Contacts of the helix formed by residues 422 - 448 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D TRP* 4.9 3.1 - - + -
200D GLY* 3.8 23.6 - - - +
420D THR 4.8 0.4 - - - +
421D LYS* 1.3 87.0 - - + +
423D LEU* 1.3 67.2 - - - +
424D GLN* 3.2 6.1 - - + +
425D LEU* 2.9 33.6 + - + +
426D TYR 3.0 9.9 + - - -
495D THR* 4.6 7.2 - - + -
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Residues in contact with LEU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LYS 3.3 3.3 + - - -
422D PRO* 1.3 68.8 - - - +
424D GLN* 1.3 62.4 + - - +
426D TYR* 4.2 12.3 - - + -
427D ARG* 2.9 51.6 + - + +
495D THR* 5.4 0.2 - - - +
499D ASN* 3.4 30.1 + - + +
502D TRP* 3.6 54.3 - - + +
503D TYR* 4.6 1.1 - - + -
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Residues in contact with GLN 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D HIS* 3.1 34.2 + - - -
205D ARG* 4.5 7.5 + - - +
422D PRO* 3.1 5.3 + - + +
423D LEU* 1.3 78.4 - - - +
425D LEU* 1.3 60.0 + - + +
427D ARG* 4.0 7.6 + - - +
428D GLN* 3.2 40.0 + - + +
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLY* 3.5 26.5 - - - +
201D LEU 3.8 12.1 - - - +
202D HIS* 4.1 27.4 - - + +
203D VAL* 4.7 5.8 - - + +
204D PHE* 3.8 25.8 - - + -
421D LYS* 4.2 13.2 - - + -
422D PRO* 2.9 31.6 + - + +
424D GLN* 1.3 78.1 - - + +
426D TYR* 1.3 67.4 + - - +
428D GLN* 2.8 19.3 + - - +
429D TRP* 3.1 24.2 + - + +
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Residues in contact with TYR 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D ASN* 3.4 25.7 + - + +
419D PRO* 3.5 25.2 - - + +
421D LYS* 4.1 2.9 - - - +
422D PRO 3.0 9.6 + - - +
423D LEU* 3.7 10.8 - - + +
425D LEU* 1.3 78.7 - - - +
427D ARG* 1.3 57.7 + - - +
429D TRP* 3.1 9.1 + - - +
430D THR* 2.9 40.5 + - - -
466D GLN* 2.7 29.9 + - - +
470D ILE* 3.4 21.4 - - + +
499D ASN* 3.7 29.4 - - + -
503D TYR* 3.5 26.5 - + - -
3004D ZAR 3.5 15.5 - - - -
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Residues in contact with ARG 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 2.9 43.5 + - + +
424D GLN* 4.1 7.3 - - - +
426D TYR* 1.3 74.0 - - - +
428D GLN* 1.3 64.8 + - + +
430D THR* 3.3 2.4 + - - -
431D ASP* 3.0 31.1 + - - +
502D TRP* 3.1 39.3 - - + -
503D TYR* 3.6 19.3 + - - +
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Residues in contact with GLN 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D HIS* 3.8 11.7 + - - -
204D PHE* 3.4 39.2 - - + +
424D GLN* 3.2 46.9 + - + +
425D LEU* 2.8 8.6 + - - +
427D ARG* 1.3 76.6 - - + +
429D TRP* 1.3 64.2 + - - +
431D ASP* 3.2 12.0 + - - +
432D ARG* 3.1 29.9 + - - +
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Residues in contact with TRP 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D VAL* 4.0 11.2 - - + +
204D PHE* 3.5 28.7 - + - -
256D TYR* 3.6 28.1 - + + -
258D ASN* 5.3 1.1 - - - -
260D ILE* 3.8 14.6 - - + -
261D HIS* 3.7 37.5 - - + -
264D ASP* 3.4 30.6 + - + -
418D ASN* 3.4 40.2 - - + +
421D LYS* 5.4 4.1 - - + +
425D LEU* 3.1 34.1 + - + +
426D TYR* 3.3 7.4 - - - +
428D GLN* 1.3 74.6 - - - +
430D THR* 1.3 60.4 + - - +
432D ARG* 3.0 13.0 + - - +
433D ILE* 2.8 26.5 + - - +
3004D ZAR 3.3 9.5 - - - -
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Residues in contact with THR 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D TYR* 2.9 32.9 + - - -
427D ARG 3.6 4.3 - - - -
429D TRP* 1.3 75.7 - - - +
431D ASP* 1.3 65.0 + - - +
433D ILE* 3.1 3.3 - - - +
434D MET* 3.0 24.0 + - + +
462D VAL* 3.8 19.7 - - + -
