Contacts of the helix formed by residues 422 - 448 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E TRP* 4.9 3.4 - - + -
200E GLY* 3.8 23.8 - - - +
420E THR 4.8 0.2 - - - +
421E LYS* 1.3 88.0 - - + +
423E LEU* 1.3 68.6 + - - +
424E GLN* 3.2 5.6 - - + +
425E LEU* 2.8 31.9 + - + +
426E TYR 3.1 9.4 + - - -
495E THR* 4.6 6.7 - - + -
509L GLN* 6.3 3.1 - - + -
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421E LYS 3.3 2.6 + - - -
422E PRO* 1.3 71.1 - - - +
424E GLN* 1.3 62.6 + - - +
426E TYR* 4.2 13.5 - - + -
427E ARG* 2.9 51.3 + - + +
495E THR* 5.4 0.4 - - - +
499E ASN* 3.5 31.2 + - + +
502E TRP* 3.6 55.0 - - + +
503E TYR* 4.6 0.9 - - + -
505L SER* 4.3 19.3 - - - +
506L THR* 4.7 4.5 - - - -
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Residues in contact with GLN 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E HIS* 3.1 34.7 + - - -
205E ARG* 4.5 3.9 + - - +
422E PRO* 3.0 5.2 + - + +
423E LEU* 1.3 78.6 - - - +
425E LEU* 1.3 62.7 + - + +
427E ARG* 3.9 8.0 + - - +
428E GLN* 3.2 37.2 + - + +
508L PRO* 4.3 22.4 - - + +
509L GLN 4.7 3.7 + - - +
510L SER* 3.7 22.0 + - - -
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Residues in contact with LEU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E GLY* 3.6 26.7 - - - +
201E LEU 3.9 11.4 - - - +
202E HIS* 4.0 28.9 - - + +
203E VAL* 4.7 5.2 - - + +
204E PHE* 3.8 26.5 - - + -
421E LYS* 4.2 13.5 - - + +
422E PRO* 2.8 31.8 + - + +
424E GLN* 1.3 79.6 - - + +
426E TYR* 1.3 66.3 + - - +
428E GLN* 2.9 18.5 + - - +
429E TRP* 3.1 23.1 + - + +
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Residues in contact with TYR 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418E ASN* 3.4 19.4 + - + +
419E PRO* 3.6 31.1 - - + +
421E LYS 4.2 2.5 - - - +
422E PRO 3.1 8.0 + - - +
423E LEU* 3.7 12.1 - - + +
425E LEU* 1.3 77.9 - - - +
427E ARG* 1.3 62.8 + - - +
429E TRP* 3.0 9.6 + - - +
430E THR* 2.9 35.3 + - - -
466E GLN* 2.7 30.0 + - - +
470E ILE* 3.4 20.6 - - + +
499E ASN* 3.7 28.9 - - + -
503E TYR* 3.4 26.9 - + - -
3005E ZAR 3.5 15.3 - - - -
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Residues in contact with ARG 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 2.9 49.1 + - + +
424E GLN* 4.1 6.7 - - - +
426E TYR* 1.3 76.2 - - - +
428E GLN* 1.3 62.3 + - + +
430E THR* 3.3 2.3 + - - -
431E ASP* 3.0 31.7 + - - +
502E TRP* 3.2 29.5 - - + -
503E TYR* 3.6 18.7 + - - +
427L ARG* 5.2 8.7 - - - +
502L TRP* 6.2 0.2 - - - -
506L THR* 3.9 24.9 - - - +
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Residues in contact with GLN 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E HIS* 3.7 12.0 + - - -
204E PHE* 3.3 40.0 - - + +
424E GLN* 3.2 46.6 + - + +
425E LEU* 2.9 9.6 + - - +
427E ARG* 1.3 77.7 - - + +
429E TRP* 1.3 63.0 + - - +
431E ASP* 3.3 11.1 + - - +
432E ARG* 3.1 30.3 + - - +
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Residues in contact with TRP 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E VAL* 4.0 12.0 - - + +
204E PHE* 3.5 27.6 - + - -
255E ALA 5.6 0.2 - - - -
256E TYR* 3.6 29.2 - + - -
258E ASN* 5.3 0.7 - - - -
260E ILE* 3.8 15.0 - - + -
261E HIS* 3.7 37.0 - - + -
264E ASP* 3.5 30.3 + - + -
418E ASN* 3.5 40.4 - - + +
421E LYS* 5.4 4.1 - - + +
425E LEU* 3.1 33.7 + - + +
426E TYR* 3.0 7.5 + - - +
428E GLN* 1.3 78.0 - - - +
430E THR* 1.3 58.5 + - - +
432E ARG* 3.0 12.8 + - - +
433E ILE* 2.8 26.9 + - - +
3005E ZAR 3.3 10.6 - - - -
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Residues in contact with THR 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426E TYR* 2.9 32.2 + - - -
427E ARG 3.6 4.5 - - - -
428E GLN 3.3 0.2 - - - -
