Contacts of the helix formed by residues 422 - 448 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 4.9 3.1 - - + -
200B GLY* 3.8 23.6 - - - +
420B THR 4.8 0.7 - - - +
421B LYS* 1.3 89.0 - - + +
423B LEU* 1.3 67.4 + - - +
424B GLN* 3.2 5.6 - - + +
425B LEU* 2.9 32.9 + - + +
426B TYR 3.1 9.2 + - - -
495B THR* 4.5 7.4 - - + -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS 3.4 2.4 + - - -
422B PRO* 1.3 70.8 - - - +
424B GLN* 1.3 64.4 + - - +
426B TYR* 4.2 12.6 - - + -
427B ARG* 2.9 51.6 + - + +
499B ASN* 3.5 32.1 + - + +
502B TRP* 3.6 54.3 - - + +
503B TYR* 4.6 0.9 - - + -
505C SER* 4.7 15.3 - - - +
506C THR* 5.1 4.0 - - + -
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B HIS* 3.1 35.2 + - - -
205B ARG* 4.5 7.4 + - - +
422B PRO* 3.0 4.9 + - + +
423B LEU* 1.3 79.2 - - - +
425B LEU* 1.3 63.1 + - + +
427B ARG* 4.1 7.6 - - - +
428B GLN* 3.2 38.4 + - + +
508C PRO* 5.4 7.8 - - + +
509C GLN 5.7 1.7 + - - -
510C SER* 4.7 12.0 + - - -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B GLY* 3.6 27.4 - - - +
201B LEU 3.9 11.0 - - - +
202B HIS* 4.0 29.2 - - + +
203B VAL* 4.7 5.4 - - + +
204B PHE* 3.8 26.0 - - + -
421B LYS* 4.2 13.7 - - + -
422B PRO* 2.9 31.4 + - + +
424B GLN* 1.3 77.1 - - + +
426B TYR* 1.3 66.7 + - - +
428B GLN* 2.9 19.8 + - - +
429B TRP* 3.1 22.6 + - + +
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Residues in contact with TYR 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ASN* 3.4 26.2 + - + +
419B PRO* 3.5 32.4 - - + +
421B LYS 4.2 2.5 - - - +
422B PRO 3.1 8.5 + - - +
423B LEU* 3.7 12.1 - - + +
425B LEU* 1.3 78.9 - - - +
427B ARG* 1.3 57.2 + - - +
429B TRP* 3.0 8.9 + - - +
430B THR* 2.9 40.1 + - - -
466B GLN* 2.7 29.7 + - - +
470B ILE* 3.4 22.1 - - + +
499B ASN* 3.7 28.7 - - + -
503B TYR* 3.5 27.1 - + - -
3002B ZAR 3.6 7.6 - - - -
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 2.9 50.1 + - + +
424B GLN* 4.1 6.7 - - - +
426B TYR* 1.3 75.2 - - - +
428B GLN* 1.3 62.8 + - + +
430B THR* 3.3 2.4 + - - -
431B ASP* 3.0 31.4 + - - +
502B TRP* 3.2 36.3 - - + -
503B TYR* 3.7 19.8 + - + +
427C ARG* 5.5 6.3 - - - +
506C THR* 4.7 13.9 - - - +
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Residues in contact with GLN 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B HIS* 3.7 11.9 + - - -
204B PHE* 3.3 39.5 - - + +
424B GLN* 3.2 46.7 + - + +
425B LEU* 2.9 8.1 + - - +
427B ARG* 1.3 76.5 - - + +
429B TRP* 1.3 64.3 + - - +
431B ASP* 3.3 11.2 + - - +
432B ARG* 3.1 29.4 + - - +
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Residues in contact with TRP 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 4.0 10.6 - - + +
204B PHE* 3.5 32.3 - + - -
255B ALA 5.6 0.2 - - - -
256B TYR* 3.6 24.7 - + + -
258B ASN* 5.3 1.1 - - - -
260B ILE* 3.9 11.7 - - + -
261B HIS* 3.7 41.3 - - + -
264B ASP* 3.4 29.9 + - + -
418B ASN* 3.5 38.9 - - + +
421B LYS* 5.4 4.3 - - + +
425B LEU* 3.1 33.1 + - + +
426B TYR* 3.0 8.4 + - - +
428B GLN* 1.3 74.9 - - - +
430B THR* 1.3 61.7 + - - +
432B ARG* 3.0 13.4 + - - +
433B ILE* 2.8 26.7 + - - +
3002B ZAR 3.4 9.0 - - - -
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Residues in contact with THR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B TYR* 2.9 32.6 + - - -
