Contacts of the helix formed by residues 422 - 448 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP* 4.9 3.4 - - + -
200G GLY* 3.8 24.5 - - - +
420G THR 4.7 0.7 - - - +
421G LYS* 1.3 87.3 - - + +
423G LEU* 1.3 67.5 - - - +
424G GLN* 3.2 5.6 - - + +
425G LEU* 2.8 34.2 + - + +
426G TYR 3.0 9.7 + - - -
495G THR* 4.6 7.4 - - + -
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Residues in contact with LEU 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421G LYS 3.3 2.0 + - - -
422G PRO* 1.3 70.0 - - - +
424G GLN* 1.3 63.9 + - - +
426G TYR* 4.1 13.2 - - + -
427G ARG* 2.9 51.4 + - + +
495G THR* 5.4 0.4 - - - +
499G ASN* 3.5 31.2 + - + +
502G TRP* 3.6 55.4 - - + +
503G TYR* 4.6 0.9 - - + -
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Residues in contact with GLN 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G HIS* 3.1 34.2 + - - -
205G ARG* 4.5 7.4 + - - +
422G PRO* 3.0 5.4 + - + +
423G LEU* 1.3 78.5 - - - +
425G LEU* 1.3 62.5 + - + +
427G ARG* 3.9 7.6 + - - +
428G GLN* 3.2 38.6 + - + +
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Residues in contact with LEU 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G GLY* 3.5 26.9 - - - +
201G LEU 3.9 10.8 - - - +
202G HIS* 4.1 28.0 - - + +
203G VAL* 4.7 4.9 - - + +
204G PHE* 3.8 25.7 - - + -
421G LYS* 4.2 13.0 - - + -
422G PRO* 2.8 32.5 + - + +
424G GLN* 1.3 76.7 - - + +
426G TYR* 1.3 67.0 + - - +
428G GLN* 2.8 19.5 + - - +
429G TRP* 3.1 21.5 + - + +
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Residues in contact with TYR 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418G ASN* 3.5 26.1 + - + +
419G PRO* 3.5 23.9 - - + +
421G LYS* 4.2 2.7 - - - +
422G PRO 3.0 8.1 + - - +
423G LEU* 3.6 12.6 - - + +
425G LEU* 1.3 78.1 - - - +
427G ARG* 1.3 58.5 + - - +
429G TRP* 3.0 9.0 + - - +
430G THR* 2.9 40.5 + - - -
466G GLN* 2.7 29.8 + - - +
470G ILE* 3.4 21.2 - - + +
499G ASN* 3.7 30.1 - - + -
503G TYR* 3.5 27.4 - + - -
3007G ZAR 3.5 15.9 - - - -
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Residues in contact with ARG 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU* 2.9 50.3 + - + +
424G GLN* 4.1 7.4 - - - +
426G TYR* 1.3 75.4 - - - +
428G GLN* 1.3 63.1 + - + +
430G THR* 3.3 2.3 + - - -
431G ASP* 3.0 31.4 + - - +
502G TRP* 3.1 35.6 - - + -
503G TYR* 3.7 19.8 + - + +
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Residues in contact with GLN 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G HIS* 3.8 12.1 + - - -
204G PHE* 3.4 39.1 - - + +
424G GLN* 3.2 45.2 + - + +
425G LEU* 2.8 8.6 + - - +
427G ARG* 1.3 77.8 - - + +
429G TRP* 1.3 62.9 + - - +
431G ASP* 3.2 12.0 + - - +
432G ARG* 3.0 29.5 + - - +
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Residues in contact with TRP 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G VAL* 4.0 11.2 - - + +
204G PHE* 3.5 31.8 - + - -
255G ALA 5.6 0.2 - - - -
256G TYR* 3.6 27.9 - + + -
258G ASN* 5.3 0.7 - - - -
260G ILE* 3.8 11.9 - - + -
261G HIS* 3.7 37.5 - - + -
264G ASP* 3.4 30.1 + - + -
418G ASN* 3.5 41.1 - - + +
421G LYS* 5.4 4.5 - - + +
425G LEU* 3.1 33.5 + - + +
426G TYR* 3.0 6.8 + - - +
428G GLN* 1.3 74.2 - - - +
430G THR* 1.3 60.8 - - - +
432G ARG* 3.0 14.1 + - - +
433G ILE* 2.8 27.4 + - - +
3007G ZAR 3.3 8.2 - - - -
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Residues in contact with THR 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G TYR* 2.9 32.6 + - - -
427G ARG 3.6 4.0 - - - -
428G GLN 3.3 0.2 - - - -
429G TRP* 1.3 74.3 - - - +
431G ASP* 1.3 66.2 + - - +