429E TRP* 1.3 75.9 - - - +
431E ASP* 1.3 65.0 + - - +
433E ILE* 3.0 4.6 - - - +
434E MET* 3.0 29.1 + - + +
462E VAL* 3.8 21.1 - - + -
466E GLN* 3.5 27.7 - - + +
503E TYR* 3.2 27.3 + - - +
3005E ZAR 3.3 10.7 - - - -
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Residues in contact with ASP 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E ARG* 3.0 22.8 + - - +
428E GLN* 3.5 10.9 - - - +
429E TRP 3.2 0.2 - - - -
430E THR* 1.3 80.2 - - - +
432E ARG* 1.3 59.1 + - + +
434E MET* 3.8 4.6 - - - +
435E GLU* 2.9 30.8 + - - +
462E VAL* 5.7 3.1 - - - +
503E TYR* 5.5 0.7 + - - -
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Residues in contact with ARG 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E PHE* 3.1 37.3 - - - -
255E ALA* 2.8 49.1 + - + +
256E TYR* 4.0 7.0 - - + -
258E ASN* 4.0 9.1 - - - +
260E ILE* 3.7 22.3 - - - +
428E GLN* 3.1 20.0 + - - +
429E TRP* 3.0 17.1 + - - +
431E ASP* 1.3 75.0 - - + +
433E ILE* 1.3 60.5 + - - +
435E GLU* 3.1 10.9 + - - +
436E GLU* 2.9 24.1 + - - +
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Residues in contact with ILE 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E TYR* 3.6 37.4 - - + -
257E HIS* 3.9 12.8 - - + -
429E TRP 2.8 12.4 + - - +
430E THR* 3.0 17.7 - - - +
432E ARG* 1.3 73.1 - - - +
434E MET* 1.3 71.5 + - + +
436E GLU* 3.2 3.2 + - + +
437E PHE* 2.9 65.5 + - + -
466E GLN* 4.6 1.1 - - - +
3005E ZAR 3.6 47.1 - - + +
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Residues in contact with MET 434 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E THR* 3.0 19.8 + - + +
431E ASP* 3.9 4.9 - - - +
433E ILE* 1.3 86.7 - - + +
435E GLU* 1.3 65.0 + - - +
437E PHE* 3.8 6.2 - - - +
438E PHE* 3.1 59.4 + - + -
454E MET* 3.6 52.0 - - + +
460E ALA* 4.2 6.7 - - + -
462E VAL* 3.9 40.4 - - + +
465E SER* 5.2 0.9 - - - +
466E GLN* 4.7 4.9 - - - -
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Residues in contact with GLU 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255E ALA* 3.7 20.2 - - + +
431E ASP 2.9 19.0 + - - +
432E ARG* 3.1 12.2 + - - +
434E MET* 1.3 78.3 - - - +
436E GLU* 1.3 51.0 + - - +
438E PHE* 4.4 5.6 - - - +
439E PRO* 2.5 34.1 - - + +
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Residues in contact with GLU 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E VAL* 3.2 15.4 - - + +
255E ALA* 4.1 9.0 - - + +
256E TYR* 2.8 31.3 + - - +
257E HIS* 2.8 38.5 + - - -
301E HIS* 4.1 0.7 - - - -
303E GLY* 3.2 34.9 - - - +
432E ARG 2.9 14.0 + - - +
433E ILE* 3.6 6.7 - - - +
435E GLU* 1.3 78.2 - - - +
437E PHE* 1.3 70.4 + - + +
438E PHE 3.3 0.4 - - - -
439E PRO* 3.1 13.1 - - - +
440E GLN* 3.5 11.6 + - - +
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Residues in contact with PHE 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E HIS* 5.3 5.2 - + - -
303E GLY 6.1 0.7 - - - -
433E ILE* 2.9 51.2 + - + +
434E MET* 3.4 12.1 + - - +
436E GLU* 1.3 81.8 - - + +
438E PHE* 1.3 57.5 + - - +
440E GLN* 3.1 12.3 + - - +
441E GLY 2.9 22.0 + - - -
454E MET* 3.7 48.5 - - + +
455E CYS* 3.2 32.9 - - - +
3005E ZAR 4.0 28.9 - + - -
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Residues in contact with PHE 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434E MET* 3.1 38.0 + - + -
435E GLU* 4.4 4.5 - - - +
437E PHE* 1.3 74.1 - - - +
439E PRO* 1.4 60.1 - - + +
441E GLY* 2.9 2.6 + - - -
442E ASP* 2.7 43.0 + - - +
454E MET 3.4 18.8 - - - -
455E CYS 3.5 9.2 - - - +
457E LYS* 3.5 48.5 - - + -
460E ALA* 3.6 27.8 - - + -
462E VAL* 4.9 5.4 - - + -
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Residues in contact with PRO 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435E GLU* 2.5 31.6 - - + +
