Contacts of the helix formed by residues 422 - 448 (chain L) in PDB entry 1MKD
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 422 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509E GLN* 5.5 13.0 - - + +
199L TRP* 4.9 3.4 - - + -
200L GLY* 3.8 24.9 - - - +
420L THR 4.8 0.4 - - - +
421L LYS* 1.4 87.0 - - + +
423L LEU* 1.3 67.8 + - - +
424L GLN* 3.2 5.4 - - + +
425L LEU* 2.9 33.6 + - + +
426L TYR 3.1 10.0 + - - -
495L THR* 4.7 7.4 - - + -
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Residues in contact with LEU 423 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E SER* 3.9 26.2 - - - +
506E THR* 4.5 2.7 - - - +
421L LYS 3.3 2.4 + - - -
422L PRO* 1.3 70.7 - - - +
424L GLN* 1.3 64.0 + - - +
426L TYR* 4.2 13.2 - - + -
427L ARG* 2.9 52.6 + - + +
499L ASN* 3.4 31.2 + - + +
502L TRP* 3.6 54.1 - - + +
503L TYR* 4.6 1.1 - - + -
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Residues in contact with GLN 424 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506E THR 6.1 0.7 - - - +
508E PRO* 3.5 27.8 - - + +
509E GLN* 3.7 16.0 + - + +
510E SER* 3.2 22.8 + - - -
202L HIS* 3.1 34.5 + - - -
205L ARG* 4.5 1.6 - - - +
422L PRO* 3.1 4.8 + - + +
423L LEU* 1.3 78.9 - - - +
425L LEU* 1.3 61.0 + - + +
427L ARG* 3.9 7.3 + - - +
428L GLN* 3.1 41.0 + - + +
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Residues in contact with LEU 425 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200L GLY* 3.6 26.5 - - - +
201L LEU 3.9 11.0 - - - +
202L HIS* 4.0 28.5 - - + +
203L VAL* 4.7 5.8 - - + +
204L PHE* 3.8 26.4 - - + -
421L LYS* 4.2 13.2 - - + -
422L PRO* 2.9 32.8 + - + +
424L GLN* 1.3 78.8 - - + +
426L TYR* 1.3 66.3 + - - +
428L GLN* 2.8 19.9 + - - +
429L TRP* 3.1 23.7 + - + +
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Residues in contact with TYR 426 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418L ASN* 3.4 20.1 + - + +
419L PRO* 3.5 31.9 - - + +
421L LYS 4.2 2.2 - - - +
422L PRO 3.1 8.9 + - - +
423L LEU* 3.7 11.4 - - + +
425L LEU* 1.3 76.7 - - - +
427L ARG* 1.3 58.0 + - - +
429L TRP* 3.1 9.4 + - - +
430L THR* 2.9 40.7 + - - -
466L GLN* 2.7 30.2 + - - +
470L ILE* 3.3 21.7 - - + +
499L ASN* 3.7 28.0 - - + -
503L TYR* 3.5 26.5 - + - -
3012L ZAR 3.5 15.0 - - - -
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Residues in contact with ARG 427 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E ARG* 5.2 9.9 - - - +
502E TRP* 5.6 1.2 - - - -
506E THR* 3.3 32.9 + - - +
423L LEU* 2.9 49.9 + - + +
424L GLN* 4.1 6.5 - - - +
426L TYR* 1.3 75.6 - - - +
428L GLN* 1.3 58.2 + - + +
430L THR* 3.3 2.6 + - - -
431L ASP* 3.0 36.5 + - - +
502L TRP* 3.1 30.6 - - + -
503L TYR* 3.7 20.7 + - + +
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Residues in contact with GLN 428 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202L HIS* 3.8 11.4 + - - -
204L PHE* 3.4 38.0 - - + +
424L GLN* 3.1 46.7 + - + +
425L LEU* 2.8 13.0 + - - +
427L ARG* 1.3 73.9 - - + +
429L TRP* 1.3 63.0 + - - +
431L ASP* 3.3 10.2 + - - +
432L ARG* 3.1 30.3 + - - +
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Residues in contact with TRP 429 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203L VAL* 4.0 10.7 - - + +
204L PHE* 3.5 29.7 - + - -
255L ALA 5.6 0.2 - - - -
256L TYR* 3.6 25.0 - + - -
258L ASN* 5.3 0.4 - - - -
260L ILE* 3.8 15.3 - - + -
261L HIS* 3.7 41.7 - - + -
264L ASP* 3.4 30.3 + - + -
418L ASN* 3.5 39.9 - - + +
421L LYS* 5.4 4.3 - - + +
425L LEU* 3.1 33.2 + - + +
426L TYR* 3.4 7.4 - - - +
428L GLN* 1.3 75.7 - - - +
430L THR* 1.3 59.7 - - - +
432L ARG* 3.0 13.7 + - - +
433L ILE* 2.8 27.2 + - - +
3012L ZAR 3.3 8.7 - - - -