427B ARG 3.6 4.7 - - - -
429B TRP* 1.3 76.6 - - - +
431B ASP* 1.3 65.5 + - - +
433B ILE* 3.1 4.2 - - - +
434B MET* 3.0 23.6 + - + +
462B VAL* 3.8 20.0 - - + -
466B GLN* 3.4 27.7 - - + +
503B TYR* 3.2 26.8 + - - +
3002B ZAR 3.4 10.9 - - - -
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Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 3.0 23.5 + - - +
428B GLN* 3.5 10.5 - - - +
430B THR* 1.3 81.4 - - - +
432B ARG* 1.3 57.9 + - + +
434B MET* 3.8 4.4 - - - +
435B GLU* 2.9 30.5 + - - +
462B VAL* 5.7 3.1 - - - +
503B TYR* 5.5 0.5 + - - -
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE* 3.1 34.0 - - - -
255B ALA* 2.8 57.6 + - + +
256B TYR* 4.0 7.9 - - + -
258B ASN* 4.0 8.3 - - - +
260B ILE* 3.7 21.3 - - - +
428B GLN* 3.1 18.1 + - - +
429B TRP* 3.0 20.7 + - - +
431B ASP* 1.3 75.5 - - + +
433B ILE* 1.3 65.5 + - - +
435B GLU* 3.1 9.7 + - - +
436B GLU* 3.0 19.2 + - - +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 3.6 42.1 - - + -
257B HIS* 3.9 11.4 - - + -
429B TRP 2.8 9.7 + - - +
430B THR* 3.1 17.3 - - - +
432B ARG* 1.3 73.7 - - - +
434B MET* 1.3 70.5 + - + +
436B GLU* 3.2 3.8 + - + +
437B PHE* 2.9 65.4 + - + -
466B GLN* 4.6 1.1 - - - +
3002B ZAR 3.6 46.0 - - + +
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Residues in contact with MET 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B THR* 3.0 19.1 + - + +
431B ASP* 3.9 4.7 - - - +
433B ILE* 1.3 85.5 - - + +
435B GLU* 1.3 66.7 + - - +
436B GLU 3.1 0.4 - - - -
437B PHE* 4.3 7.0 - - - -
438B PHE* 3.0 64.8 + - + -
454B MET* 3.6 46.4 - - + +
460B ALA* 4.1 6.3 - - + -
462B VAL* 3.9 41.1 - - + -
465B SER* 5.2 1.1 - - - +
466B GLN* 4.8 5.2 - - - -
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Residues in contact with GLU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA* 3.7 19.9 - - + +
431B ASP 2.9 18.7 + - - +
432B ARG* 3.1 11.7 + - - +
434B MET* 1.3 78.1 - - - +
436B GLU* 1.3 51.0 + - - +
438B PHE* 4.4 5.6 - - - +
439B PRO* 2.6 33.8 - - + +
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 3.2 15.0 - - + +
255B ALA* 4.1 8.9 - - + +
256B TYR* 2.8 31.0 + - - +
257B HIS* 2.8 38.3 + - - -
301B HIS* 4.1 0.3 - - - -
303B GLY* 3.2 35.4 - - - +
432B ARG 3.0 14.3 + - - +
433B ILE* 3.2 7.4 + - + +
434B MET 3.1 0.2 - - - -
435B GLU* 1.3 77.6 - - - +
437B PHE* 1.3 68.8 + - + +
438B PHE 3.3 0.2 - - - -
439B PRO* 3.1 13.8 - - - +
440B GLN* 3.5 11.6 + - - +
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Residues in contact with PHE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B HIS* 5.3 5.2 - + - -
433B ILE* 2.9 50.9 + - + +
434B MET* 3.4 11.0 + - - +
436B GLU* 1.3 81.6 - - + +
438B PHE* 1.3 57.7 + - - +
440B GLN* 3.1 11.9 + - - +
441B GLY 2.9 22.2 + - - -
454B MET* 3.7 49.1 - - + +
455B CYS* 3.2 33.5 - - - +
3002B ZAR 4.0 29.4 - + - -
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B MET* 3.0 43.2 + - + -
435B GLU* 4.4 4.3 - - - +
437B PHE* 1.3 77.2 - - + +
439B PRO* 1.4 57.1 - - + +
441B GLY* 2.9 3.1 + - - -
442B ASP* 2.7 40.4 + - - +
454B MET 3.4 19.7 - - - -
455B CYS 3.5 9.4 - - - +
457B LYS* 3.5 51.1 - - + -
460B ALA* 3.6 21.8 - - + -
462B VAL* 4.8 5.8 - - + -