436E GLU* 3.1 11.9 - - - +
438E PHE* 1.4 87.8 - - + +
440E GLN* 1.3 55.4 + - - +
442E ASP* 3.5 14.8 - - + +
443E ARG* 2.8 35.4 + - + +
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Residues in contact with GLN 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E GLY 4.0 3.9 + - - +
304E VAL* 3.2 17.3 - - + -
305E SER* 2.9 45.7 + - - -
308E PHE* 3.8 20.7 - - + +
436E GLU 3.5 8.7 + - - +
437E PHE* 3.1 16.3 + - - +
438E PHE 3.0 0.4 - - - -
439E PRO* 1.3 78.4 - - - +
441E GLY* 1.3 60.4 + - - +
443E ARG* 3.1 8.4 + - - +
444E GLU* 2.8 52.6 + - - +
452E SER* 3.8 9.1 + - - -
455E CYS* 4.1 15.4 - - + -
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Residues in contact with GLY 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437E PHE 2.9 7.9 + - - -
438E PHE 2.9 3.8 + - - -
440E GLN* 1.3 78.0 - - - +
442E ASP* 1.3 56.9 + - - +
444E GLU* 3.3 14.5 + - - -
445E ARG* 2.9 28.1 + - - +
451E ILE* 3.0 16.2 - - - +
455E CYS* 3.2 25.7 - - - +
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Residues in contact with ASP 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438E PHE* 2.7 21.6 + - - +
439E PRO* 3.5 17.3 - - + +
441E GLY* 1.3 70.8 - - - +
443E ARG* 1.3 65.8 + - - +
445E ARG* 2.9 39.1 + - - +
446E GLU* 2.9 26.0 + - + +
457E LYS* 3.0 37.0 + - - +
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Residues in contact with ARG 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E PRO 5.3 3.8 + - - -
304E VAL* 3.8 18.6 - - - +
308E PHE* 3.4 35.0 - - + -
439E PRO* 2.8 26.1 + - + +
440E GLN* 3.2 11.4 - - - +
442E ASP* 1.3 76.6 - - - +
444E GLU* 1.3 56.9 + - - +
446E GLU* 3.4 18.8 + - - +
447E ARG* 3.0 62.2 + - - +
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Residues in contact with GLU 444 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E PHE* 3.6 23.3 - - + +
311E ASN* 5.7 1.4 + - - -
440E GLN* 2.8 33.1 + - - +
441E GLY* 3.6 14.6 + - - +
443E ARG* 1.3 75.5 - - - +
445E ARG* 1.3 62.4 + - - +
447E ARG 3.4 0.5 + - - -
448E GLY 3.0 3.1 + - - -
449E MET* 2.8 56.2 + - + +
450E GLU 4.1 5.6 - - - +
451E ILE* 3.6 9.1 - - + -
452E SER* 2.6 51.5 + - - -
455E CYS* 4.2 0.3 - - - +
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Residues in contact with ARG 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441E GLY 2.9 15.0 + - - +
442E ASP* 2.9 39.8 + - - +
444E GLU* 1.3 76.0 - - - +
446E GLU* 1.3 63.0 + - + +
448E GLY* 3.1 12.4 + - - -
449E MET 4.6 1.6 - - - -
451E ILE* 3.2 18.4 - - + +
456E ASP* 3.0 29.1 + - - +
457E LYS* 3.9 15.2 - - - +
458E HIS* 3.8 27.2 + - - -
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Residues in contact with GLU 446 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442E ASP* 2.9 28.6 + - + +
443E ARG* 3.4 26.0 + - - +
445E ARG* 1.3 74.5 - - + +
447E ARG* 1.3 66.6 + - - +
448E GLY* 2.9 11.0 + - - -
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Residues in contact with ARG 447 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E PHE* 4.0 8.8 - - + -
312E THR* 4.1 17.2 - - + +
443E ARG* 3.0 62.3 + - - +
444E GLU 3.4 1.3 + - - +
446E GLU* 1.3 84.6 + - - +
448E GLY* 1.3 58.7 + - - +
449E MET* 3.1 37.9 + - + +
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Residues in contact with GLY 448 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444E GLU 3.0 2.6 + - - -
445E ARG* 3.1 11.2 + - - -
446E GLU 2.9 6.9 - - - -
447E ARG* 1.3 79.6 - - - +
449E MET* 1.3 64.9 + - - +
450E GLU 4.1 0.3 + - - -
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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