Contacts of the helix formed by residues 422 - 448 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 4.9 3.4 - - + -
200H GLY* 3.8 23.8 - - - +
420H THR 4.8 0.4 - - - +
421H LYS* 1.3 89.4 - - + +
423H LEU* 1.3 67.8 + - - +
424H GLN* 3.2 5.6 - - + +
425H LEU* 2.9 32.2 + - + +
426H TYR 3.1 9.7 + - - -
495H THR* 4.7 6.5 - - + -
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Residues in contact with LEU 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H LYS 3.3 2.4 + - - -
422H PRO* 1.3 71.1 - - - +
424H GLN* 1.3 62.4 + - - +
426H TYR* 4.1 13.0 - - + -
427H ARG* 2.9 52.3 + - + +
495H THR* 5.4 0.4 - - - +
499H ASN* 3.5 31.5 + - + +
502H TRP* 3.6 54.3 - - + +
503H TYR* 4.6 0.9 - - + -
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Residues in contact with GLN 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H HIS* 3.1 34.8 + - - -
205H ARG* 4.5 6.8 + - - +
422H PRO* 3.0 5.4 + - + +
423H LEU* 1.3 79.5 - - - +
425H LEU* 1.3 62.9 + - + +
427H ARG* 3.9 7.0 + - - +
428H GLN* 3.2 40.3 + - + +
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Residues in contact with LEU 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H GLY* 3.6 26.7 - - - +
201H LEU 3.9 11.0 - - - +
202H HIS* 4.1 28.5 - - + +
203H VAL* 4.7 5.2 - - + +
204H PHE* 3.8 26.5 - - + -
421H LYS* 4.2 13.9 - - + +
422H PRO* 2.9 32.5 + - + +
424H GLN* 1.3 76.5 - - + +
426H TYR* 1.3 66.2 + - - +
428H GLN* 2.9 19.1 + - - +
429H TRP* 3.1 23.1 + - + +
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Residues in contact with TYR 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418H ASN* 3.5 19.4 + - + +
419H PRO* 3.6 30.9 - - + +
421H LYS 4.2 2.5 - - - +
422H PRO 3.1 8.3 + - - +
423H LEU* 3.6 11.4 - - + +
425H LEU* 1.3 78.3 - - - +
427H ARG* 1.3 57.8 + - - +
429H TRP* 3.0 8.9 + - - +
430H THR* 2.9 40.2 + - - -
466H GLN* 2.7 31.5 + - - +
470H ILE* 3.4 21.5 - - + +
499H ASN* 3.7 28.0 - - + -
503H TYR* 3.5 26.4 - + - -
3008H ZAR 3.5 15.5 - - - -
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Residues in contact with ARG 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H LEU* 2.9 50.1 + - + +
424H GLN* 4.1 6.5 - - - +
426H TYR* 1.3 75.4 - - - +
428H GLN* 1.3 62.1 + - + +
430H THR* 3.3 2.3 + - - -
431H ASP* 3.0 31.8 + - - +
502H TRP* 3.2 35.1 - - + -
503H TYR* 3.6 20.4 + - + +
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Residues in contact with GLN 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H HIS* 3.7 12.0 + - - -
204H PHE* 3.3 38.4 - - + +
424H GLN* 3.2 46.5 + - + +
425H LEU* 2.9 9.0 + - - +
427H ARG* 1.3 76.5 - - + +
429H TRP* 1.3 63.5 + - - +
431H ASP* 3.3 10.5 + - - +
432H ARG* 3.1 30.9 + - - +
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Residues in contact with TRP 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H VAL* 4.0 11.6 - - + +
204H PHE* 3.5 31.1 - + - -
256H TYR* 3.6 29.8 - + + -
258H ASN* 5.3 0.7 - - - -
260H ILE* 3.9 11.7 - - + -
261H HIS* 3.7 37.9 - - + -
264H ASP* 3.5 30.3 + - + -
418H ASN* 3.5 40.5 - - + +
421H LYS* 5.5 4.5 - - + +
425H LEU* 3.1 33.3 + - + +
426H TYR* 3.0 8.8 + - - +
428H GLN* 1.3 74.2 - - - +
430H THR* 1.3 60.5 + - - +
432H ARG* 3.0 13.2 + - - +
433H ILE* 2.8 27.0 + - - +
3008H ZAR 3.3 9.8 - - - -
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Residues in contact with THR 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426H TYR* 2.9 32.4 + - - -
427H ARG 3.6 4.3 - - - -
429H TRP* 1.3 76.9 - - - +
431H ASP* 1.3 63.9 + - - +
433H ILE* 3.1 4.0 - - - +
434H MET* 3.0 28.6 + - + +
462H VAL* 3.8 20.4 - - + -
