Contacts of the helix formed by residues 422 - 448 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLN* 5.2 17.3 - - + +
199C TRP* 4.9 3.4 - - + -
200C GLY* 3.8 23.3 - - - +
420C THR 4.8 0.7 - - - +
421C LYS* 1.3 88.4 - - + +
423C LEU* 1.3 66.1 - - - +
424C GLN* 3.2 5.8 - - + +
425C LEU* 2.8 33.8 + - + +
426C TYR 3.1 9.2 + - - -
495C THR* 4.7 6.7 - - + -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B SER* 3.9 26.0 - - - +
506B THR* 4.6 3.1 - - - +
421C LYS 3.3 2.4 + - - -
422C PRO* 1.3 69.9 - - - +
424C GLN* 1.3 64.8 + - - +
426C TYR* 4.2 13.7 - - + -
427C ARG* 2.9 52.0 + - + +
495C THR* 5.4 0.4 - - - +
499C ASN* 3.5 31.7 + - + +
502C TRP* 3.6 53.4 - - + +
503C TYR* 4.6 1.3 - - + -
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Residues in contact with GLN 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B PRO* 3.8 24.5 - - + +
509B GLN* 4.1 12.4 + - + +
510B SER* 3.4 21.1 + - - -
202C HIS* 3.1 34.7 + - - -
205C ARG* 4.5 3.8 - - - +
422C PRO* 3.0 5.2 + - + +
423C LEU* 1.3 79.0 - - - +
425C LEU* 1.3 61.1 + - + +
427C ARG* 4.2 7.2 - - - +
428C GLN* 3.1 41.1 + - + +
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Residues in contact with LEU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C GLY* 3.6 25.6 - - - +
201C LEU 3.9 12.6 - - - +
202C HIS* 4.0 26.9 - - + +
203C VAL* 4.7 5.4 - - + +
204C PHE* 3.8 26.0 - - + -
421C LYS* 4.1 13.5 - - + -
422C PRO* 2.8 33.7 + - + +
424C GLN* 1.3 77.0 - - + +
426C TYR* 1.3 66.8 + - - +
428C GLN* 2.9 18.9 + - - +
429C TRP* 3.1 24.1 + - + +
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Residues in contact with TYR 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418C ASN* 3.4 26.2 + - + +
419C PRO* 3.6 24.9 - - + +
421C LYS 4.1 3.6 - - - +
422C PRO 3.1 9.1 + - - +
423C LEU* 3.7 9.9 - - + +
425C LEU* 1.3 78.6 - - - +
427C ARG* 1.3 57.0 + - - +
429C TRP* 3.1 8.9 + - - +
430C THR* 2.9 40.5 + - - -
466C GLN* 2.7 30.3 + - - +
470C ILE* 3.4 21.5 - - + +
499C ASN* 3.7 28.3 - - + -
503C TYR* 3.5 25.6 - + - -
3003C ZAR 3.6 15.0 - - - -
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Residues in contact with ARG 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ARG* 5.5 6.1 - - - +
502B TRP* 5.9 1.2 - - - -
506B THR* 3.9 26.5 - - - +
423C LEU* 2.9 48.7 + - + +
424C GLN* 4.2 7.1 - - - +
426C TYR* 1.3 75.6 - - - +
428C GLN* 1.3 63.2 + - + +
430C THR* 3.3 2.6 + - - -
431C ASP* 3.0 31.4 + - - +
502C TRP* 3.1 32.3 - - + -
503C TYR* 3.6 20.6 + - - +
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Residues in contact with GLN 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C HIS* 3.7 11.7 + - - -
204C PHE* 3.4 38.4 - - + +
424C GLN* 3.1 46.3 + - + +
425C LEU* 2.9 9.0 + - - +
427C ARG* 1.3 77.1 - - + +
429C TRP* 1.3 62.9 - - - +
431C ASP* 3.3 11.0 + - - +
432C ARG* 3.1 29.8 + - - +
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Residues in contact with TRP 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 4.0 11.8 - - + +
204C PHE* 3.5 31.9 - + - -
255C ALA 5.6 0.2 - - - -
256C TYR* 3.6 28.7 - + - -
258C ASN* 5.3 0.4 - - - -
260C ILE* 3.8 11.4 - - + -
261C HIS* 3.7 38.6 - - + -
264C ASP* 3.5 30.3 + - + -
418C ASN* 3.5 40.4 - - + +
421C LYS* 5.4 4.3 - - + +
425C LEU* 3.1 33.4 + - + +
426C TYR* 3.3 7.2 - - - +
428C GLN* 1.3 73.9 - - - +
430C THR* 1.3 59.8 + - - +
432C ARG* 3.0 13.9 + - - +
433C ILE* 2.8 26.9 + - - +
3003C ZAR 3.3 10.0 - - - -
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Residues in contact with THR 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C TYR* 2.9 32.8 + - - -
