Contacts of the helix formed by residues 422 - 448 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199J TRP* 4.9 3.4 - - + -
200J GLY* 3.8 23.6 - - - +
420J THR 4.8 0.4 - - - +
421J LYS* 1.4 88.3 - - + +
423J LEU* 1.3 66.7 + - - +
424J GLN* 3.2 5.6 - - + +
425J LEU* 2.9 33.5 + - + +
426J TYR 3.0 9.9 + - - -
495J THR* 4.7 7.2 - - + -
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Residues in contact with LEU 423 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F SER* 4.0 24.9 - - - +
506F THR* 5.0 0.4 - - - +
421J LYS 3.3 3.7 + - - -
422J PRO* 1.3 70.4 - - - +
424J GLN* 1.3 64.8 + - - +
426J TYR* 4.2 12.6 - - + -
427J ARG* 2.9 51.7 + - + +
495J THR* 5.4 0.4 - - - +
499J ASN* 3.4 30.5 + - + +
502J TRP* 3.6 54.3 - - + +
503J TYR* 4.6 0.7 - - + -
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Residues in contact with GLN 424 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505F SER 5.9 0.6 + - - -
508F PRO* 4.1 10.6 - - + +
509F GLN* 3.3 40.5 + - + +
510F SER* 4.2 6.3 + - - -
202J HIS* 3.1 34.2 + - - -
205J ARG* 4.5 3.6 - - - +
422J PRO* 3.1 5.4 + - + +
423J LEU* 1.3 77.6 - - - +
425J LEU* 1.3 63.5 + - + +
427J ARG* 3.9 8.0 + - - +
428J GLN* 3.2 37.1 + - + +
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Residues in contact with LEU 425 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200J GLY* 3.6 26.7 - - - +
201J LEU 3.9 11.2 - - - +
202J HIS* 4.1 28.7 - - + +
203J VAL* 4.7 4.7 - - + +
204J PHE* 3.8 25.8 - - + -
421J LYS* 4.2 13.9 - - + +
422J PRO* 2.9 32.9 + - + +
424J GLN* 1.3 79.6 - - + +
426J TYR* 1.3 65.7 + - - +
428J GLN* 2.9 19.7 + - - +
429J TRP* 3.1 23.3 + - + +
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Residues in contact with TYR 426 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418J ASN* 3.4 21.0 + - + +
419J PRO* 3.5 31.8 - - + +
421J LYS* 4.1 3.8 - - - +
422J PRO 3.0 8.3 + - - +
423J LEU* 3.3 11.6 + - + +
425J LEU* 1.3 78.2 - - - +
427J ARG* 1.3 57.2 + - - +
429J TRP* 3.1 8.3 + - - +
430J THR* 2.9 40.4 + - - -
466J GLN* 2.6 30.3 + - - +
470J ILE* 3.5 20.7 - - + +
499J ASN* 3.7 27.8 - - + -
503J TYR* 3.5 27.1 - + - -
3010J ZAR 3.5 15.0 - - - -
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Residues in contact with ARG 427 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F ARG* 5.5 5.5 - - - +
502F TRP* 5.2 4.9 - - - -
506F THR* 3.5 34.8 + - - +
423J LEU* 2.9 48.8 + - + +
424J GLN* 4.1 6.9 - - - +
426J TYR* 1.3 75.5 - - - +
428J GLN* 1.3 63.4 + - + +
430J THR* 3.3 2.9 + - - -
431J ASP* 3.0 31.0 + - - +
502J TRP* 3.2 32.3 - - + -
503J TYR* 3.7 20.0 + - + +
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Residues in contact with GLN 428 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202J HIS* 3.8 12.4 + - - -
204J PHE* 3.4 38.7 - - + +
424J GLN* 3.2 46.7 + - + +
425J LEU* 2.9 9.2 + - - +
427J ARG* 1.3 76.2 - - + +
429J TRP* 1.3 63.0 + - - +
431J ASP* 3.3 12.0 + - - +
432J ARG* 3.1 29.9 + - - +
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Residues in contact with TRP 429 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203J VAL* 4.0 11.0 - - + +
204J PHE* 3.5 27.7 - + - -
255J ALA 5.6 0.2 - - - -
256J TYR* 3.6 28.3 - + - -
258J ASN* 5.3 0.7 - - - -
260J ILE* 3.8 15.7 - - + -
261J HIS* 3.7 37.7 - - + -
264J ASP* 3.5 29.9 + - + -
418J ASN* 3.5 40.5 - - + +
421J LYS* 5.4 4.5 - - + +
425J LEU* 3.1 34.6 + - + +
426J TYR* 3.4 7.2 - - - +
428J GLN* 1.3 77.9 - - - +
430J THR* 1.3 61.8 - - - +
432J ARG* 3.0 14.1 + - - +
433J ILE* 2.8 21.3 + - - +
3010J ZAR 3.3 9.1 - - - -
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Residues in contact with THR 430 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426J TYR* 2.9 32.7 + - - -
