F LEU* 3.0 16.5 + - + +
420F THR* 3.2 21.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F TYR* 3.7 24.9 + - + -
108F HIS* 2.8 30.1 + - + -
370F GLY 4.5 0.2 - - - -
371F PRO* 3.5 26.6 - - + +
374F SER* 3.7 17.9 + - - -
375F VAL* 4.1 10.5 - - + +
413F ALA 2.8 20.7 + - - +
416F ILE* 1.3 73.3 - - - +
418F CYS* 1.3 62.5 + - - +
419F LEU 3.4 0.2 + - - -
420F THR* 3.9 8.0 + - - -
421F ALA* 3.4 22.2 + - - +
460F ASN* 4.2 5.2 - - - +
461F ALA 4.5 1.2 + - - -
462F PRO* 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 418 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F TYR* 4.1 4.9 - - - -
105F MET* 4.0 13.8 - - - +
108F HIS* 3.1 39.7 - - + +
109F LEU 4.8 0.2 - - - -
253F ILE* 4.0 28.0 - - - +
257F TYR* 4.0 15.0 - - + -
414F ARG 3.0 15.7 + - - +
415F GLY 3.7 5.4 - - - +
416F ILE 3.1 0.2 - - - -
417F GLN* 1.3 79.3 - - - +
419F LEU* 1.3 55.9 + - - +
421F ALA* 4.0 4.4 - - - +
422F ALA* 3.4 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F ILE* 4.5 12.6 - - + -
254F GLU* 3.5 41.3 - - + +
258F ILE* 4.6 17.7 - - + -
389F ALA* 4.7 19.5 - - + -
392F LEU* 5.6 8.3 - - + -
415F GLY 3.3 14.3 + - - +
416F ILE* 3.0 5.9 + - + +
418F CYS* 1.3 76.6 - - - +
420F THR* 1.3 57.1 + - + +
421F ALA 3.3 1.3 - - - -
422F ALA* 3.3 8.7 + - + +
423F GLN* 2.8 57.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F TYR* 3.2 26.9 + - - -
298F THR* 4.7 10.7 - - - +
383F HIS* 4.9 0.4 - - - -
385F PRO* 3.9 34.1 - - + +
386F THR* 4.0 14.6 + - - +
389F ALA* 4.5 4.7 - - + -
416F ILE* 3.5 22.7 + - + +
417F GLN* 3.9 8.7 + - - -
419F LEU* 1.3 75.7 - - + +
421F ALA* 1.3 66.5 + - - +
423F GLN* 3.2 11.8 + - - +
424F GLU* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F GLY* 4.7 5.8 - - - +
104F TYR* 3.7 33.0 - - + -
105F MET* 5.3 0.2 - - - -
286F PHE* 4.6 15.9 - - + -
297F TYR* 4.8 4.2 - - - -
417F GLN 3.4 16.9 + - - +
418F CYS 4.0 2.2 - - - +
420F THR* 1.3 79.7 + - - +
422F ALA* 1.3 63.3 + - - +
424F GLU* 3.0 16.3 + - - +
425F VAL* 3.2 18.8 + - - +
428F TRP* 4.6 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F MET* 4.1 26.6 - - + +
246F TYR* 2.6 32.4 + - - -
250F ARG* 4.0 23.0 - - + +
253F ILE* 4.7 5.4 - - + -
418F CYS 3.4 15.2 + - - +
419F LEU* 3.3 15.4 + - + +
420F THR 3.3 0.4 - - - -
421F ALA* 1.3 79.3 - - - +
423F GLN* 1.3 57.4 + - - +
424F GLU 3.5 0.2 + - - -
425F VAL* 3.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 423 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F TYR* 4.0 0.2 + - - -
250F ARG* 3.5 31.8 + - - +
254F GLU* 4.6 1.7 - - - +
297F TYR* 4.7 2.6 + - - +
385F PRO* 3.9 28.5 + - - +
388F LYS* 5.6 3.4 - - - +
389F ALA* 6.0 0.3 - - - +
419F LEU* 2.8 53.5 + - + +
420F THR* 3.6 12.2 + - - +
421F ALA 3.1 0.6 - - - -
422F ALA* 1.3 76.6 - - - +
424F GLU* 1.3 64.2 - - - +
425F VAL 3.4 0.3 + - - -
426F GLU* 3.7 17.0 + - - +
427F VAL* 4.5 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F TYR* 3.5 38.9 + - + -
420F THR 3.0 11.4 + - - +
421F ALA 3.0 8.5 + - - +
423F GLN* 1.3 76.1 - - - +
425F VAL* 1.3 63.6 + - - +
426F GLU 3.1 3.1 - - - -
427F VAL* 3.1 51.2 + - - +
428F TRP* 3.2 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 425 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F LEU* 3.6 21.3 - - + +
101F GLY* 3.8 32.1 - - - -
102F ALA 4.4 1.8 - - - +
105F MET* 4.5 5.6 - - - -
242F PHE* 3.9 15.7 - - + -
246F TYR* 3.7 35.4 - - + -
421F ALA 3.2 14.9 + - - +
422F ALA 4.0 1.1 - - - +
423F GLN 3.3 1.4 - - - -
424F GLU* 1.3 76.6 - - - +
426F GLU* 1.3 61.4 + - - +
428F TRP* 3.5 13.9 + - + -
429F LEU* 3.1 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F ARG* 3.4 24.0 + - - -
246F TYR* 2.9 40.9 + - - +
247F LYS* 3.9 22.2 + - - -
250F ARG* 4.0 11.0 + - - +
423F GLN 3.7 9.4 - - - +
424F GLU 3.1 0.4 - - - -
425F VAL* 1.3 78.5 - - - +