433G ILE* 3.1 4.0 - - - +
434G MET* 3.1 23.6 + - + +
462G VAL* 3.8 19.3 - - + -
466G GLN* 3.4 28.2 - - + +
503G TYR* 3.2 27.1 + - - +
3007G ZAR 3.3 10.8 - - - -
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Residues in contact with ASP 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427G ARG* 3.0 22.6 + - - +
428G GLN* 3.5 10.8 - - - +
429G TRP 3.1 0.2 - - - -
430G THR* 1.3 79.6 - - - +
432G ARG* 1.3 59.5 + - + +
434G MET* 3.8 5.4 - - - +
435G GLU* 2.9 30.8 + - - +
462G VAL* 5.7 2.9 - - - +
503G TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G PHE* 3.1 35.3 - - - -
255G ALA* 2.8 55.2 + - + +
256G TYR* 4.0 7.6 - - + -
258G ASN* 4.0 8.7 - - - +
260G ILE* 3.7 21.6 - - - +
428G GLN* 3.0 19.7 + - - +
429G TRP* 3.0 20.6 + - - +
431G ASP* 1.3 74.8 - - + +
433G ILE* 1.3 64.4 + - - +
435G GLU* 3.1 10.9 + - - +
436G GLU* 2.9 19.9 + - - +
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Residues in contact with ILE 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256G TYR* 3.6 36.7 - - + -
257G HIS* 3.9 13.0 - - + -
429G TRP 2.8 13.5 + - - +
430G THR* 3.1 17.3 - - - +
432G ARG* 1.3 73.7 - - - +
434G MET* 1.3 71.7 + - + +
436G GLU* 3.2 3.1 + - + +
437G PHE* 2.9 65.2 + - + -
466G GLN* 4.6 1.1 - - - +
3007G ZAR 3.5 46.7 - - + +
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Residues in contact with MET 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G THR* 3.1 19.7 + - + +
431G ASP* 3.9 4.5 - - - +
433G ILE* 1.3 84.4 - - + +
435G GLU* 1.3 64.9 + - - +
437G PHE* 3.9 7.7 - - + +
438G PHE* 3.0 66.2 + - + -
454G MET* 3.6 45.5 - - + +
460G ALA* 4.1 6.7 - - + -
462G VAL* 3.9 39.5 - - + -
465G SER* 5.2 1.1 - - - +
466G GLN* 4.8 4.5 - - - -
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Residues in contact with GLU 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G ALA* 3.7 19.6 - - + +
431G ASP 2.9 19.5 + - - +
432G ARG* 3.1 11.1 + - - +
434G MET* 1.3 79.1 - - - +
436G GLU* 1.3 51.2 + - - +
438G PHE* 4.4 6.0 - - - +
439G PRO* 2.5 33.5 - - + +
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Residues in contact with GLU 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254G VAL* 3.2 13.7 - - + +
255G ALA* 4.1 9.0 - - + +
256G TYR* 2.7 31.9 + - - +
257G HIS* 2.7 37.3 + - - -
301G HIS* 4.1 0.5 - - - -
303G GLY* 3.3 35.6 - - - +
432G ARG 2.9 13.4 + - - +
433G ILE* 3.6 7.4 - - - +
434G MET 3.1 0.2 - - - -
435G GLU* 1.3 76.9 - - - +
437G PHE* 1.3 68.9 + - + +
438G PHE 3.3 0.4 - - - -
439G PRO* 3.0 13.6 - - - +
440G GLN* 3.5 10.9 + - - +
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Residues in contact with PHE 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G HIS* 5.3 4.7 - + - -
433G ILE* 2.9 50.4 + - + +
434G MET* 3.4 12.3 + - - +
436G GLU* 1.3 83.2 - - + +
438G PHE* 1.3 57.6 + - - +
440G GLN* 3.1 11.8 + - - +
441G GLY 2.9 22.2 + - - -
454G MET* 3.7 48.2 - - + +
455G CYS* 3.2 34.3 - - - +
3007G ZAR 4.0 30.1 - + - -
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Residues in contact with PHE 438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G MET* 3.0 44.3 + - + +
435G GLU* 4.4 4.9 - - - +
437G PHE* 1.3 77.0 - - - +
439G PRO* 1.3 57.4 - - + +
441G GLY* 2.9 3.5 + - - -
442G ASP* 2.7 42.1 + - - +
454G MET 3.4 19.3 - - - -
455G CYS 3.5 9.2 - - - +
457G LYS* 3.5 49.4 - - + -
460G ALA* 3.6 21.8 - - + -
462G VAL* 4.8 5.2 - - + -
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Residues in contact with PRO 439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435G GLU* 2.5 33.0 - - + +
436G GLU* 3.0 12.3 - - - +
