Contacts of the helix formed by residues 422 - 448 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 4.9 3.4 - - + -
200F GLY* 3.8 24.2 - - - +
421F LYS* 1.4 88.9 - - + +
423F LEU* 1.3 66.4 + - - +
424F GLN* 3.2 5.4 - - + +
425F LEU* 2.8 33.4 + - + +
426F TYR 3.1 9.7 + - - -
495F THR* 4.7 7.2 - - + -
509J GLN* 5.6 12.1 - - + +
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Residues in contact with LEU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421F LYS 3.4 2.4 + - - -
422F PRO* 1.3 71.4 - - - +
424F GLN* 1.3 63.0 + - - +
426F TYR* 4.2 12.8 - - + -
427F ARG* 2.9 51.0 + - + +
495F THR* 5.4 0.4 - - - +
499F ASN* 3.5 31.2 + - + +
502F TRP* 3.6 54.5 - - + +
503F TYR* 4.6 1.1 - - + -
505J SER* 4.5 10.1 - - - +
506J THR* 4.5 17.3 - - + -
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Residues in contact with GLN 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F HIS* 3.1 34.5 + - - -
205F ARG* 4.5 4.3 + - - +
422F PRO* 3.0 5.4 + - + +
423F LEU* 1.3 79.0 - - - +
425F LEU* 1.3 60.7 + - + +
427F ARG* 4.1 7.0 - - - +
428F GLN* 3.1 41.5 + - + +
508J PRO* 3.9 26.5 - - + +
509J GLN 4.7 3.3 + - - +
510J SER* 3.5 21.8 + - - -
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Residues in contact with LEU 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F GLY* 3.5 26.9 - - - +
201F LEU 3.8 12.6 - - - +
202F HIS* 4.0 27.6 - - + +
203F VAL* 4.7 5.6 - - + +
204F PHE* 3.8 26.5 - - + -
421F LYS* 4.2 13.2 - - + +
422F PRO* 2.8 31.8 + - + +
424F GLN* 1.3 78.5 - - + +
426F TYR* 1.3 66.6 + - - +
428F GLN* 2.9 19.2 + - - +
429F TRP* 3.1 22.8 + - + +
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Residues in contact with TYR 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F ASN* 3.4 19.6 + - + +
419F PRO* 3.5 30.5 - - + +
421F LYS 4.2 4.0 - - - +
422F PRO 3.1 7.9 + - - +
423F LEU* 3.7 10.1 - - + +
425F LEU* 1.3 77.6 - - - +
427F ARG* 1.3 57.1 + - - +
429F TRP* 3.0 9.8 + - - +
430F THR* 2.9 41.0 + - - -
466F GLN* 2.6 30.7 + - - +
470F ILE* 3.4 21.6 - - + +
499F ASN* 3.7 28.3 - - + -
503F TYR* 3.5 26.9 - + - -
3006F ZAR 3.5 15.3 - - - -
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Residues in contact with ARG 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU* 2.9 49.8 + - + +
424F GLN* 4.1 6.3 - - - +
426F TYR* 1.3 74.8 - - - +
428F GLN* 1.3 61.8 + - + +
430F THR* 3.3 2.4 + - - -
431F ASP* 3.0 31.8 + - - +
502F TRP* 3.1 35.9 - - + -
503F TYR* 3.6 19.7 + - - +
427J ARG* 5.5 5.7 - - - +
506J THR* 4.4 15.2 - - - +
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Residues in contact with GLN 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F HIS* 3.7 12.6 + - - -
204F PHE* 3.4 39.3 - - + +
424F GLN* 3.1 46.3 + - + +
425F LEU* 2.9 9.0 + - - +
427F ARG* 1.3 76.4 - - + +
429F TRP* 1.3 62.8 + - - +
431F ASP* 3.3 10.7 + - - +
432F ARG* 3.1 29.5 + - - +
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Residues in contact with TRP 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F VAL* 4.0 11.4 - - + +
204F PHE* 3.5 33.2 - + - -
256F TYR* 3.6 28.5 - + + -
258F ASN* 5.3 0.7 - - - -
260F ILE* 3.9 11.7 - - + -
261F HIS* 3.7 38.1 - - + -
264F ASP* 3.5 30.4 + - + -
418F ASN* 3.5 41.1 - - + +
421F LYS* 5.4 4.3 - - + +
425F LEU* 3.1 33.0 + - + +
426F TYR* 3.0 7.5 + - - +
428F GLN* 1.3 74.4 - - - +
430F THR* 1.3 55.5 + - - +
432F ARG* 3.0 13.9 + - - +
433F ILE* 2.8 32.1 + - - +
3006F ZAR 3.4 10.0 - - - -
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Residues in contact with THR 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426F TYR* 2.9 32.6 + - - -