427F VAL* 1.3 61.3 + - + +
429F LEU* 3.6 4.1 - - - +
430F ASP* 3.2 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 427 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F GLN 5.3 1.3 - - - +
424F GLU* 3.1 41.8 + - - +
426F GLU* 1.3 80.7 - - + +
428F TRP* 1.3 72.5 + - + +
429F LEU 3.4 0.2 + - - -
430F ASP* 3.5 6.3 + - - +
431F LYS* 3.2 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 428 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 4.0 28.2 - - + +
97F ASN* 3.3 44.6 - - + +
98F LEU* 3.8 19.8 - - + +
101F GLY* 4.4 1.6 - - - -
286F PHE* 3.1 52.8 + + + +
297F TYR* 4.6 4.3 - + + +
421F ALA* 4.6 2.5 - - - -
424F GLU* 3.2 38.9 + - + +
425F VAL* 3.7 33.7 - - + +
427F VAL* 1.3 82.5 - - + +
429F LEU* 1.3 61.3 + - - +
431F LYS* 3.7 2.6 - - + +
432F LEU* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F LEU* 4.0 21.1 - - + +
213F PHE* 4.3 7.9 - - + -
239F ILE* 4.1 19.2 - - + +
242F PHE* 3.9 28.9 - - + -
243F ARG* 3.4 53.4 - - + +
246F TYR* 4.9 6.7 - - + -
425F VAL 3.1 17.9 + - - +
426F GLU* 3.6 6.3 - - - +
427F VAL 3.2 0.2 - - - -
428F TRP* 1.3 79.1 - - - +
430F ASP* 1.3 55.2 + - - +
432F LEU* 3.2 3.5 + - + +
433F GLU* 2.7 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 430 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F ARG* 2.9 32.7 + - - -
426F GLU* 3.2 27.8 + - - +
427F VAL* 3.5 7.4 - - - +
429F LEU* 1.3 82.7 - - - +
431F LYS* 1.3 55.0 + - - +
433F GLU* 3.3 8.3 + - - +
434F ALA* 3.0 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 5.2 14.1 - - - +
94F LEU* 3.9 28.3 - - + -
288F THR* 6.1 5.6 - - - -
427F VAL* 3.2 25.1 + - + +
428F TRP* 3.7 7.0 - - + +
430F ASP* 1.3 70.2 - - - +
432F LEU* 1.4 71.4 + - - +
433F GLU 3.0 1.3 - - - -
434F ALA* 3.1 5.9 + - - +
435F ASN* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 432 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ASN* 3.6 45.8 - - + +
94F LEU* 3.8 15.0 - - + +
95F MET* 4.4 5.6 - - + +
98F LEU* 4.5 10.5 - - + -
213F PHE* 4.4 18.4 - - + -
234F LEU* 3.9 22.9 - - + -
239F ILE* 3.6 26.5 - - + -
428F TRP 2.8 23.0 + - - +
429F LEU* 3.6 7.2 - - + +
431F LYS* 1.4 76.3 - - - +
433F GLU* 1.3 56.4 - - - +
435F ASN* 3.3 4.3 + - - +
436F VAL* 3.0 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 433 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F PRO* 5.1 8.9 - - + +
239F ILE* 3.7 30.3 - - + +
243F ARG* 3.0 24.8 + - - -
429F LEU 2.7 16.6 + - - +
430F ASP* 3.3 7.9 - - - +
432F LEU* 1.3 80.5 - - - +
434F ALA* 1.3 55.8 + - - +
436F VAL* 3.4 4.9 + - + +
437F LYS* 3.0 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 434 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430F ASP 3.0 15.1 + - - +
431F LYS* 3.1 7.8 + - - +
433F GLU* 1.3 72.8 - - - +
435F ASN* 1.3 69.4 + - - +
437F LYS* 3.3 9.7 + - - +
438F ALA* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 2.9 30.0 + - - +
91F ASN* 2.8 26.9 + - - +
94F LEU* 3.9 8.7 - - - +
431F LYS* 2.9 19.7 + - - +
432F LEU 3.4 8.5 - - - +
434F ALA* 1.3 79.3 - - - +
436F VAL* 1.3 62.8 + - - +
438F ALA* 3.4 7.4 + - - -
440F LYS* 2.8 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ASN* 4.1 5.4 - - - +
234F LEU* 3.3 55.6 - - + +
236F PRO* 5.6 5.8 - - + -
239F ILE* 5.3 2.5 - - + -
432F LEU* 3.0 18.9 + - + +
433F GLU* 3.4 6.7 + - + +
434F ALA 3.2 0.2 - - - -
435F ASN* 1.3 80.5 - - - +
437F LYS* 1.3 59.2 + - + +
439F GLY* 3.0 19.8 + - - -
440F LYS 3.9 13.0 - - - +
441F ASP* 4.9 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F PRO* 4.8 17.6 - - - +
433F GLU* 3.0 53.5 + - - +
434F ALA* 3.7 8.3 - - - +
435F ASN 3.2 0.2 - - - -
436F VAL* 1.3 73.8 - - + +
438F ALA* 1.3 55.8 + - - +
439F GLY* 3.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
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