Contacts of the helix formed by residues 434 - 460 (chain C) in PDB entry 5IWM
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 THR 434 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ILE* 3.7 26.0 - - + +
401A SER 3.4 9.2 - - - -
402A ASP 3.7 10.7 + - - -
403A THR 3.9 13.9 - - - +
404A ASP* 3.9 17.0 + - - +
407A ALA* 4.3 7.9 - - + -
426A LEU* 5.6 0.4 - - + -
431C ARG* 3.3 18.8 + - - +
432C ARG 3.4 0.2 - - - -
433C LEU* 1.3 79.8 - - - +
435C GLY* 1.3 66.0 + - - +
436C LEU* 5.0 0.5 - - - +
437C GLU* 3.1 18.0 + - - +
438C ARG* 3.0 21.2 + - - -
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Residues in contact with GLY 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG 5.0 0.4 - - - -
401A SER 2.8 14.7 + - - -
402A ASP* 3.2 15.0 + - - -
433C LEU 3.9 0.4 + - - -
434C THR* 1.3 73.4 - - - +
436C LEU* 1.3 62.8 + - - +
438C ARG* 3.4 19.1 + - - +
439C ASP* 3.0 30.8 + - - +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP* 2.8 37.2 + - + +
403A THR* 3.7 25.8 - - + -
434C THR* 5.0 1.3 - - - +
435C GLY* 1.3 73.0 - - - +
437C GLU* 1.3 62.7 + - - +
439C ASP* 3.4 10.8 + - - +
440C LYS* 3.1 35.3 + - + +
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Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ASP* 4.6 12.8 - - - +
431C ARG* 3.3 20.6 - - + +
432C ARG* 3.1 44.9 + - + +
434C THR* 3.1 13.8 + - - +
436C LEU* 1.3 76.8 - - + +
438C ARG* 1.3 62.7 - - - +
440C LYS* 3.2 49.3 + - - +
441C ILE* 3.4 18.7 + - - +
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Residues in contact with ARG 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A ARG* 2.8 39.9 + - - +
388C LEU* 4.0 37.9 - - + +
432C ARG 3.8 9.0 - - - +
433C LEU* 2.8 26.7 + - - +
434C THR 3.0 9.5 + - - +
435C GLY* 3.7 17.4 - - - +
437C GLU* 1.3 77.1 - - - +
439C ASP* 1.3 64.7 + - - +
440C LYS 3.6 0.2 + - - -
441C ILE* 3.7 5.0 + - - +
442C GLU* 3.6 18.0 + - - +
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Residues in contact with ASP 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C GLY* 3.0 19.7 + - - +
436C LEU* 3.7 13.2 - - - +
437C GLU 3.2 0.4 - - - -
438C ARG* 1.3 79.0 + - - +
440C LYS* 1.3 60.2 + - - +
442C GLU* 3.9 6.4 - - - +
443C ALA* 3.0 29.5 + - - +
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Residues in contact with LYS 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436C LEU* 3.1 19.2 + - + +
437C GLU* 3.2 44.0 + - - +
439C ASP* 1.3 77.1 - - - +
441C ILE* 1.3 60.6 + - + +
443C ALA* 3.8 5.5 - - - +
444C GLU* 2.9 34.6 + - - +
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Residues in contact with ILE 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C LEU* 3.8 26.2 - - + +
384C LEU* 4.1 27.6 - - + -
385C ARG* 4.1 17.7 - - + -
388C LEU* 4.0 24.9 - - + -
428C MET* 4.9 8.3 - - - -
432C ARG* 4.0 38.1 - - + +
437C GLU 3.4 13.8 + - - +
438C ARG 4.0 6.5 - - - +
439C ASP 3.4 0.2 - - - -
440C LYS* 1.3 76.9 - - + +
442C GLU* 1.3 61.5 + - - +
444C GLU* 4.8 2.0 - - - +
445C TYR* 3.3 22.3 + - - +
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Residues in contact with GLU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ARG* 3.2 36.8 + - + +
438C ARG 3.6 10.7 + - - +
