Contacts of the helix formed by residues 407 - 437 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H TRP* 4.7 9.2 - - + -
271H TRP* 4.1 20.2 - - + -
274H ILE 2.6 23.2 + - - -
275H GLY* 3.5 9.5 - - - -
406H SER* 1.3 69.2 - - - +
408H LEU* 1.3 64.6 + - - +
410H ARG* 3.2 22.0 + - - +
411H THR* 2.8 30.8 + - - +
522H ARG 3.6 29.6 - - - +
523H THR* 3.5 9.7 + - - -
526H SER* 3.7 9.4 - - - +
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Residues in contact with LEU 408 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H TRP* 5.1 9.2 - - + -
265H ALA* 4.0 38.1 - - + +
268H TYR* 3.7 28.7 - - + +
269H LYS* 4.1 7.9 - - + -
271H TRP* 3.1 28.1 + - + +
272H ALA* 3.6 21.1 - - + +
397H LEU* 4.9 12.1 - - + -
399H VAL* 6.5 0.4 - - + -
403H ALA 5.1 0.2 - - - +
406H SER 3.1 0.2 - - - -
407H THR* 1.3 81.1 - - - +
409H GLY* 1.3 57.6 + - - +
411H THR* 3.0 14.6 + - + -
412H ALA* 2.9 27.8 + - + +
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Residues in contact with GLY 409 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372H LEU* 3.7 3.6 - - - +
403H ALA 3.8 7.8 + - - -
404H LEU* 3.5 33.8 - - - +
406H SER* 2.9 12.7 + - - -
408H LEU* 1.3 73.6 - - - +
410H ARG* 1.3 59.9 + - - +
412H ALA* 3.8 4.4 - - - +
413H ALA* 2.9 33.4 + - - +
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Residues in contact with ARG 410 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H GLY 2.7 25.0 + - - -
276H LYS* 4.6 0.4 - - - +
277H THR* 3.2 22.8 + - - -
368H GLU* 3.1 21.0 + - - +
371H PRO* 4.9 1.2 - - + +
372H LEU* 4.2 20.6 + - + +
404H LEU 4.2 0.6 + - - -
406H SER* 3.0 15.1 + - - +
407H THR* 3.2 34.3 + - - +
408H LEU 3.2 0.4 - - - -
409H GLY* 1.3 77.0 - - - +
411H THR* 1.3 58.9 + - - +
413H ALA* 4.0 2.8 + - - +
414H ARG* 3.7 26.1 + - - +
505H ALA* 4.4 2.0 - - - +
523H THR* 4.7 0.6 + - - +
526H SER* 3.3 38.7 + - - +
527H TYR* 3.3 37.5 + - - -
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Residues in contact with THR 411 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H PHE* 5.0 7.9 - - + -
116H HIS* 3.5 36.7 - - + +
120H TRP* 5.1 4.8 - - + +
257H TYR* 4.8 1.4 + - - -
261H LEU* 3.6 24.7 - - + +
265H ALA* 6.5 0.9 - - + -
407H THR* 2.8 18.7 + - - +
408H LEU* 3.0 17.6 + - + -
410H ARG* 1.3 77.1 - - - +
412H ALA* 1.3 64.2 + - - +
413H ALA 3.3 0.4 - - - -
414H ARG* 3.6 17.5 + - - +
415H GLY 3.7 3.8 + - - -
526H SER* 3.7 5.4 - - - -
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Residues in contact with ALA 412 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261H LEU* 4.2 17.1 - - + +
262H LEU* 5.4 1.8 - - + -
265H ALA* 6.1 4.0 - - + -
393H VAL* 4.1 27.9 - - + +
397H LEU* 5.2 7.9 - - + -
404H LEU* 5.4 4.3 - - + -
408H LEU* 2.9 15.3 + - + +
409H GLY* 3.4 5.8 + - - +
411H THR* 1.3 76.7 - - - +
413H ALA* 1.3 53.7 + - - +
415H GLY* 2.7 24.6 + - - -
416H ILE* 3.0 16.5 + - + +
----------------------------------------------------------
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Residues in contact with ALA 413 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H PRO* 3.6 5.6 - - - +
372H LEU* 3.6 37.7 - - + +
375H VAL* 3.7 11.3 - - + +
404H LEU* 5.5 2.6 - - + +
409H GLY 2.9 18.6 + - - +
410H ARG 4.1 2.5 - - - +
412H ALA* 1.3 76.3 - - - +
414H ARG* 1.3 56.5 + - - +
416H ILE* 3.7 13.8 - - + +
417H GLN* 2.8 31.4 + - - +
