Contacts of the helix formed by residues 422 - 448 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199K TRP* 4.9 3.4 - - + -
200K GLY* 3.8 24.5 - - - +
420K THR 4.8 0.7 - - - +
421K LYS* 1.3 86.4 - - + +
423K LEU* 1.3 68.4 + - - +
424K GLN* 3.2 5.4 - - + +
425K LEU* 2.9 33.6 + - + +
426K TYR 3.0 9.5 + - - -
495K THR* 4.7 7.4 - - + -
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Residues in contact with LEU 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421K LYS 3.3 2.2 + - - -
422K PRO* 1.3 71.3 - - - +
424K GLN* 1.3 62.3 + - - +
426K TYR* 4.1 12.8 - - + -
427K ARG* 2.9 53.2 + - + +
495K THR* 5.4 0.2 - - - +
499K ASN* 3.5 32.1 + - + +
502K TRP* 3.6 54.5 - - + +
503K TYR* 4.6 1.1 - - + -
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Residues in contact with GLN 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K HIS* 3.1 33.6 + - - -
205K ARG* 4.5 7.0 + - - +
422K PRO* 3.0 5.6 + - + +
423K LEU* 1.3 78.4 - - - +
425K LEU* 1.3 63.1 + - + +
427K ARG* 4.1 7.6 - - - +
428K GLN* 3.1 38.9 + - + +
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Residues in contact with LEU 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200K GLY* 3.5 26.7 - - - +
201K LEU 3.9 11.0 - - - +
202K HIS* 4.0 29.4 - - + +
203K VAL* 4.7 4.7 - - + +
204K PHE* 3.8 25.7 - - + -
421K LYS* 4.2 13.2 - - + -
422K PRO* 2.9 32.9 + - + +
424K GLN* 1.3 77.2 - - + +
426K TYR* 1.3 66.0 + - - +
428K GLN* 2.8 19.7 + - - +
429K TRP* 3.1 23.0 + - + +
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Residues in contact with TYR 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418K ASN* 3.4 26.8 + - + +
419K PRO* 3.5 24.9 - - + +
421K LYS 4.1 3.4 - - - +
422K PRO 3.0 8.7 + - - +
423K LEU* 3.7 11.7 - - + +
425K LEU* 1.3 78.7 - - - +
427K ARG* 1.3 56.8 + - - +
429K TRP* 3.1 9.1 + - - +
430K THR* 2.9 39.6 + - - -
466K GLN* 2.7 30.7 + - - +
470K ILE* 3.4 21.2 - - + +
499K ASN* 3.7 28.9 - - + -
503K TYR* 3.5 26.2 - + - -
3011K ZAR 3.5 14.4 - - - -
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Residues in contact with ARG 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423K LEU* 2.9 51.7 + - + +
424K GLN* 4.1 6.5 - - - +
426K TYR* 1.3 74.1 - - - +
428K GLN* 1.3 62.7 + - + +
430K THR* 3.3 2.6 + - - -
431K ASP* 3.0 31.2 + - - +
502K TRP* 3.1 36.5 - - + -
503K TYR* 3.6 19.2 + - - +
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Residues in contact with GLN 428 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K HIS* 3.8 12.2 + - - -
204K PHE* 3.4 39.3 - - + +
424K GLN* 3.1 47.1 + - + +
425K LEU* 2.8 9.0 + - - +
427K ARG* 1.3 76.4 - - + +
429K TRP* 1.3 62.4 + - - +
431K ASP* 3.3 11.0 + - - +
432K ARG* 3.0 29.6 + - - +
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Residues in contact with TRP 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K VAL* 4.0 11.0 - - + +
204K PHE* 3.5 31.6 - + - -
256K TYR* 3.6 27.7 - + - -
258K ASN* 5.3 0.4 - - - -
260K ILE* 3.8 12.1 - - + -
261K HIS* 3.7 38.4 - - + -
264K ASP* 3.4 30.5 + - + -
418K ASN* 3.5 40.9 - - + +
421K LYS* 5.4 3.9 - - + +
425K LEU* 3.1 35.1 + - + +
426K TYR* 3.4 7.4 - - - +
428K GLN* 1.3 76.7 - - - +
430K THR* 1.3 56.7 + - - +
432K ARG* 3.0 12.9 + - - +
433K ILE* 2.8 27.4 + - - +
3011K ZAR 3.3 8.2 - - - -
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Residues in contact with THR 430 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426K TYR* 2.9 33.4 + - - -
427K ARG 3.6 4.0 - - - -
429K TRP* 1.3 76.0 - - - +
431K ASP* 1.3 65.9 + - - +
433K ILE* 3.1 4.0 - - - +
434K MET* 3.0 28.9 + - + +
462K VAL* 3.8 20.2 - - + -