466H GLN* 3.4 28.6 - - + +
503H TYR* 3.2 26.1 + - - +
3008H ZAR 3.3 11.4 - - - -
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Residues in contact with ASP 431 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ARG* 3.0 23.1 + - - +
428H GLN* 3.5 10.9 - - - +
430H THR* 1.3 79.9 - - - +
432H ARG* 1.3 59.4 + - + +
434H MET* 3.4 4.5 + - - +
435H GLU* 2.9 30.8 + - - +
462H VAL* 5.7 2.8 - - - +
503H TYR* 5.5 0.3 + - - -
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Residues in contact with ARG 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H PHE* 3.1 35.8 - - - -
255H ALA* 2.8 56.9 + - + +
256H TYR* 4.0 7.9 - - + -
258H ASN* 4.0 8.7 - - - +
260H ILE* 3.7 21.8 - - - +
428H GLN* 3.1 19.1 + - - +
429H TRP* 3.0 17.3 + - - +
431H ASP* 1.3 75.2 - - + +
433H ILE* 1.3 66.6 + - - +
435H GLU* 3.1 10.9 + - - +
436H GLU* 3.0 19.2 + - - +
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Residues in contact with ILE 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256H TYR* 3.6 38.5 - - + -
257H HIS* 3.9 12.1 - - + -
429H TRP 2.8 13.0 + - - +
430H THR* 3.1 17.3 - - - +
432H ARG* 1.3 72.9 - - - +
434H MET* 1.3 70.8 + - + +
436H GLU* 3.2 3.8 + - + +
437H PHE* 2.9 66.3 + - + -
466H GLN* 4.6 1.1 - - - +
3008H ZAR 3.5 46.4 - - + +
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Residues in contact with MET 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430H THR* 3.0 20.4 + - + +
431H ASP* 3.9 4.3 - - - +
433H ILE* 1.3 86.2 - - + +
435H GLU* 1.3 65.9 + - - +
437H PHE* 4.2 6.5 - - - -
438H PHE* 3.1 64.9 + - + -
454H MET* 3.6 47.3 - - + +
460H ALA* 4.2 6.5 - - + -
462H VAL* 3.8 39.7 - - + -
465H SER* 5.2 1.1 - - - +
466H GLN* 4.8 4.9 - - - -
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Residues in contact with GLU 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255H ALA* 3.7 19.7 - - + +
431H ASP 2.9 18.9 + - - +
432H ARG* 3.1 11.9 + - - +
434H MET* 1.3 78.7 - - - +
436H GLU* 1.3 50.5 + - - +
438H PHE* 4.4 6.2 - - - +
439H PRO* 2.6 33.3 - - + +
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Residues in contact with GLU 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254H VAL* 3.2 15.4 - - + +
255H ALA* 4.1 8.7 - - + +
256H TYR* 2.8 29.9 + - - +
257H HIS* 2.8 38.3 + - - -
301H HIS* 4.1 0.5 - - - -
303H GLY* 3.2 35.2 - - - +
432H ARG 3.0 14.4 + - - +
433H ILE* 3.6 7.6 - - + +
434H MET 3.1 0.2 - - - -
435H GLU* 1.3 76.6 - - - +
437H PHE* 1.3 69.2 + - + +
438H PHE 3.3 0.4 - - - -
439H PRO* 3.0 13.6 - - - +
440H GLN* 3.5 11.6 + - - +
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Residues in contact with PHE 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H HIS* 5.3 4.9 - + - -
433H ILE* 2.9 51.8 + - + +
434H MET* 3.4 10.5 + - - +
436H GLU* 1.3 82.3 - - + +
438H PHE* 1.3 56.4 + - - +
440H GLN* 3.1 11.4 + - - +
441H GLY 2.9 22.5 + - - -
454H MET* 3.7 49.4 - - + +
455H CYS* 3.2 34.8 - - - +
3008H ZAR 3.9 30.3 - + - -
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Residues in contact with PHE 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434H MET* 3.1 42.8 + - + -
435H GLU* 4.4 4.3 - - - +
437H PHE* 1.3 75.1 - - - +
439H PRO* 1.4 60.3 - - + +
441H GLY* 2.9 3.1 + - - -
442H ASP* 2.7 41.2 + - - +
454H MET 3.4 19.7 - - - -
455H CYS 3.5 9.2 - - - +
457H LYS* 3.5 49.8 - - + +
460H ALA* 3.6 22.0 - - + -
462H VAL* 4.8 5.8 - - + -
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Residues in contact with PRO 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435H GLU* 2.6 31.9 - - + +
436H GLU* 3.0 12.1 - - - +