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Residues in contact with ARG 414 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H HIS* 3.5 25.5 + - + -
111H HIS* 3.5 33.0 - - - -
112H PHE* 5.5 0.7 - - - +
116H HIS* 5.2 0.6 + - - -
257H TYR* 3.8 14.2 + - - +
371H PRO* 3.6 37.1 - - + +
410H ARG* 3.7 18.4 + - - +
411H THR* 3.6 15.8 + - - +
412H ALA 3.1 1.0 + - - -
413H ALA* 1.3 77.9 - - - +
415H GLY* 1.3 58.6 + - - +
417H GLN* 4.4 0.7 - - - +
418H CYS* 3.0 29.6 + - - +
462H PRO 5.5 0.4 + - - -
463H ARG* 5.7 0.8 - - - +
526H SER* 2.6 35.7 + - - +
527H TYR* 3.8 5.1 + - - +
528H ASP* 3.4 32.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 415 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H TYR* 3.7 10.3 + - - -
258H ILE* 3.2 24.8 - - - +
261H LEU* 3.6 23.6 - - - -
411H THR 3.7 2.0 + - - -
412H ALA 2.7 10.3 + - - -
414H ARG* 1.3 81.3 - - - +
416H ILE* 1.3 60.5 + - - +
418H CYS* 3.5 3.1 + - - +
419H LEU* 3.3 15.9 + - - +
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Residues in contact with ILE 416 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ILE* 6.3 0.2 - - + -
375H VAL* 4.0 21.1 - - + -
386H THR* 4.7 9.4 - - + +
389H ALA* 3.8 25.4 - - + +
390H VAL* 3.9 28.3 - - + -
393H VAL* 4.1 28.5 - - + -
404H LEU* 5.3 6.5 - - + -
412H ALA* 3.0 17.6 + - + +
413H ALA* 3.7 15.7 - - + +
415H GLY* 1.3 75.7 - - - +
417H GLN* 1.3 65.2 + - - +
419H LEU* 3.0 17.0 + - + +
420H THR* 3.2 21.0 + - + +
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Residues in contact with GLN 417 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H TYR* 3.7 24.1 - - + -
108H HIS* 2.8 30.5 + - + -
370H GLY 4.5 0.3 - - - -
371H PRO* 3.5 25.5 - - + +
374H SER* 3.7 17.7 + - - -
375H VAL* 4.1 11.2 - - + +
413H ALA 2.8 20.1 + - - +
416H ILE* 1.3 73.7 - - - +
418H CYS* 1.3 61.3 + - - +
419H LEU 3.4 0.3 + - - -
420H THR* 3.9 8.0 + - - -
421H ALA* 3.4 23.4 + - - +
460H ASN* 4.2 5.4 - - - +
461H ALA 4.5 0.8 + - - -
462H PRO* 3.1 25.3 + - - +
----------------------------------------------------------
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Residues in contact with CYS 418 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H TYR* 4.1 4.9 - - - -
105H MET* 4.0 13.0 - - - +
108H HIS* 3.1 40.2 - - + +
109H LEU 4.8 0.2 - - - -
253H ILE* 4.0 27.8 - - - -
257H TYR* 4.0 15.9 - - + -
414H ARG 3.0 15.3 + - - +
415H GLY 3.7 5.2 - - - +
416H ILE 3.1 0.4 - - - -
417H GLN* 1.3 79.5 - - - +
419H LEU* 1.3 56.0 + - - +
421H ALA* 4.0 3.7 - - - +
422H ALA* 3.4 22.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 419 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253H ILE* 4.5 13.2 - - + -
254H GLU* 3.5 41.3 - - + +
258H ILE* 4.6 17.9 - - + -
389H ALA* 4.7 19.1 - - + -
392H LEU* 5.6 8.1 - - + -
415H GLY 3.3 13.7 + - - +
416H ILE* 3.0 6.1 + - + +
418H CYS* 1.3 77.0 - - - +
420H THR* 1.3 54.8 + - + +
421H ALA 3.3 1.3 - - - -
422H ALA* 3.3 8.8 + - + +
423H GLN* 2.8 57.5 + - + +
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Residues in contact with THR 420 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H TYR* 3.2 26.3 + - - -
298H THR* 4.7 10.6 - - - +
383H HIS* 4.9 1.1 - - - -
385H PRO* 3.9 33.4 - - + +
386H THR* 4.0 14.4 + - - +
389H ALA* 4.5 4.5 - - + -
416H ILE* 3.2 23.2 + - + +
417H GLN* 3.9 9.0 + - - -
419H LEU* 1.3 74.8 - - + +
421H ALA* 1.3 66.7 + - - +
423H GLN* 3.2 12.2 + - - +
424H GLU* 3.0 19.6 + - - +