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Residues in contact with THR 430 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426L TYR* 2.9 36.4 + - - -
427L ARG 3.3 4.7 + - - -
429L TRP* 1.3 76.4 - - - +
431L ASP* 1.3 65.3 + - - +
433L ILE* 3.1 4.1 - - - +
434L MET* 3.1 29.4 + - + +
462L VAL* 3.8 20.0 - - + -
466L GLN* 3.4 27.9 - - + +
503L TYR* 3.2 26.2 + - - +
3012L ZAR 3.3 11.4 - - - -
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Residues in contact with ASP 431 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427L ARG* 3.0 23.0 + - - +
428L GLN* 3.5 10.8 - - - +
430L THR* 1.3 82.1 - - - +
432L ARG* 1.3 59.0 + - + +
434L MET* 3.8 4.1 - - - +
435L GLU* 2.8 31.1 + - - +
462L VAL* 5.7 3.3 - - - +
503L TYR* 5.5 0.5 + - - -
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Residues in contact with ARG 432 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204L PHE* 3.0 36.6 - - - -
255L ALA* 2.8 57.5 + - + +
256L TYR* 4.0 7.6 - - + -
258L ASN* 4.0 9.1 - - - +
260L ILE* 3.7 21.8 - - - +
428L GLN* 3.1 20.3 + - - +
429L TRP* 3.0 18.2 + - - +
431L ASP* 1.3 74.2 - - + +
433L ILE* 1.3 65.6 + - - +
435L GLU* 3.1 9.8 + - - +
436L GLU* 3.0 18.7 + - - +
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Residues in contact with ILE 433 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256L TYR* 3.6 37.8 - - + -
257L HIS* 3.9 12.3 - - + -
429L TRP 2.8 12.7 + - - +
430L THR* 3.1 17.0 - - - +
432L ARG* 1.3 73.3 - - - +
434L MET* 1.3 70.8 + - + +
436L GLU* 3.2 4.3 + - + +
437L PHE* 2.9 64.9 + - + -
466L GLN* 4.6 1.3 - - - +
3012L ZAR 3.5 46.9 - - + +
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Residues in contact with MET 434 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430L THR* 3.1 18.9 + - + +
431L ASP* 3.8 4.9 - - - +
433L ILE* 1.3 85.3 - - + +
435L GLU* 1.3 66.2 + - - +
437L PHE* 3.8 7.7 - - - +
438L PHE* 3.1 65.6 + - + -
454L MET* 3.6 47.1 - - + +
460L ALA* 4.1 6.5 - - + -
462L VAL* 3.9 39.7 - - + -
465L SER* 5.2 1.1 - - - +
466L GLN* 4.8 4.5 - - - -
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Residues in contact with GLU 435 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255L ALA* 3.7 20.4 - - + +
431L ASP 2.8 19.6 + - - +
432L ARG* 3.4 12.3 - - - +
434L MET* 1.3 77.9 - - - +
436L GLU* 1.3 52.4 + - - +
438L PHE* 4.4 6.6 - - - +
439L PRO* 2.6 33.9 - - + +
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Residues in contact with GLU 436 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254L VAL* 3.2 14.6 - - + +
255L ALA* 4.1 9.4 - - + +
256L TYR* 2.8 30.9 + - - +
257L HIS* 2.7 37.9 + - - -
301L HIS* 4.1 0.5 - - - -
303L GLY* 3.2 36.6 - - - +
432L ARG 3.0 10.7 + - - +
433L ILE* 3.6 10.1 - - + +
434L MET 3.1 0.2 - - - -
435L GLU* 1.3 76.3 - - - +
437L PHE* 1.3 69.6 + - + +
438L PHE 3.3 0.4 - - - -
439L PRO* 3.0 13.8 - - - +
440L GLN* 3.5 11.6 + - - +
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Residues in contact with PHE 437 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257L HIS* 5.3 5.6 - + - -
433L ILE* 2.9 50.0 + - + +
434L MET* 3.3 11.9 + - - +
436L GLU* 1.3 81.7 - - + +
438L PHE* 1.3 56.4 + - - +
440L GLN* 3.1 11.8 + - - +
441L GLY 2.9 22.3 + - - -
454L MET* 3.7 48.0 - - + +
455L CYS* 3.2 33.9 - - - +
3012L ZAR 4.0 29.6 - + - -
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Residues in contact with PHE 438 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434L MET* 3.1 44.6 + - + +
435L GLU* 4.4 3.8 - - - +
437L PHE* 1.3 74.1 - - - +
439L PRO* 1.4 60.6 - - + +
441L GLY* 2.9 3.5 + - - -
442L ASP* 2.6 40.6 + - - +
454L MET 3.4 19.3 - - - -
455L CYS 3.5 8.6 - - - +
457L LYS* 3.5 50.6 - - + +
460L ALA* 3.6 22.2 - - + -
462L VAL* 4.8 5.6 - - + -