427C ARG 3.6 4.3 - - - -
429C TRP* 1.3 75.7 - - - +
431C ASP* 1.3 66.6 + - - +
433C ILE* 3.1 4.0 - - - +
434C MET* 3.0 24.4 + - + +
462C VAL* 3.8 20.2 - - + -
466C GLN* 3.4 28.8 - - + +
503C TYR* 3.2 25.4 + - - +
3003C ZAR 3.3 11.1 - - - -
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Residues in contact with ASP 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C ARG* 3.0 23.2 + - - +
428C GLN* 3.5 10.8 - - - +
429C TRP 3.2 0.2 - - - -
430C THR* 1.3 80.8 - - - +
432C ARG* 1.3 57.8 + - + +
434C MET* 3.4 4.4 + - - +
435C GLU* 2.9 30.5 + - - +
462C VAL* 5.7 3.3 - - - +
503C TYR* 5.5 0.5 + - - -
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Residues in contact with ARG 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C PHE* 3.1 33.7 - - - -
255C ALA* 2.8 55.0 + - + +
256C TYR* 4.0 7.9 - - + -
258C ASN* 4.0 9.1 - - - +
260C ILE* 3.7 21.9 - - - +
428C GLN* 3.1 19.3 + - - +
429C TRP* 3.0 20.0 + - - +
431C ASP* 1.3 75.5 - - + +
433C ILE* 1.3 65.5 + - - +
435C GLU* 3.1 10.0 + - - +
436C GLU* 3.0 19.6 + - - +
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Residues in contact with ILE 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C TYR* 3.6 38.3 - - + -
257C HIS* 3.9 12.3 - - + -
429C TRP 2.8 13.1 + - - +
430C THR* 3.1 17.3 - - - +
432C ARG* 1.3 72.7 - - - +
434C MET* 1.3 70.9 + - + +
436C GLU* 3.3 4.0 + - + +
437C PHE* 2.9 64.1 + - + -
466C GLN* 4.6 1.1 - - - +
3003C ZAR 3.5 46.4 - - + +
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Residues in contact with MET 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C THR* 3.0 18.9 + - + +
431C ASP* 3.9 4.7 - - - +
433C ILE* 1.3 86.6 - - + +
435C GLU* 1.3 66.2 + - - +
437C PHE* 4.2 8.1 - - + -
438C PHE* 3.1 59.0 + - + -
454C MET* 3.5 52.7 - - + +
460C ALA* 4.2 6.7 - - + -
462C VAL* 3.9 38.8 - - + -
465C SER* 5.2 1.1 - - - +
466C GLN* 4.8 4.5 - - - -
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Residues in contact with GLU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ALA* 3.7 20.2 - - + +
431C ASP 2.9 19.9 + - - +
432C ARG* 3.1 11.2 + - - +
434C MET* 1.3 79.1 - - - +
436C GLU* 1.3 50.3 + - - +
438C PHE* 4.4 6.0 - - - +
439C PRO* 2.5 34.8 - - + +
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Residues in contact with GLU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C VAL* 3.2 14.8 - - + +
255C ALA* 4.1 9.2 - - + +
256C TYR* 2.8 32.1 + - - +
257C HIS* 2.8 37.3 + - - -
301C HIS* 4.1 0.5 - - - -
303C GLY* 3.2 34.9 - - - +
432C ARG 3.0 14.1 + - - +
433C ILE* 3.7 7.2 - - - +
434C MET 3.1 0.4 - - - -
435C GLU* 1.3 77.3 - - - +
437C PHE* 1.3 70.4 + - + +
438C PHE 3.3 0.2 - - - -
439C PRO* 3.1 13.7 - - - +
440C GLN* 3.5 11.4 + - - +
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Residues in contact with PHE 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C HIS* 5.2 5.4 - + - -
303C GLY 6.1 0.2 - - - -
433C ILE* 2.9 51.0 + - + +
434C MET* 3.4 11.4 + - - +
436C GLU* 1.3 81.5 - - + +
438C PHE* 1.3 57.4 + - - +
440C GLN* 3.1 14.2 + - - +
441C GLY 2.9 22.2 + - - -
454C MET* 3.7 47.3 - - + +
455C CYS* 3.3 32.4 - - - +
3003C ZAR 4.0 28.9 - + - -
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Residues in contact with PHE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C MET* 3.1 43.7 + - + +
435C GLU* 4.4 4.9 - - - +
437C PHE* 1.3 77.9 - - - +
439C PRO* 1.4 58.0 - - + +
441C GLY* 2.8 2.8 + - - -
442C ASP* 2.6 40.9 + - - +
454C MET 3.5 19.5 - - - -
455C CYS 3.5 9.1 - - - +
457C LYS* 3.5 49.6 - - + -
460C ALA* 3.6 21.5 - - + -
462C VAL* 4.9 5.6 - - + -