427F ARG 3.3 4.2 + - - -
429F TRP* 1.3 76.2 - - - +
431F ASP* 1.3 64.2 + - - +
433F ILE* 3.1 4.8 - - - +
434F MET* 3.0 30.1 + - + +
462F VAL* 3.8 20.0 - - + -
466F GLN* 3.4 27.9 - - + +
503F TYR* 3.2 25.9 + - - +
3006F ZAR 3.3 10.1 - - - -
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Residues in contact with ASP 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427F ARG* 3.0 22.7 + - - +
428F GLN* 3.5 11.1 - - - +
429F TRP 3.2 0.2 - - - -
430F THR* 1.3 79.3 - - - +
432F ARG* 1.3 59.8 + - + +
434F MET* 3.8 4.4 - - - +
435F GLU* 2.9 30.2 + - - +
462F VAL* 5.7 2.9 - - - +
503F TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F PHE* 3.1 38.1 - - - -
255F ALA* 2.7 57.6 + - + +
256F TYR* 4.0 7.0 - - + -
258F ASN* 4.0 9.7 - - - +
260F ILE* 3.7 21.9 - - - +
428F GLN* 3.1 18.4 + - - +
429F TRP* 3.0 18.2 + - - +
431F ASP* 1.3 75.0 - - + +
433F ILE* 1.3 65.2 + - - +
435F GLU* 3.1 10.2 + - - +
436F GLU* 3.0 19.6 + - - +
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Residues in contact with ILE 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F TYR* 3.6 36.1 - - + -
257F HIS* 3.9 12.8 - - + +
429F TRP 2.8 13.1 + - - +
430F THR* 3.1 15.0 - - - +
432F ARG* 1.3 73.1 - - - +
434F MET* 1.3 70.2 + - + +
436F GLU* 3.2 3.8 + - + +
437F PHE* 2.9 65.2 + - + -
466F GLN* 4.6 0.7 - - - +
3006F ZAR 3.6 47.6 - - + +
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Residues in contact with MET 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430F THR* 3.0 18.7 + - + +
431F ASP* 3.9 5.2 - - - +
433F ILE* 1.3 85.9 - - + +
435F GLU* 1.3 66.0 + - - +
437F PHE* 3.8 6.9 - - + +
438F PHE* 3.1 65.5 + - + -
454F MET* 3.5 47.3 - - + +
460F ALA* 4.2 6.5 - - + -
462F VAL* 3.9 39.9 - - + -
465F SER* 5.2 0.9 - - - +
466F GLN* 4.8 5.2 - - - -
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Residues in contact with GLU 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ALA* 3.7 20.4 - - + +
431F ASP 2.9 19.4 + - - +
432F ARG* 3.1 11.6 + - - +
434F MET* 1.3 79.5 - - - +
436F GLU* 1.3 51.2 + - - +
438F PHE* 4.4 5.6 - - - +
439F PRO* 2.5 34.5 - - + +
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Residues in contact with GLU 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F VAL* 3.2 14.9 - - + +
255F ALA* 4.1 9.2 - - + +
256F TYR* 2.8 32.4 + - + +
257F HIS* 2.7 38.1 + - - -
301F HIS* 4.1 0.3 - - - -
303F GLY* 3.2 36.4 - - - +
432F ARG 3.0 14.3 + - - +
433F ILE* 3.6 5.8 - - - +
435F GLU* 1.3 76.5 - - - +
437F PHE* 1.3 70.2 + - + +
438F PHE 3.3 0.4 - - - -
439F PRO* 3.1 14.1 - - - +
440F GLN* 3.5 11.1 + - - +
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Residues in contact with PHE 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F HIS* 5.3 4.9 - + - -
303F GLY 6.1 0.2 - - - -
433F ILE* 2.9 51.8 + - + +
434F MET* 3.4 11.0 + - - +
436F GLU* 1.3 81.9 - - + +
438F PHE* 1.3 57.8 + - - +
440F GLN* 3.1 14.1 + - - +
441F GLY 2.9 23.0 + - - -
454F MET* 3.7 49.4 - - + +
455F CYS* 3.3 31.9 - - - +
3006F ZAR 3.9 29.6 - + - -
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Residues in contact with PHE 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F MET* 3.1 43.4 + - + -
435F GLU* 4.4 4.3 - - - +
437F PHE* 1.3 76.2 - - - +
439F PRO* 1.4 57.6 - - + +
441F GLY* 2.9 2.1 + - - -
442F ASP* 2.7 43.3 + - - +
454F MET 3.4 19.3 - - - -
455F CYS 3.5 9.7 - - - +
457F LYS* 3.5 46.7 - - + -
460F ALA* 3.6 22.0 - - + -
462F VAL* 4.8 5.2 - - + -
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Residues in contact with PRO 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435F GLU* 2.5 31.0 - - + +