438H PHE* 1.4 89.2 - - + +
440H GLN* 1.3 55.3 + - - +
442H ASP* 3.5 14.5 - - + +
443H ARG* 2.8 35.8 + - + +
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Residues in contact with GLN 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H GLY 4.0 4.1 + - - +
304H VAL* 3.2 17.9 - - + -
305H SER* 3.0 45.4 + - - -
308H PHE* 3.8 20.9 - - + +
436H GLU 3.5 8.7 + - - +
437H PHE* 3.1 16.5 + - - +
438H PHE 3.1 0.2 - - - -
439H PRO* 1.3 75.8 - - - +
441H GLY* 1.3 62.0 + - - +
443H ARG* 3.1 9.5 + - - +
444H GLU* 2.8 51.9 + - - +
452H SER* 3.8 9.5 + - - -
455H CYS* 4.0 14.9 - - - -
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Residues in contact with GLY 441 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H PHE 2.9 7.7 + - - -
438H PHE 2.9 3.6 + - - -
440H GLN* 1.3 77.7 - - - +
442H ASP* 1.3 57.4 + - - +
444H GLU* 3.2 14.4 + - - -
445H ARG* 2.9 27.5 + - - +
451H ILE* 3.1 16.3 - - - +
455H CYS* 3.2 25.8 - - - +
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Residues in contact with ASP 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H PHE* 2.7 21.9 + - - +
439H PRO* 3.5 16.8 - - + +
441H GLY* 1.3 70.3 - - - +
443H ARG* 1.3 65.8 + - - +
445H ARG* 2.8 39.3 + - - +
446H GLU* 2.9 26.0 + - + +
457H LYS* 3.0 36.3 + - - +
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Residues in contact with ARG 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302H PRO 5.4 3.8 + - - -
304H VAL* 3.7 18.4 - - - +
308H PHE* 3.3 35.5 - - + -
439H PRO* 2.8 25.5 + - + +
440H GLN* 3.2 12.6 - - - +
442H ASP* 1.3 77.2 - - - +
444H GLU* 1.3 56.7 + - - +
446H GLU* 3.3 19.2 + - - +
447H ARG* 3.0 62.2 + - - +
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Residues in contact with GLU 444 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H PHE* 3.6 24.0 - - + +
311H ASN* 5.7 1.2 + - - -
440H GLN* 2.8 32.1 + - - +
441H GLY* 3.5 14.2 - - - +
443H ARG* 1.3 74.7 - - - +
445H ARG* 1.3 64.7 + - - +
447H ARG* 3.4 3.4 + - - -
448H GLY 3.0 2.6 + - - -
449H MET* 2.8 54.0 + - + +
450H GLU 4.1 5.4 - - - +
451H ILE* 3.6 9.6 - - + -
452H SER* 2.6 51.0 + - - -
455H CYS* 4.2 0.7 - - - +
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Residues in contact with ARG 445 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441H GLY 2.9 13.9 + - - +
442H ASP* 2.8 39.2 + - - +
444H GLU* 1.3 77.7 - - - +
446H GLU* 1.3 63.9 + - + +
448H GLY* 3.1 12.3 + - - -
449H MET 4.6 1.6 - - - -
451H ILE* 3.3 17.0 - - + +
456H ASP* 3.0 29.3 + - - +
457H LYS* 3.8 14.5 - - - +
458H HIS* 3.8 27.5 + - - -
----------------------------------------------------------
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Residues in contact with GLU 446 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H ASP* 2.9 27.3 + - + +
443H ARG* 3.3 26.6 + - - +
445H ARG* 1.3 75.7 - - + +
447H ARG* 1.3 67.1 + - - +
448H GLY* 2.9 10.2 + - - -
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Residues in contact with ARG 447 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H PHE* 4.1 7.6 - - + -
312H THR* 4.1 17.4 - - + +
443H ARG* 3.0 61.9 + - - +
444H GLU 3.7 0.9 - - - +
446H GLU* 1.3 84.0 + - - +
448H GLY* 1.3 58.5 + - - +
449H MET* 3.1 37.9 + - + +
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Residues in contact with GLY 448 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444H GLU 3.0 2.8 + - - -
445H ARG 3.1 11.2 + - - -
446H GLU 2.9 6.7 + - - -
447H ARG* 1.3 80.2 - - - +
449H MET* 1.3 64.1 + - - +
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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