466D GLN* 3.4 28.5 - - + +
503D TYR* 3.2 27.1 + - - +
3004D ZAR 3.3 11.2 - - - -
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Residues in contact with ASP 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D ARG* 3.0 22.2 + - - +
428D GLN* 3.5 11.2 - - - +
429D TRP 3.1 0.2 - - - -
430D THR* 1.3 81.3 - - - +
432D ARG* 1.3 58.2 + - + +
434D MET* 3.8 4.6 - - - +
435D GLU* 2.8 31.5 + - - +
462D VAL* 5.6 3.1 - - - +
503D TYR* 5.5 0.5 + - - -
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Residues in contact with ARG 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D PHE* 3.1 36.5 - - - -
255D ALA* 2.8 57.2 + - + +
256D TYR* 4.0 7.6 - - + -
258D ASN* 4.0 8.9 - - - +
260D ILE* 3.7 21.3 - - - +
428D GLN* 3.1 19.3 + - - +
429D TRP* 3.0 18.6 + - - +
431D ASP* 1.3 74.6 - - + +
433D ILE* 1.3 65.5 + - - +
435D GLU* 3.1 10.7 + - - +
436D GLU* 3.0 19.9 + - - +
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Residues in contact with ILE 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D TYR* 3.5 42.0 - - + -
257D HIS* 3.9 11.4 - - + -
429D TRP 2.8 9.5 + - - +
430D THR* 3.1 15.0 - - - +
432D ARG* 1.3 72.9 - - - +
434D MET* 1.3 71.6 + - + +
436D GLU* 3.2 3.8 + - + +
437D PHE* 2.9 65.4 + - + -
466D GLN* 4.6 1.1 - - - +
3004D ZAR 3.5 47.1 - - + +
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Residues in contact with MET 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D THR* 3.0 19.3 + - + +
431D ASP* 3.8 4.7 - - - +
433D ILE* 1.3 85.1 - - + +
435D GLU* 1.3 66.1 + - - +
437D PHE* 3.8 6.2 - - - +
438D PHE* 3.1 64.9 + - + -
454D MET* 3.6 45.3 - - + +
460D ALA* 4.1 6.1 - - + -
462D VAL* 3.8 41.3 - - + +
465D SER* 5.2 1.1 - - - +
466D GLN* 4.8 5.2 - - - -
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Residues in contact with GLU 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ALA* 3.7 19.6 - - + +
431D ASP 2.8 18.3 + - - +
432D ARG* 3.1 12.0 + - - +
434D MET* 1.3 77.8 - - - +
436D GLU* 1.3 51.5 + - - +
438D PHE* 4.4 6.6 - - - +
439D PRO* 2.6 33.7 - - + +
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Residues in contact with GLU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D VAL* 3.2 15.1 - - + +
255D ALA* 4.1 8.7 - - + +
256D TYR* 2.7 32.0 + - - +
257D HIS* 2.7 38.9 + - - -
301D HIS* 4.2 0.3 - - - -
303D GLY* 3.2 35.5 - - - +
432D ARG 3.0 13.8 + - - +
433D ILE* 3.6 6.5 - - - +
435D GLU* 1.3 77.6 - - - +
437D PHE* 1.3 69.5 + - + +
438D PHE 3.3 0.4 - - - -
439D PRO* 3.1 13.5 - - - +
440D GLN* 3.5 11.4 + - - +
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Residues in contact with PHE 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D HIS* 5.3 4.7 - + - -
303D GLY 6.1 0.7 - - - -
433D ILE* 2.9 50.6 + - + +
434D MET* 3.8 11.9 - - - +
436D GLU* 1.3 82.5 - - + +
438D PHE* 1.3 57.2 + - - +
440D GLN* 3.1 12.1 + - - +
441D GLY 2.9 21.5 + - - -
454D MET* 3.7 49.4 - - + +
455D CYS* 3.2 35.2 - - - +
3004D ZAR 4.0 29.8 - + - -
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Residues in contact with PHE 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D MET* 3.1 43.9 + - + -
435D GLU* 4.4 3.8 - - - +
437D PHE* 1.3 76.4 - - - +
439D PRO* 1.4 58.3 - - + +
441D GLY* 2.8 3.6 + - - -
442D ASP* 2.7 39.1 + - - +
454D MET 3.4 19.5 - - - -
455D CYS 3.5 9.2 - - - +
457D LYS* 3.5 50.9 - - + +
460D ALA* 3.6 21.8 - - + -
462D VAL* 4.8 5.4 - - + -