436F GLU* 3.1 11.9 - - - +
438F PHE* 1.4 89.1 - - + +
440F GLN* 1.3 57.1 + - - +
442F ASP* 3.5 14.9 - - + +
443F ARG* 2.8 35.4 + - + +
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Residues in contact with GLN 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F GLY 4.0 4.2 + - - +
304F VAL* 3.2 17.0 - - + -
305F SER* 3.0 46.3 + - - -
308F PHE* 3.8 21.3 - - + +
436F GLU 3.5 8.4 + - - +
437F PHE* 3.1 16.6 + - - +
438F PHE 3.0 0.4 - - - -
439F PRO* 1.3 80.4 - - - +
441F GLY* 1.3 53.5 + - - +
443F ARG* 3.0 9.3 + - - +
444F GLU* 2.8 56.4 + - - +
452F SER* 3.8 9.1 + - - -
455F CYS* 4.1 13.9 - - - -
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Residues in contact with GLY 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437F PHE 2.9 10.7 + - - -
438F PHE 2.9 0.6 + - - -
440F GLN* 1.3 78.6 - - - +
442F ASP* 1.3 56.7 + - - +
444F GLU* 3.3 14.5 + - - -
445F ARG* 2.9 27.9 + - - +
451F ILE* 3.1 16.6 - - - +
455F CYS* 3.2 25.5 - - - +
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Residues in contact with ASP 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438F PHE* 2.7 21.0 + - - +
439F PRO* 3.5 16.4 - - + +
441F GLY* 1.3 71.5 - - - +
443F ARG* 1.3 65.9 + - - +
445F ARG* 2.8 35.7 + - - +
446F GLU* 2.9 35.1 + - + +
457F LYS* 3.1 35.3 + - - +
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Residues in contact with ARG 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F PRO 5.4 3.6 + - - -
304F VAL* 3.8 19.0 - - - +
308F PHE* 3.3 34.6 - - + -
439F PRO 2.8 24.8 + - - +
440F GLN* 3.1 12.3 - - - +
442F ASP* 1.3 76.6 - - + +
444F GLU* 1.3 56.4 + - - +
446F GLU* 3.4 18.7 + - - +
447F ARG* 3.0 61.6 + - - +
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Residues in contact with GLU 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F PHE* 3.6 24.5 - - + +
311F ASN* 5.7 1.2 + - - -
440F GLN* 2.8 31.8 + - - +
441F GLY* 3.5 16.7 + - - +
443F ARG* 1.3 75.4 - - - +
445F ARG* 1.3 58.7 + - - +
447F ARG* 3.4 3.7 + - - -
448F GLY 3.0 6.2 + - - -
449F MET* 2.8 53.6 + - + +
450F GLU 4.1 5.2 - - - +
451F ILE* 3.6 9.2 - - + -
452F SER* 2.6 50.8 + - - -
455F CYS* 4.2 0.2 - - - +
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Residues in contact with ARG 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441F GLY 2.9 15.3 + - - +
442F ASP* 2.8 39.4 + - - +
444F GLU* 1.3 76.2 - - - +
446F GLU* 1.3 63.5 + - + +
448F GLY* 3.1 12.9 + - - -
449F MET 4.6 1.1 - - - -
451F ILE* 3.3 18.1 - - + +
456F ASP* 3.0 28.9 + - - +
457F LYS* 3.8 16.0 - - - +
458F HIS* 3.8 26.5 + - - -
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Residues in contact with GLU 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442F ASP* 2.9 28.1 + - + +
443F ARG* 3.4 25.7 + - - +
445F ARG* 1.3 73.8 - - + +
447F ARG* 1.3 65.3 + - - +
448F GLY* 2.9 12.2 + - - -
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Residues in contact with ARG 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F PHE* 4.0 8.4 - - + -
312F THR* 4.1 16.6 - - + +
443F ARG* 3.0 61.9 + - - +
444F GLU 3.4 1.1 + - - +
446F GLU* 1.3 85.1 + - - +
448F GLY* 1.3 58.6 + - - +
449F MET* 3.1 38.3 + - + +
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Residues in contact with GLY 448 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444F GLU 3.0 2.6 + - - -
445F ARG 3.6 9.6 - - - -
446F GLU 2.9 7.1 + - - -
447F ARG* 1.3 79.1 - - - +
449F MET* 1.3 64.9 + - - +
450F GLU 4.1 0.2 + - - -
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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