466K GLN* 3.4 28.3 - - + +
503K TYR* 3.2 26.5 + - - +
3011K ZAR 3.3 10.3 - - - -
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Residues in contact with ASP 431 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427K ARG* 3.0 22.6 + - - +
428K GLN* 3.5 10.8 - - - +
429K TRP 3.2 0.2 - - - -
430K THR* 1.3 79.2 - - - +
432K ARG* 1.3 59.4 + - + +
434K MET* 3.8 5.0 - - - +
435K GLU* 2.8 30.4 + - - +
462K VAL* 5.7 3.1 - - - +
503K TYR* 5.5 0.9 + - - -
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Residues in contact with ARG 432 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204K PHE* 3.1 36.9 - - - -
255K ALA* 2.7 53.0 + - + +
256K TYR* 4.0 7.4 - - + -
258K ASN* 4.0 8.5 - - - +
260K ILE* 3.8 21.4 - - - +
428K GLN* 3.0 19.3 + - - +
429K TRP* 3.0 17.8 + - - +
431K ASP* 1.3 75.2 - - + +
433K ILE* 1.3 65.4 + - - +
435K GLU* 3.1 12.1 + - - +
436K GLU* 2.9 19.8 + - - +
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Residues in contact with ILE 433 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256K TYR* 3.5 37.2 - - + -
257K HIS* 3.9 12.6 - - + -
429K TRP 2.8 13.3 + - - +
430K THR* 3.1 17.7 - - - +
432K ARG* 1.3 74.6 - - - +
434K MET* 1.3 71.3 + - + +
436K GLU* 3.2 3.8 + - + +
437K PHE* 2.9 64.3 + - + -
466K GLN* 4.6 0.9 - - - +
3011K ZAR 3.5 46.9 - - + +
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Residues in contact with MET 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430K THR* 3.0 18.9 + - + +
431K ASP* 3.9 4.7 - - - +
433K ILE* 1.3 84.9 - - + +
435K GLU* 1.3 66.4 + - - +
437K PHE* 4.2 6.3 - - + -
438K PHE* 3.1 58.6 + - + -
454K MET* 3.5 53.2 - - + +
460K ALA* 4.2 6.5 - - + -
462K VAL* 3.9 40.8 - - + -
465K SER* 5.2 1.1 - - - +
466K GLN* 4.8 4.5 - - - -
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Residues in contact with GLU 435 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K ALA* 3.7 19.8 - - + +
431K ASP 2.8 19.5 + - - +
432K ARG* 3.1 12.0 + - - +
434K MET* 1.3 77.8 - - - +
436K GLU* 1.3 52.5 + - - +
438K PHE* 4.4 6.0 - - - +
439K PRO* 2.6 34.0 - - + +
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Residues in contact with GLU 436 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K VAL* 3.2 14.8 - - + +
255K ALA* 4.1 8.7 - - + +
256K TYR* 2.8 32.4 + - - +
257K HIS* 2.7 38.1 + - - -
301K HIS* 4.1 0.5 - - - -
303K GLY* 3.2 35.3 - - - +
432K ARG 2.9 13.7 + - - +
433K ILE* 3.6 7.9 - - - +
434K MET 3.1 0.2 - - - -
435K GLU* 1.3 77.6 - - - +
437K PHE* 1.3 69.8 + - + +
438K PHE 3.3 0.4 - - - -
439K PRO* 3.1 14.2 - - - +
440K GLN* 3.5 10.7 + - - +
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Residues in contact with PHE 437 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257K HIS* 5.2 5.2 - + - -
303K GLY 6.1 0.2 - - - -
433K ILE* 2.9 51.7 + - + +
434K MET* 3.4 11.6 + - - +
436K GLU* 1.3 81.8 - - + +
438K PHE* 1.3 57.0 + - - +
440K GLN* 3.1 12.1 + - - +
441K GLY 2.9 22.2 + - - -
454K MET* 3.7 49.6 - - + +
455K CYS* 3.2 34.0 - - - +
3011K ZAR 3.9 30.1 - + - -
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Residues in contact with PHE 438 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434K MET* 3.1 43.4 + - + +
435K GLU* 4.4 4.7 - - - +
437K PHE* 1.3 74.5 - - - +
439K PRO* 1.4 60.5 - - + +
441K GLY* 2.9 3.3 + - - -
442K ASP* 2.7 39.4 + - - +
454K MET 3.4 20.9 - - - -
455K CYS 3.5 8.5 - - - +
457K LYS* 3.5 50.9 - - + +
460K ALA* 3.6 22.4 - - + -
462K VAL* 4.8 5.2 - - + -
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Residues in contact with PRO 439 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435K GLU* 2.6 31.2 - - + +