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Residues in contact with PRO 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLU* 2.6 32.1 - - + +
436D GLU* 3.1 11.7 - - - +
438D PHE* 1.4 87.4 - - + +
440D GLN* 1.3 54.6 + - - +
442D ASP* 3.3 15.1 + - + +
443D ARG* 2.8 35.9 + - + +
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Residues in contact with GLN 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D GLY 4.0 3.7 + - - +
304D VAL* 3.2 18.9 - - + -
305D SER* 3.0 45.4 + - - -
308D PHE* 3.8 20.4 - - + +
436D GLU 3.5 9.1 + - - +
437D PHE* 3.1 16.0 + - - +
438D PHE 3.0 0.6 - - - -
439D PRO* 1.3 78.6 - - - +
441D GLY* 1.3 59.1 + - - +
443D ARG* 3.1 9.6 + - - +
444D GLU* 2.8 52.4 + - - +
452D SER* 3.8 8.9 + - - -
455D CYS* 4.0 14.9 - - - -
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Residues in contact with GLY 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D PHE 2.9 7.9 + - - -
438D PHE 2.8 3.8 + - - -
440D GLN* 1.3 77.8 - - - +
442D ASP* 1.3 56.7 + - - +
444D GLU* 3.3 14.0 + - - -
445D ARG* 2.9 27.9 + - - +
451D ILE* 3.0 16.7 - - - +
455D CYS* 3.2 25.7 - - - +
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Residues in contact with ASP 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D PHE* 2.7 21.9 + - - +
439D PRO* 3.5 16.8 - - + +
441D GLY* 1.3 70.3 - - - +
443D ARG* 1.3 66.9 + - - +
445D ARG* 2.8 44.8 + - - +
446D GLU* 2.9 26.4 + - + +
457D LYS* 3.1 37.0 + - - +
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Residues in contact with ARG 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D PRO 5.3 4.0 + - - -
304D VAL* 3.8 19.2 - - - +
308D PHE* 3.3 34.0 - - + -
439D PRO* 2.8 25.5 + - + +
440D GLN* 3.2 11.7 - - - +
442D ASP* 1.3 77.4 - - - +
444D GLU* 1.3 57.5 + - - +
446D GLU* 3.4 18.8 + - - +
447D ARG* 3.0 61.4 + - - +
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Residues in contact with GLU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D PHE* 3.6 23.3 - - + +
311D ASN* 5.7 0.9 + - - -
440D GLN* 2.8 32.9 + - - +
441D GLY* 3.6 14.2 - - - +
443D ARG* 1.3 75.4 - - - +
445D ARG* 1.3 63.6 + - - +
447D ARG 3.4 0.5 + - - -
448D GLY 3.0 2.6 + - - -
449D MET* 2.8 56.6 + - + +
450D GLU 4.1 6.1 - - - +
451D ILE* 3.6 9.8 - - + -
452D SER* 2.6 51.5 + - - -
455D CYS* 4.2 0.5 - - - +
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Residues in contact with ARG 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D GLY 2.9 15.7 + - - +
442D ASP* 2.8 39.6 + - - +
444D GLU* 1.3 75.0 - - - +
446D GLU* 1.3 64.3 + - + +
448D GLY* 3.1 12.3 + - - -
449D MET 4.7 1.6 - - - -
451D ILE* 3.3 16.7 - - + +
456D ASP* 3.0 28.7 + - - +
457D LYS* 3.8 15.6 - - - +
458D HIS* 3.8 27.9 + - - -
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Residues in contact with GLU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D ASP* 2.9 28.7 + - + +
443D ARG* 3.4 26.4 + - - +
445D ARG* 1.3 74.3 - - + +
447D ARG* 1.3 70.1 + - - +
448D GLY* 2.9 6.6 + - - -
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D PHE* 4.0 8.2 - - + -
312D THR* 4.1 17.0 - - + +
443D ARG* 3.0 63.3 + - - +
444D GLU 3.7 1.3 - - - +
446D GLU* 1.3 85.0 + - - +
448D GLY* 1.3 59.3 + - - +
449D MET* 3.1 37.7 + - + +
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Residues in contact with GLY 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D GLU 3.0 2.8 + - - -
445D ARG* 3.1 11.2 + - - -
446D GLU 2.9 7.9 + - - -
447D ARG* 1.3 79.5 - - - +
449D MET* 1.3 63.7 + - - +
450D 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