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Residues in contact with ALA 421 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H GLY* 4.7 5.8 - - - +
104H TYR* 3.7 33.7 - - + -
286H PHE* 4.6 14.8 - - + -
297H TYR* 4.8 4.5 - - - -
417H GLN 3.4 17.1 + - - +
418H CYS 4.0 2.7 - - - +
420H THR* 1.3 81.0 + - - +
422H ALA* 1.3 61.1 + - - +
424H GLU* 3.0 17.1 + - - +
425H VAL* 3.2 18.4 + - - +
428H TRP* 4.6 1.4 - - - -
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Residues in contact with ALA 422 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H MET* 4.1 27.1 - - + +
246H TYR* 2.6 32.4 + - - -
250H ARG* 4.0 22.6 - - + +
253H ILE* 4.7 5.6 - - + -
418H CYS 3.4 15.6 + - - +
419H LEU* 3.4 14.8 - - + +
420H THR 3.3 0.2 - - - -
421H ALA* 1.3 79.3 - - - +
423H GLN* 1.3 56.7 + - - +
424H GLU 3.5 0.2 + - - -
425H VAL* 3.6 2.8 + - - -
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Residues in contact with GLN 423 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H TYR* 4.0 0.5 + - - -
250H ARG* 3.5 32.4 + - - +
254H GLU* 4.6 1.6 - - - +
297H TYR* 4.7 2.2 + - - +
385H PRO* 3.9 28.3 + - - +
388H LYS* 5.6 3.2 - - - +
389H ALA* 6.0 0.2 - - - +
419H LEU* 2.8 53.6 + - + +
420H THR* 3.2 13.2 + - - +
421H ALA 3.1 0.4 - - - -
422H ALA* 1.3 75.0 - - - +
424H GLU* 1.3 66.2 + - - +
425H VAL 3.4 0.7 + - - -
426H GLU* 3.7 16.6 + - - +
427H VAL* 4.5 1.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 424 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H TYR* 3.5 37.6 + - + -
420H THR 3.0 11.8 + - - +
421H ALA 3.0 9.0 + - - +
423H GLN* 1.3 77.3 - - - +
425H VAL* 1.3 64.3 + - - +
426H GLU 3.1 3.1 - - - -
427H VAL* 3.1 51.1 + - - +
428H TRP* 3.2 41.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 425 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 3.6 21.4 - - + +
101H GLY* 3.8 31.6 - - - -
102H ALA* 4.4 2.0 - - - +
105H MET* 4.5 5.8 - - - -
242H PHE* 3.9 15.3 - - + -
246H TYR* 3.7 34.3 - - + -
421H ALA 3.2 16.2 + - - +
422H ALA 4.0 0.9 - - - +
423H GLN 3.3 1.6 - - - -
424H GLU* 1.3 76.0 - - - +
426H GLU* 1.3 61.0 + - - +
428H TRP* 3.5 13.4 + - + -
429H LEU* 3.1 22.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 426 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H ARG* 3.4 23.3 + - - -
246H TYR* 2.9 38.2 + - - +
247H LYS* 3.9 22.8 + - - +
250H ARG* 4.0 10.6 + - - +
423H GLN 3.7 12.6 - - - +
425H VAL* 1.3 79.3 - - - +
427H VAL* 1.3 60.3 + - + +
429H LEU* 3.5 5.4 + - - +
430H ASP* 3.2 40.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 427 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H GLN 5.3 1.6 - - - +
424H GLU* 3.1 41.3 + - - +
426H GLU* 1.3 81.1 - - + +
428H TRP* 1.3 73.0 + - + +
429H LEU 3.4 0.2 + - - -
430H ASP* 3.5 6.0 + - - +
431H LYS* 3.2 31.9 + - + +
----------------------------------------------------------
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Residues in contact with TRP 428 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H LEU* 4.0 29.7 - - + +
97H ASN* 3.3 45.5 - - + +
98H LEU* 3.8 20.7 - - + +
101H GLY* 4.4 1.3 - - - -
286H PHE* 3.1 52.1 + + + +
297H TYR* 4.6 3.9 - + + +
421H ALA 4.6 2.7 - - - -
424H GLU* 3.2 39.5 + - + +
425H VAL* 3.7 33.4 - - + +
427H VAL* 1.3 81.9 - - + +
429H LEU* 1.3 60.2 + - - +
431H LYS* 3.7 1.9 - - + +
432H LEU* 2.8 30.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 429 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H LEU* 4.0 20.6 - - + +