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Residues in contact with PRO 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C GLU* 2.5 31.9 - - + +
436C GLU* 3.1 11.7 - - - +
438C PHE* 1.4 88.7 - - + +
440C GLN* 1.3 56.3 + - - +
442C ASP* 3.5 14.7 - - + +
443C ARG* 2.9 34.0 + - + +
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Residues in contact with GLN 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLY 4.0 3.3 + - - +
304C VAL* 3.2 19.1 - - + -
305C SER* 2.9 45.2 + - - -
308C PHE* 3.8 21.2 - - + +
436C GLU 3.5 9.6 + - - +
437C PHE* 3.1 16.4 + - - +
438C PHE 3.0 0.6 - - - -
439C PRO* 1.3 77.2 - - - +
441C GLY* 1.3 60.4 + - - +
443C ARG* 3.1 8.8 + - - +
444C GLU* 2.8 53.0 + - - +
452C SER* 3.8 9.1 + - - -
455C CYS* 4.0 13.2 - - - -
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Residues in contact with GLY 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C PHE 2.9 7.7 + - - -
438C PHE 2.8 3.8 + - - -
440C GLN* 1.3 79.1 - - - +
442C ASP* 1.3 57.1 + - - +
444C GLU* 3.3 14.3 + - - -
445C ARG* 2.9 27.9 + - - +
451C ILE* 3.1 16.0 - - - +
455C CYS* 3.2 25.7 - - - +
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Residues in contact with ASP 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 2.6 22.1 + - - +
439C PRO* 3.5 17.7 - - + +
441C GLY* 1.3 70.9 - - - +
443C ARG* 1.3 66.2 + - - +
445C ARG* 2.8 39.3 + - - +
446C GLU* 2.9 26.4 + - + +
457C LYS* 3.0 36.9 + - - +
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Residues in contact with ARG 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C PRO 5.4 4.0 + - - -
304C VAL* 3.8 18.4 - - - +
308C PHE* 3.3 35.6 - - + -
439C PRO* 2.9 25.5 + - + +
440C GLN* 3.2 11.4 - - - +
442C ASP* 1.3 76.1 - - - +
444C GLU* 1.3 57.3 + - - +
446C GLU* 3.3 20.3 + - - +
447C ARG* 3.0 61.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.6 24.8 - - + +
311C ASN* 5.7 1.2 + - - -
440C GLN* 2.8 32.5 + - - +
441C GLY* 3.5 14.2 - - - +
442C ASP 3.1 0.2 - - - -
443C ARG* 1.3 75.4 - - - +
445C ARG* 1.3 62.8 + - - +
448C GLY 3.0 2.8 + - - -
449C MET* 2.8 56.7 + - + +
450C GLU 4.1 5.8 - - - +
451C ILE* 3.6 9.6 - - + -
452C SER* 2.6 50.1 + - - -
455C CYS* 4.2 0.3 - - - +
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Residues in contact with ARG 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C GLY 2.9 15.2 + - - +
442C ASP* 2.8 39.4 + - - +
444C GLU* 1.3 77.1 - - - +
446C GLU* 1.3 63.8 + - + +
448C GLY* 3.1 12.9 + - - -
449C MET 4.6 1.8 - - - -
451C ILE* 3.3 17.8 - - + +
456C ASP* 3.0 28.9 + - - +
457C LYS* 3.8 15.0 - - - +
458C HIS* 3.8 26.5 + - - -
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Residues in contact with GLU 446 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ASP* 2.9 27.9 + - + +
443C ARG* 3.3 26.6 + - - +
445C ARG* 1.3 74.0 - - + +
447C ARG* 1.3 70.4 + - - +
448C GLY* 2.9 7.1 + - - -
----------------------------------------------------------
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Residues in contact with ARG 447 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 4.1 8.6 - - + -
312C THR* 4.1 16.9 - - + +
443C ARG* 3.0 65.0 + - - +
444C GLU 3.4 1.1 + - - +
446C GLU* 1.3 82.2 + - - +
448C GLY* 1.3 58.5 + - - +
449C MET* 3.1 37.6 - - + +
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Residues in contact with GLY 448 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLU 3.0 3.0 + - - -
445C ARG 3.1 10.5 + - - -
446C GLU 2.9 7.1 - - - -
447C ARG* 1.3 80.0 - - - +
449C MET* 1.3 63.7 + - - +
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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