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Residues in contact with PRO 439 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435L GLU* 2.6 31.9 - - + +
436L GLU* 3.0 17.5 - - - +
438L PHE* 1.4 82.7 - - + +
440L GLN* 1.3 55.0 + - - +
442L ASP* 3.5 13.7 - - + +
443L ARG* 2.8 35.4 + - + +
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Residues in contact with GLN 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303L GLY 4.0 3.4 - - - +
304L VAL* 3.2 17.9 - - + -
305L SER* 3.0 45.8 + - - -
308L PHE* 3.8 20.4 - - + +
436L GLU 3.5 9.5 + - - +
437L PHE* 3.1 16.1 + - - +
438L PHE 3.1 0.4 - - - -
439L PRO* 1.3 75.6 - - - +
441L GLY* 1.3 54.5 + - - +
443L ARG* 3.1 9.8 + - - +
444L GLU* 2.8 58.0 + - - +
452L SER* 3.8 9.3 + - - -
455L CYS* 4.0 14.8 - - - -
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Residues in contact with GLY 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437L PHE 2.9 7.7 + - - -
438L PHE 2.9 3.6 + - - -
440L GLN* 1.3 78.6 - - - +
442L ASP* 1.3 57.6 + - - +
444L GLU* 3.3 14.3 + - - -
445L ARG* 2.9 28.2 + - - +
451L ILE* 3.1 15.9 - - - +
455L CYS* 3.2 25.8 - - - +
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Residues in contact with ASP 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438L PHE* 2.6 22.4 + - - +
439L PRO* 3.5 16.9 - - + +
441L GLY* 1.3 70.7 - - - +
443L ARG* 1.3 65.9 + - - +
445L ARG* 2.8 29.4 + - - +
446L GLU* 2.9 35.5 + - + +
457L LYS* 3.0 35.6 + - - +
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Residues in contact with ARG 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L PRO 5.3 4.0 + - - -
304L VAL* 3.8 18.2 - - - +
308L PHE* 3.4 35.2 - - + -
439L PRO 2.8 25.5 + - - +
440L GLN* 3.2 12.8 - - - +
442L ASP* 1.3 77.2 - - - +
444L GLU* 1.3 57.2 + - - +
446L GLU* 3.4 20.0 + - - +
447L ARG* 3.0 60.6 + - - +
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Residues in contact with GLU 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308L PHE* 3.6 24.1 - - + +
311L ASN* 5.7 1.0 + - - -
440L GLN* 2.8 32.4 + - - +
441L GLY* 3.6 14.6 - - - +
443L ARG* 1.3 74.8 - - - +
445L ARG* 1.3 60.9 + - - +
447L ARG 3.4 0.3 + - - -
448L GLY 3.0 2.9 + - - -
449L MET* 2.8 56.9 + - + +
450L GLU 4.1 5.8 - - - +
451L ILE* 3.6 9.1 - - + -
452L SER* 2.6 49.8 + - - -
455L CYS* 4.2 0.3 - - - +
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Residues in contact with ARG 445 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441L GLY 2.9 15.4 + - - +
442L ASP* 2.8 39.2 + - - +
444L GLU* 1.3 76.7 - - - +
446L GLU* 1.3 64.5 + - + +
448L GLY* 3.1 13.0 + - - -
449L MET 4.6 2.0 - - - -
451L ILE* 3.3 16.4 - - + +
456L ASP* 2.9 29.5 + - - +
457L LYS* 3.8 15.2 - - - +
458L HIS* 3.8 25.3 + - - -
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Residues in contact with GLU 446 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442L ASP* 2.9 28.8 + - + +
443L ARG* 3.4 26.2 + - - +
444L GLU 3.2 0.2 - - - -
445L ARG* 1.3 74.4 - - + +
447L ARG* 1.3 66.6 + - - +
448L GLY* 2.9 11.0 + - - -
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Residues in contact with ARG 447 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308L PHE* 4.0 8.4 - - + -
312L THR* 4.1 16.7 - - + +
443L ARG* 3.0 62.1 + - - +
444L GLU 3.7 1.1 - - - +
446L GLU* 1.3 84.0 + - - +
448L GLY* 1.3 58.6 + - - +
449L MET* 3.1 38.4 + - + +
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Residues in contact with GLY 448 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444L GLU 3.0 2.8 + - - -
445L ARG 3.1 10.3 + - - -
446L GLU 2.9 6.5 + - - -
447L ARG* 1.3 80.2 - - - +
449L MET* 1.3 64.5 + - - +
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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