438G PHE* 1.3 88.1 - - + +
440G GLN* 1.3 55.6 + - - +
442G ASP* 3.3 15.5 + - + +
443G ARG* 2.8 35.8 + - + +
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Residues in contact with GLN 440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G GLY 4.0 3.4 - - - +
304G VAL* 3.2 17.7 - - + -
305G SER* 3.0 45.6 + - - -
308G PHE* 3.7 20.6 - - + +
436G GLU 3.5 9.3 + - - +
437G PHE* 3.1 15.9 + - - +
438G PHE 3.0 0.4 - - - -
439G PRO* 1.3 78.0 - - - +
441G GLY* 1.3 59.9 + - - +
443G ARG* 3.1 9.3 + - - +
444G GLU* 2.8 53.2 + - - +
452G SER* 3.8 9.3 + - - -
455G CYS* 4.1 13.9 - - - -
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Residues in contact with GLY 441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437G PHE 2.9 7.7 + - - -
438G PHE 2.9 3.6 + - - -
440G GLN* 1.3 77.6 - - - +
442G ASP* 1.3 57.7 + - - +
444G GLU* 3.3 13.9 + - - -
445G ARG* 2.9 27.6 + - - +
451G ILE* 3.1 15.8 - - - +
455G CYS* 3.2 26.4 - - - +
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Residues in contact with ASP 442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438G PHE* 2.7 22.2 + - - +
439G PRO* 3.5 16.2 - - + +
441G GLY* 1.3 71.3 - - - +
443G ARG* 1.3 64.8 + - - +
445G ARG* 2.8 45.2 + - - +
446G GLU* 2.9 26.1 + - + +
457G LYS* 3.1 37.2 + - - +
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Residues in contact with ARG 443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G PRO 5.3 3.6 + - - -
304G VAL* 3.8 18.6 - - - +
308G PHE* 3.3 35.2 - - + -
439G PRO* 2.8 26.6 + - + +
440G GLN* 3.2 12.1 - - - +
442G ASP* 1.3 76.5 - - - +
444G GLU* 1.3 55.9 + - - +
446G GLU* 3.4 19.2 + - - +
447G ARG* 3.0 62.1 + - - +
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Residues in contact with GLU 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 3.6 24.1 - - + +
311G ASN* 5.7 1.2 + - - -
440G GLN* 2.8 33.0 + - - +
441G GLY* 3.6 14.6 - - - +
442G ASP 3.1 0.2 - - - -
443G ARG* 1.3 75.7 - - - +
445G ARG* 1.3 62.0 + - - +
447G ARG* 3.4 2.8 + - - -
448G GLY 3.0 2.6 + - - -
449G MET* 2.8 54.3 + - + +
450G GLU 4.1 5.6 - - - +
451G ILE* 3.7 9.9 - - + -
452G SER* 2.6 51.3 + - - -
455G CYS* 4.2 0.7 - - - +
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Residues in contact with ARG 445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441G GLY 2.9 15.7 + - - +
442G ASP* 2.8 39.6 + - - +
444G GLU* 1.3 76.2 - - - +
446G GLU* 1.3 65.1 + - + +
448G GLY* 3.1 12.0 + - - -
449G MET 4.6 1.8 - - - -
451G ILE* 3.3 17.5 - - + +
456G ASP* 3.0 28.5 + - - +
457G LYS* 3.8 15.6 - - - +
458G HIS* 3.7 26.9 + - - -
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Residues in contact with GLU 446 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442G ASP* 2.9 28.3 + - + +
443G ARG* 3.4 26.3 + - - +
445G ARG* 1.3 74.5 - - + +
447G ARG* 1.3 70.1 + - - +
448G GLY* 2.9 7.3 + - - -
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Residues in contact with ARG 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 4.1 7.3 - - + -
312G THR* 4.1 17.3 - - + +
443G ARG* 3.0 62.3 + - - +
444G GLU 3.7 1.1 - - - +
446G GLU* 1.3 84.3 + - - +
448G GLY* 1.3 58.8 + - - +
449G MET* 3.1 38.2 + - + +
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Residues in contact with GLY 448 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444G GLU 3.0 2.8 + - - -
445G ARG 3.1 11.2 + - - -
446G GLU 2.9 7.3 + - - -
447G ARG* 1.3 78.9 - - - +
449G MET* 1.3 64.7 + - - +
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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