213H PHE* 4.3 8.1 - - + -
239H ILE* 4.1 18.3 - - + +
242H PHE* 3.9 28.9 - - + -
243H ARG* 3.4 54.5 - - + +
246H TYR* 4.9 6.7 - - + -
425H VAL 3.1 19.4 + - - +
426H GLU* 3.6 6.1 - - - +
427H VAL 3.2 0.2 - - - -
428H TRP* 1.3 77.3 - - - +
430H ASP* 1.3 56.2 + - - +
432H LEU* 3.2 3.3 + - + +
433H GLU* 2.7 37.5 + - - +
----------------------------------------------------------
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Residues in contact with ASP 430 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243H ARG* 2.9 32.9 + - - -
426H GLU* 3.2 26.9 - - - +
427H VAL* 3.5 7.3 - - - +
429H LEU* 1.3 80.9 - - - +
431H LYS* 1.3 55.8 + - - +
433H GLU* 3.3 7.8 + - - +
434H ALA* 3.0 28.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 431 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H GLU* 5.2 13.9 - - - +
94H LEU* 3.9 28.0 - - + -
288H THR* 6.1 5.8 - - - -
427H VAL* 3.2 25.4 + - + +
428H TRP* 3.7 7.2 - - + +
430H ASP* 1.3 69.7 - - - +
432H LEU* 1.4 71.7 + - - +
433H GLU 3.0 1.3 - - - -
434H ALA* 3.1 6.6 + - + +
435H ASN* 2.9 32.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 432 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ASN* 3.7 46.2 - - + +
94H LEU* 3.8 15.9 - - + +
95H MET* 4.4 5.6 - - + +
98H LEU* 4.5 10.1 - - + -
213H PHE* 4.4 18.4 - - + -
234H LEU* 3.9 22.0 - - + -
239H ILE* 3.6 26.0 - - + -
428H TRP 2.8 23.4 + - - +
429H LEU* 3.2 7.2 + - + +
431H LYS* 1.4 76.6 - - - +
433H GLU* 1.3 57.7 - - - +
435H ASN* 3.3 4.8 + - - +
436H VAL* 3.0 25.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 433 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PRO* 5.1 8.3 - - + +
239H ILE* 3.7 30.5 - - + +
243H ARG* 3.0 24.3 + - - -
429H LEU 2.7 17.7 + - - +
430H ASP* 3.3 7.3 - - - +
432H LEU* 1.3 78.4 - - - +
434H ALA* 1.3 56.2 + - - +
436H VAL* 3.4 4.7 + - + +
437H LYS* 3.0 63.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 434 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430H ASP 3.0 15.4 + - - +
431H LYS* 3.1 8.0 + - - +
433H GLU* 1.3 74.1 - - - +
435H ASN* 1.3 69.4 + - - +
437H LYS* 3.3 9.6 + - - +
438H ALA* 3.0 25.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 435 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H GLU* 2.9 29.4 + - - +
91H ASN* 2.8 27.1 + - - +
94H LEU* 3.9 8.3 - - - +
431H LYS* 2.9 19.6 + - - +
432H LEU 3.4 8.3 - - - +
434H ALA* 1.3 78.8 - - - +
436H VAL* 1.3 63.9 + - - +
438H ALA* 3.4 4.1 + - - -
439H GLY 3.4 3.1 + - - -
440H LYS* 2.8 51.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 436 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H ASN* 4.1 5.6 - - - +
234H LEU* 3.3 55.2 - - + +
236H PRO* 5.6 6.5 - - + -
239H ILE* 5.3 2.5 - - + -
432H LEU* 3.0 19.3 + - + +
433H GLU* 3.4 6.5 + - + +
434H ALA 3.2 0.2 - - - -
435H ASN* 1.3 80.5 - - - +
437H LYS* 1.3 59.1 + - + +
439H GLY* 3.0 19.6 + - - +
440H LYS 3.9 13.7 - - - +
441H ASP* 4.9 6.2 - - + +
----------------------------------------------------------
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Residues in contact with LYS 437 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H PRO* 4.8 17.8 - - - +
433H GLU* 3.0 53.9 + - - +
434H ALA* 3.7 8.7 - - - +
435H ASN 3.2 0.2 - - - -
436H VAL* 1.3 74.2 - - + +
438H ALA* 1.3 56.0 + - - +
439H GLY 3.0 9.6 + - - -
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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