439C ASP* 3.9 8.7 - - - +
440C LYS 3.2 0.4 - - - -
441C ILE* 1.3 78.0 - - - +
443C ALA* 1.3 65.0 + - - +
445C TYR* 3.2 5.9 + - - +
446C ASN* 3.0 49.0 + - - +
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Residues in contact with ALA 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ASP 3.0 20.3 + - - +
440C LYS* 3.4 6.3 + - - +
442C GLU* 1.3 77.9 - - - +
444C GLU* 1.3 62.0 + - - +
446C ASN* 3.5 6.5 + - - +
447C GLU* 3.2 39.1 + - - +
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ARG* 2.8 49.7 + - - +
381C LEU* 3.8 12.5 - - + +
440C LYS 2.9 18.4 + - - +
441C ILE* 4.1 4.4 - - - +
443C ALA* 1.3 75.4 - - - +
445C TYR* 1.3 57.3 + - - +
447C GLU* 3.4 12.1 + - - +
448C LEU* 2.9 37.6 + - + +
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Residues in contact with TYR 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C ALA* 3.6 18.6 - - + -
381C LEU* 3.7 29.5 - - + +
382C GLU* 2.7 46.3 + - + +
385C ARG* 3.6 39.0 + - - -
441C ILE 3.3 15.8 + - - +
442C GLU 3.2 5.9 + - - +
444C GLU* 1.3 79.0 - - - +
446C ASN* 1.3 65.6 + - - +
448C LEU* 3.3 3.8 + - - +
449C LEU* 3.0 60.7 + - + +
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Residues in contact with ASN 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ARG* 5.6 0.7 + - - -
442C GLU* 3.0 44.8 + - - +
443C ALA* 4.0 5.8 - - - +
445C TYR* 1.3 84.4 - - - +
447C GLU* 1.3 65.7 + - + +
449C LEU* 3.3 21.9 + - - +
450C ASN* 3.3 12.6 + - - +
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Residues in contact with GLU 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ALA* 3.2 28.7 + - - +
444C GLU* 3.6 10.0 - - - +
446C ASN* 1.3 77.1 - - + +
448C LEU* 1.3 62.9 + - - +
450C ASN* 3.3 7.7 + - - +
451C TYR* 3.2 22.7 + - - +
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Residues in contact with LEU 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ALA* 3.4 42.4 - - + +
377C ARG* 3.6 20.2 - - + -
378C ALA* 3.5 23.6 - - + +
381C LEU* 3.9 7.9 - - + -
444C GLU* 2.9 21.6 + - + +
445C TYR* 3.5 6.5 - - - +
446C ASN 3.2 0.2 - - - -
447C GLU* 1.3 74.9 - - - +
449C LEU* 1.3 59.2 - - - +
451C TYR* 3.5 15.5 - - + +
452C ILE* 2.9 38.3 + - + +
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C ALA* 5.2 3.1 - - + -
382C GLU* 5.3 0.7 - - - +
445C TYR* 3.0 59.3 + - + +
446C ASN* 3.3 15.2 + - - +
448C LEU* 1.3 73.7 - - - +
450C ASN* 1.3 64.3 + - - +
452C ILE* 3.4 17.9 + - + +
453C SER* 3.1 22.3 + - - -
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Residues in contact with ASN 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446C ASN 3.3 9.8 + - - +
447C GLU* 3.3 10.3 + - - +
449C LEU* 1.3 74.8 - - - +
451C TYR* 1.2 61.0 + - - +
453C SER* 3.1 9.7 + - - -
454C GLU* 2.8 52.0 + - - +
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Residues in contact with TYR 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ASN* 3.6 35.4 + - + +
374C ALA* 4.2 13.0 - - + -
447C GLU 3.2 14.6 + - - +
448C LEU* 3.5 17.3 - - + +
450C ASN* 1.2 76.2 + - - +
452C ILE* 1.3 65.3 + - - +
454C GLU* 3.2 22.3 + - + +
455C LEU* 3.0 62.0 + - + +
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C LEU* 4.0 9.5 - - + +
374C ALA* 3.8 38.4 - - + +