427J ARG 3.6 4.5 - - - -
429J TRP* 1.3 75.2 - - - +
431J ASP* 1.3 65.1 + - - +
433J ILE* 3.1 4.1 - - - +
434J MET* 3.1 23.4 + - + +
462J VAL* 3.8 20.6 - - + -
466J GLN* 3.4 29.1 - - + +
503J TYR* 3.2 27.3 + - - +
3010J ZAR 3.3 10.6 - - - -
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Residues in contact with ASP 431 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427J ARG* 3.0 22.6 + - - +
428J GLN* 3.5 11.4 - - - +
429J TRP 3.1 0.2 - - - -
430J THR* 1.3 80.9 - - - +
432J ARG* 1.3 59.7 + - + +
434J MET* 3.8 5.3 - - - +
435J GLU* 2.9 30.6 + - - +
462J VAL* 5.7 3.1 - - - +
503J TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 432 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204J PHE* 3.1 34.2 - - - -
255J ALA* 2.7 56.1 + - + +
256J TYR* 4.0 8.1 - - + -
258J ASN* 4.0 9.5 - - - +
260J ILE* 3.7 21.9 - - - +
428J GLN* 3.1 18.7 + - - +
429J TRP* 3.0 19.1 + - - +
431J ASP* 1.3 74.4 - - + +
433J ILE* 1.3 64.3 + - - +
435J GLU* 3.1 10.9 + - - +
436J GLU* 3.0 19.8 + - - +
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Residues in contact with ILE 433 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256J TYR* 3.6 38.3 - - + -
257J HIS* 3.8 11.7 - - + -
429J TRP 2.8 12.0 + - - +
430J THR* 3.1 14.8 - - - +
432J ARG* 1.3 73.5 - - - +
434J MET* 1.3 71.0 + - + +
436J GLU* 3.2 3.6 + - + +
437J PHE* 2.9 65.0 + - + -
466J GLN* 4.6 0.9 - - - +
3010J ZAR 3.5 48.0 - - + +
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Residues in contact with MET 434 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430J THR* 3.1 18.9 + - + +
431J ASP* 3.9 5.2 - - - +
433J ILE* 1.3 85.1 - - + +
435J GLU* 1.3 65.7 + - - +
437J PHE* 3.8 6.9 - - - +
438J PHE* 3.1 64.9 + - + -
454J MET* 3.6 46.2 - - + +
460J ALA* 4.1 6.1 - - + -
462J VAL* 3.9 39.5 - - + -
465J SER* 5.2 1.3 - - - +
466J GLN* 4.8 4.9 - - - -
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Residues in contact with GLU 435 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255J ALA* 3.7 19.2 - - + +
431J ASP 2.9 19.5 + - - +
432J ARG* 3.4 11.7 - - - +
434J MET* 1.3 79.1 - - - +
436J GLU* 1.3 50.5 + - - +
438J PHE* 4.6 5.8 - - - -
439J PRO* 2.6 33.3 - - + +
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Residues in contact with GLU 436 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254J VAL* 3.1 14.5 - - + +
255J ALA* 4.1 9.2 - - + +
256J TYR* 2.8 31.6 + - - +
257J HIS* 2.7 37.7 + - - -
301J HIS* 4.1 0.3 - - - -
303J GLY* 3.2 35.1 - - - +
432J ARG 3.0 14.0 + - - +
433J ILE* 3.6 7.2 - - - +
434J MET 3.1 0.2 - - - -
435J GLU* 1.3 77.2 - - - +
437J PHE* 1.3 67.9 + - + +
438J PHE 3.3 0.4 - - - -
439J PRO* 3.0 14.2 - - - +
440J GLN* 3.5 10.0 + - - +
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Residues in contact with PHE 437 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J HIS* 5.2 5.4 - + - -
303J GLY 6.2 0.4 - - - -
433J ILE* 2.9 51.4 + - + +
434J MET* 3.3 11.0 + - - +
436J GLU* 1.3 81.5 - - + +
438J PHE* 1.3 57.3 + - - +
440J GLN* 3.1 13.9 + - - +
441J GLY 2.9 21.8 + - - -
454J MET* 3.7 49.4 - - + +
455J CYS* 3.3 30.1 - - - +
3010J ZAR 4.0 29.6 - + - -
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Residues in contact with PHE 438 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434J MET* 3.1 44.4 + - + -
435J GLU* 4.4 3.8 - - - +
437J PHE* 1.3 73.0 - - - +
439J PRO* 1.3 60.7 - - + +
441J GLY* 2.9 2.6 + - - -
442J ASP* 2.7 40.4 + - - +
454J MET 3.4 19.3 - - - -
455J CYS 3.5 9.9 - - - +
457J LYS* 3.5 50.3 - - + -
460J ALA* 3.6 21.8 - - + -
462J VAL* 4.8 5.8 - - + -