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Residues in contact with PRO 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLU* 2.6 32.3 - - + +
436B GLU* 3.1 17.5 - - - +
438B PHE* 1.4 82.6 - - + +
440B GLN* 1.3 55.2 + - - +
442B ASP* 3.5 14.3 - - + +
443B ARG* 2.8 35.3 + - + +
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Residues in contact with GLN 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLY 4.0 3.7 + - - +
304B VAL* 3.2 18.3 - - + -
305B SER* 2.9 45.0 + - - -
308B PHE* 3.8 20.7 - - + +
436B GLU 3.5 9.1 + - - +
437B PHE* 3.1 15.9 + - - +
438B PHE 3.0 0.2 - - - -
439B PRO* 1.3 77.1 - - - +
441B GLY* 1.3 60.2 + - - +
443B ARG* 3.0 9.3 + - - +
444B GLU* 2.8 52.6 + - - +
452B SER* 3.8 9.3 + - - -
455B CYS* 4.0 14.3 - - - -
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE 2.9 7.7 + - - -
438B PHE 2.9 3.6 + - - -
440B GLN* 1.3 77.6 - - - +
442B ASP* 1.3 55.8 + - - +
444B GLU* 3.2 14.9 + - - -
445B ARG* 2.8 28.4 + - - +
451B ILE* 3.1 16.0 - - - +
455B CYS* 3.2 26.2 - - - +
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Residues in contact with ASP 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 2.7 22.0 + - - +
439B PRO* 3.5 16.8 - - + +
441B GLY* 1.3 69.9 - - - +
443B ARG* 1.3 65.9 + - - +
445B ARG* 2.8 39.8 + - - +
446B GLU* 2.9 25.0 + - + +
457B LYS* 3.0 37.0 + - - +
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Residues in contact with ARG 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO 5.3 4.0 + - - -
304B VAL* 3.7 19.0 - - + +
308B PHE* 3.3 34.7 - - + -
439B PRO 2.8 25.7 + - - +
440B GLN* 3.2 11.9 - - - +
442B ASP* 1.3 74.8 - - - +
444B GLU* 1.3 58.5 + - - +
446B GLU* 3.4 20.0 + - - +
447B ARG* 3.0 62.2 + - - +
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.6 23.8 - - + +
311B ASN* 5.7 1.2 + - - -
440B GLN* 2.8 31.0 + - - +
441B GLY* 3.5 15.9 - - - +
443B ARG* 1.3 75.2 - - - +
445B ARG* 1.3 63.1 + - - +
447B ARG* 3.4 4.0 + - - -
448B GLY 3.0 2.9 + - - -
449B MET* 2.8 51.8 + - + +
450B GLU 4.1 5.8 - - - +
451B ILE* 3.6 10.2 - - + -
452B SER* 2.6 50.7 + - - -
455B CYS* 4.2 0.3 - - - +
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLY 2.8 14.5 + - - +
442B ASP* 2.8 39.0 + - - +
444B GLU* 1.3 76.2 - - - +
446B GLU* 1.3 64.3 + - + +
448B GLY* 3.1 12.6 + - - -
449B MET 4.6 2.0 - - - -
451B ILE* 3.2 17.1 - - + +
456B ASP* 3.0 29.3 + - - +
457B LYS* 3.8 14.3 - - - +
458B HIS* 3.8 27.5 + - - -
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ASP* 2.9 27.3 + - + +
443B ARG* 3.4 27.0 + - - +
445B ARG* 1.3 75.9 - - + +
447B ARG* 1.3 70.4 + - - +
448B GLY* 2.9 7.1 + - - -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 4.0 7.9 - - + -
312B THR* 4.1 17.9 - - + +
443B ARG* 3.0 63.1 + - - +
444B GLU 3.7 0.9 - - - +
446B GLU* 1.3 85.2 + - - +
448B GLY* 1.3 58.4 + - - +
449B MET* 3.1 36.7 + - + +
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Residues in contact with GLY 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLU 3.0 2.6 + - - -
445B ARG 3.1 10.7 + - - -
446B GLU 2.9 7.1 + - - -
447B ARG* 1.3 79.7 - - - +
449B MET* 1.3 63.5 + - - +
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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