375C LYS* 4.3 15.5 - - + +
378C ALA* 4.1 16.8 - - + -
448C LEU* 2.9 30.0 + - + +
449C LEU* 3.7 16.4 - - + +
451C TYR* 1.3 75.8 - - - +
453C SER* 1.3 61.7 + - - +
455C LEU* 3.3 10.2 + - - +
456C GLU* 3.1 43.1 + - - +
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Residues in contact with SER 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C LEU 3.1 14.1 + - - -
450C ASN* 3.1 15.0 + - - -
452C ILE* 1.3 75.1 - - - +
454C GLU* 1.3 62.5 + - - +
456C GLU* 3.3 13.1 + - - +
457C THR* 3.0 30.5 + - - -
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Residues in contact with GLU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C ASN* 2.8 42.4 + - - +
451C TYR* 3.2 30.0 + - + +
453C SER* 1.3 75.5 - - - +
455C LEU* 1.3 62.1 + - + +
457C THR* 3.5 11.7 + - - -
458C ILE* 3.4 23.9 + - + +
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367C THR* 3.7 26.9 - - + +
370C ASN* 3.7 11.4 - - + +
371C LEU* 3.6 43.3 - - + +
374C ALA* 4.7 0.7 - - + -
451C TYR* 3.0 63.5 + - + +
452C ILE* 3.7 5.4 - - - +
453C SER 3.2 0.2 - - - -
454C GLU* 1.3 75.6 - - + +
456C GLU* 1.3 64.9 + - - +
458C ILE* 3.4 16.5 + - + +
459C LEU* 3.3 19.5 + - - +
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Residues in contact with GLU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C LEU* 3.8 16.8 - - + -
375C LYS* 4.0 16.3 + - - -
452C ILE* 3.1 34.5 + - - +
453C SER* 3.3 10.9 + - - +
455C LEU* 1.3 73.4 - - - +
457C THR* 1.3 64.6 + - - +
459C LEU* 3.4 7.3 + - - +
460C ALA* 3.1 26.3 + - - +
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Residues in contact with THR 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453C SER* 3.0 19.0 + - - -
454C GLU* 3.6 11.6 - - - -
455C LEU 3.3 0.2 - - - -
456C GLU* 1.3 76.1 - - - +
458C ILE* 1.3 62.3 + - - +
460C ALA* 3.7 11.3 + - - +
461C ASP* 3.8 14.7 + - - +
464C VAL* 4.4 13.6 - - + +
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Residues in contact with ILE 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363C VAL* 5.8 0.4 - - + -
367C THR* 4.3 20.6 - - + +
454C GLU* 3.4 18.6 - - + +
455C LEU* 3.4 22.9 + - + +
456C GLU 3.2 0.6 - - - -
457C THR* 1.3 79.5 - - - +
459C LEU* 1.3 59.2 + - + +
461C ASP 3.2 22.9 - - - +
464C VAL* 4.1 17.3 - - + -
465C LEU* 4.1 32.1 + - + +
468C LEU* 4.1 26.7 - - + -
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Residues in contact with LEU 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C ARG* 4.1 21.5 - - + +
367C THR* 3.9 19.3 - - + -
368C GLN* 3.7 35.4 - - + +
371C LEU* 3.8 29.6 - - + -
455C LEU 3.3 16.3 + - - +
456C GLU* 3.4 6.0 + - + +
458C ILE* 1.3 75.4 - - + +
460C ALA* 1.3 60.2 + - - +
461C ASP 3.2 5.3 + - - -
462C GLU* 5.2 2.3 + - - +
465C LEU* 5.4 4.9 - - + -
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Residues in contact with ALA 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C GLU 3.1 17.6 + - - +
457C THR* 4.1 7.0 - - - +
458C ILE 3.3 0.6 - - - -
459C LEU* 1.3 76.6 - - - +
461C ASP* 1.3 58.6 + - + +
462C GLU 4.4 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) + - + + + + + -
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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