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Residues in contact with PRO 439 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435J GLU* 2.6 31.9 - - + +
436J GLU* 3.0 17.0 - - - +
438J PHE* 1.3 83.3 - - + +
440J GLN* 1.3 54.6 + - - +
442J ASP* 3.3 13.8 + - + +
443J ARG* 2.8 35.3 + - + +
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Residues in contact with GLN 440 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J GLY 4.0 3.7 + - - +
304J VAL* 3.3 17.8 - - + -
305J SER* 3.0 44.9 + - - -
308J PHE* 3.8 21.2 - - + +
436J GLU 3.5 8.5 + - - +
437J PHE* 3.1 16.8 + - - +
438J PHE 3.0 0.4 - - - -
439J PRO* 1.3 79.0 - - - +
441J GLY* 1.3 60.4 + - - +
443J ARG* 3.0 9.3 + - - +
444J GLU* 2.8 52.4 + - - +
452J SER* 3.8 8.7 + - - -
455J CYS* 4.0 13.7 - - - -
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Residues in contact with GLY 441 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437J PHE 2.9 7.9 + - - -
438J PHE 2.9 3.6 + - - -
440J GLN* 1.3 77.5 - - - +
442J ASP* 1.3 56.6 + - - +
444J GLU* 3.3 14.3 + - - -
445J ARG* 2.9 27.7 + - - +
451J ILE* 3.1 16.6 - - - +
455J CYS* 3.2 25.5 - - - +
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Residues in contact with ASP 442 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438J PHE* 2.7 22.5 + - - +
439J PRO* 3.5 16.6 - - + +
440J GLN 3.1 0.2 - - - -
441J GLY* 1.3 69.9 - - - +
443J ARG* 1.3 65.5 + - - +
445J ARG* 2.8 39.6 + - - +
446J GLU* 2.9 26.2 + - - +
457J LYS* 3.1 36.2 + - - +
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Residues in contact with ARG 443 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J PRO 5.3 4.6 + - - -
304J VAL* 3.8 18.6 - - - +
308J PHE* 3.4 34.5 - - + -
439J PRO* 2.8 25.2 + - + +
440J GLN* 3.2 13.0 - - - +
442J ASP* 1.3 76.3 - - - +
444J GLU* 1.3 56.4 + - - +
446J GLU* 3.4 19.2 + - - +
447J ARG* 3.0 61.1 + - - +
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Residues in contact with GLU 444 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 3.6 23.9 - - + +
311J ASN* 5.7 1.4 + - - -
440J GLN* 2.8 31.7 + - - +
441J GLY* 3.5 14.6 + - - +
443J ARG* 1.3 75.3 - - - +
445J ARG* 1.3 62.3 + - - +
447J ARG* 3.4 3.0 + - - -
448J GLY 3.0 2.6 + - - -
449J MET* 2.8 54.0 + - + +
450J GLU 4.1 5.9 - - - +
451J ILE* 3.6 10.7 - - + -
452J SER* 2.6 50.6 + - - -
455J CYS* 4.2 0.2 - - - +
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Residues in contact with ARG 445 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441J GLY 2.9 14.3 + - - +
442J ASP* 2.8 44.5 + - - +
444J GLU* 1.3 73.8 - - - +
446J GLU* 1.3 65.7 + - + +
448J GLY* 3.1 13.7 + - - -
449J MET 4.6 1.6 - - - -
451J ILE* 3.3 17.9 - - + +
456J ASP* 3.0 29.7 + - - +
457J LYS* 3.8 15.4 - - - +
458J HIS* 3.8 26.9 + - - -
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Residues in contact with GLU 446 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442J ASP* 2.9 29.2 + - + +
443J ARG* 3.4 25.5 + - - +
445J ARG* 1.3 73.9 - - + +
447J ARG* 1.3 65.5 + - - +
448J GLY* 2.9 11.0 + - - -
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Residues in contact with ARG 447 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J PHE* 4.0 8.2 - - + -
312J THR* 4.1 16.7 - - + +
443J ARG* 3.0 66.3 + - - +
444J GLU 3.7 0.9 - - - +
445J ARG 3.4 0.2 - - - -
446J GLU* 1.3 82.4 + - - +
448J GLY* 1.3 58.6 + - - +
449J MET* 3.1 37.2 + - + +
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Residues in contact with GLY 448 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444J GLU 3.0 2.6 + - - -
445J ARG* 3.1 11.2 + - - -
446J GLU 2.9 6.9 + - - -
447J ARG* 1.3 78.7 - - - +
449J 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