436K GLU* 3.1 12.1 - - - +
438K PHE* 1.4 88.9 - - + +
440K GLN* 1.3 55.6 + - - +
442K ASP* 3.4 14.7 - - + +
443K ARG* 2.8 34.7 + - + +
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Residues in contact with GLN 440 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K GLY 3.9 3.8 + - - +
304K VAL* 3.2 18.1 - - + -
305K SER* 3.0 45.7 + - - -
308K PHE* 3.8 21.7 - - + +
436K GLU 3.5 9.5 + - - +
437K PHE* 3.1 16.0 + - - +
438K PHE 3.1 0.6 - - - -
439K PRO* 1.3 78.6 - - - +
441K GLY* 1.3 54.3 + - - +
443K ARG* 3.1 10.0 + - - +
444K GLU* 2.8 58.0 + - - +
452K SER* 3.8 8.7 + - - -
455K CYS* 4.1 15.2 - - - -
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Residues in contact with GLY 441 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437K PHE 2.9 7.9 + - - -
438K PHE 2.9 3.8 + - - -
440K GLN* 1.3 78.7 - - - +
442K ASP* 1.3 56.0 + - - +
444K GLU* 3.3 14.8 + - - -
445K ARG* 2.9 28.0 + - - +
451K ILE* 3.1 15.6 - - - +
455K CYS* 3.2 25.5 - - - +
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Residues in contact with ASP 442 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438K PHE* 2.7 22.7 + - - +
439K PRO* 3.4 16.8 - - + +
441K GLY* 1.3 70.7 - - - +
443K ARG* 1.3 65.6 + - - +
445K ARG* 2.8 30.8 + - - +
446K GLU* 2.9 35.7 + - + +
457K LYS* 3.1 34.9 + - - +
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Residues in contact with ARG 443 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302K PRO 5.4 4.0 + - - -
304K VAL* 3.8 18.8 - - - +
308K PHE* 3.3 34.7 - - + -
439K PRO* 2.8 26.4 + - + +
440K GLN* 3.2 11.9 - - - +
442K ASP* 1.3 76.5 - - - +
444K GLU* 1.3 56.4 + - - +
446K GLU* 3.3 19.4 + - - +
447K ARG* 3.0 62.6 + - - +
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Residues in contact with GLU 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K PHE* 3.6 24.1 - - + +
311K ASN* 5.7 1.4 + - - -
440K GLN* 2.8 35.2 + - - +
441K GLY* 3.5 16.2 - - - +
442K ASP 3.1 0.2 - - - -
443K ARG* 1.3 70.5 - - - +
445K ARG* 1.3 61.2 + - - +
447K ARG 3.4 0.3 + - - -
448K GLY 3.0 2.9 + - - -
449K MET* 2.8 57.8 + - + +
450K GLU 4.1 5.1 - - - +
451K ILE* 3.7 8.7 - - + -
452K SER* 2.6 51.4 + - - -
455K CYS* 4.2 0.7 - - - +
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Residues in contact with ARG 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441K GLY 2.9 15.6 + - - +
442K ASP* 2.8 40.1 + - - +
444K GLU* 1.3 76.0 - - - +
446K GLU* 1.3 63.5 + - + +
448K GLY* 3.1 13.0 + - - -
449K MET 4.6 1.6 - - - -
451K ILE* 3.2 18.0 - - + +
456K ASP* 3.0 29.1 + - - +
457K LYS* 3.8 15.8 - - - +
458K HIS* 3.7 26.0 + - - -
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Residues in contact with GLU 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442K ASP* 2.9 29.4 + - + +
443K ARG* 3.3 26.7 + - - +
445K ARG* 1.3 74.4 - - - +
447K ARG* 1.3 66.1 + - - +
448K GLY* 2.9 11.4 + - - -
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Residues in contact with ARG 447 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K PHE* 4.0 8.0 - - + -
312K THR* 4.1 17.8 - - + +
443K ARG* 3.0 61.6 + - - +
444K GLU 3.7 0.9 - - - +
446K GLU* 1.3 85.4 + - - +
448K GLY* 1.3 58.9 + - - +
449K MET* 3.1 38.1 - - + +
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Residues in contact with GLY 448 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444K GLU 3.0 2.8 + - - -
445K ARG 3.5 10.5 - - - -
446K GLU 2.9 7.7 + - - -
447K ARG* 1.3 79.8 - - - +
449K MET* 1.3 64.8 + - - +
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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