Contacts of the helix formed by residues 421 - 449 (chain M) in PDB entry 4BOG
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 SER 421 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422M GLY* 1.3 65.2 + - - +
423M ILE* 3.5 10.4 - - - +
424M ASP* 3.7 14.9 + - - +
425M SER* 2.8 25.0 + - - -
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Residues in contact with GLY 422 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406L GLU* 3.2 25.9 - - - +
421M SER* 1.3 77.5 - - - +
423M ILE* 1.3 66.9 + - - +
424M ASP 3.1 0.2 - - - -
425M SER* 2.9 24.6 + - - -
426M THR* 3.0 10.0 + - - -
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Residues in contact with ILE 423 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405L VAL* 3.8 14.4 - - + -
406L GLU* 4.3 4.0 - - + +
409L LYS* 3.1 35.2 - - - +
421M SER* 4.7 7.0 - - - +
422M GLY* 1.3 76.9 - - - +
424M ASP* 1.3 64.0 + - + +
426M THR* 3.3 3.6 + - - -
427M ASN* 3.1 27.7 + - - +
376N ILE* 3.6 40.1 - - + +
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Residues in contact with ASP 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421M SER* 3.7 17.3 + - - +
422M GLY 3.1 0.6 - - - -
423M ILE* 1.3 80.5 - - + +
425M SER* 1.3 63.7 + - - +
427M ASN* 3.4 3.7 + - - +
428M TYR* 2.9 41.6 + - - +
431M LYS* 4.6 15.4 + - - -
375N ALA* 5.8 3.3 - - - +
376N ILE* 4.0 15.3 - - + +
379N VAL* 5.2 5.2 - - - +
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Residues in contact with SER 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406L GLU* 4.7 3.4 - - - -
421M SER* 2.8 21.1 + - - -
422M GLY* 2.9 16.9 + - - -
424M ASP* 1.3 81.4 + - - +
426M THR* 1.3 49.9 + - - +
428M TYR* 3.3 7.9 + - - +
429M ILE* 2.6 33.9 + - - +
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Residues in contact with THR 426 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406L GLU* 3.6 6.4 + - - -
409L LYS* 2.6 65.6 - - + +
412L ALA* 5.7 1.3 - - + -
413L GLU* 4.4 7.5 + - + +
422M GLY 3.0 11.6 + - - -
423M ILE 3.6 3.6 - - - -
424M ASP 3.2 0.2 - - - -
425M SER* 1.3 74.9 - - - +
427M ASN* 1.3 64.1 + - - +
429M ILE* 2.4 46.9 - - + +
430M VAL* 3.1 3.9 - - + +
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Residues in contact with ASN 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409L LYS* 5.0 9.5 - - - +
423M ILE* 3.1 15.5 + - - +
424M ASP* 4.4 3.1 - - - +
426M THR* 1.3 80.0 - - - +
428M TYR* 1.3 61.4 + - - +
430M VAL* 2.9 20.9 + - - +
431M LYS* 2.8 32.0 + - - +
376N ILE* 5.3 13.3 + - - +
379N VAL* 4.0 36.8 - - + +
380N LYS* 5.9 2.6 - - - +
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Residues in contact with TYR 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424M ASP* 2.9 34.0 + - - +
425M SER* 3.5 8.3 - - - +
426M THR 3.1 0.2 - - - -
427M ASN* 1.3 74.1 - - - +
429M ILE* 1.3 57.0 + - - +
431M LYS* 3.8 30.7 - - + +
432M GLN* 2.7 58.7 + - - +
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Residues in contact with ILE 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412L ALA* 6.0 2.7 - - + -
413L GLU* 4.5 31.6 - - + +
416L GLU* 4.9 0.4 - - - +
425M SER 2.6 28.8 + - - +
426M THR* 2.4 44.0 - - + +
428M TYR* 1.3 77.0 - - - +
430M VAL* 1.3 64.7 + - + +
432M GLN* 3.0 12.2 - - - +
433M ILE* 2.8 63.0 + - + +
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Residues in contact with VAL 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416L GLU* 5.4 2.2 - - - +
426M THR* 3.1 17.3 - - + +
427M ASN* 3.1 31.9 - - - +
429M ILE* 1.3 84.7 - - + +
431M LYS* 1.3 53.1 + - - +
432M GLN 2.9 1.8 - - - -
433M ILE* 3.0 10.1 + - + +
434M LYS* 2.4 37.9 + - - +
379N VAL* 6.1 1.3 - - + -
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Residues in contact with LYS 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424M ASP* 4.6 11.7 + - - -
427M ASN 2.8 22.2 + - - +
428M TYR* 3.7 37.4 - - + +
430M VAL* 1.3 72.7 - - - +
432M GLN* 1.3 57.8 + - - +
434M LYS* 2.8 35.4 - - + +
435M GLU* 3.0 17.6 + - - +
379N VAL* 3.5 20.2 - - + +
382N ILE* 3.3 37.4 - - + +
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Residues in contact with GLN 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428M TYR* 2.7 37.8 + - - +
429M ILE* 3.0 18.3 - - - +
431M LYS* 1.3 75.6 - - - +
433M ILE* 1.3 64.6 + - + +
434M LYS 2.9 1.1 - - - -
435M GLU* 4.1 4.4 + - - +
436M LYS* 3.0 43.9 + - + +
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Residues in contact with ILE 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413L GLU* 6.4 0.4 - - - -
416L GLU* 2.6 61.0 - - + +
429M ILE* 2.8 46.5 + - + +
430M VAL* 3.0 9.6 + - + +
432M GLN* 1.3 73.1 - - + +
434M LYS* 1.3 65.9 + - - +
436M LYS* 3.7 19.7 - - - +
437M ASN* 3.4 29.7 + - + +
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Residues in contact with LYS 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430M VAL 2.4 26.7 + - - +
431M LYS* 2.8 23.1 - - + +
432M GLN 2.9 0.4 - - - -
433M ILE* 1.3 72.9 - - - +
435M GLU* 1.3 111.0 + - + +
437M ASN* 3.5 0.7 + - - +
438M ALA* 3.4 21.2 + - + +
441M GLU* 4.3 3.5 - - - +
382N ILE* 6.1 5.0 - - + +
386N MET* 3.5 37.7 - - + -
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Residues in contact with GLU 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431M LYS* 3.0 15.5 + - - +
432M GLN* 4.2 3.8 + - - +
434M LYS* 1.3 126.0 + - + +
436M LYS* 1.3 54.2 + - - +
438M ALA* 2.7 33.1 + - - +
439M TYR* 3.0 24.8 + - + -
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Residues in contact with LYS 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416L GLU* 5.7 0.4 + - - -
420L GLU* 5.8 2.0 + - - -
432M GLN* 3.0 37.6 + - + +
433M ILE* 3.7 21.8 - - - +
434M LYS 3.3 0.2 - - - -
435M GLU* 1.3 76.3 - - - +
437M ASN* 1.3 68.2 + - - +
439M TYR* 3.0 29.4 + - - +
440M ASP* 3.5 5.6 + - - +
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Residues in contact with ASN 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420L GLU* 4.6 20.3 + - - +
433M ILE* 3.4 24.6 + - + +
434M LYS 4.6 0.2 - - - +
436M LYS* 1.3 87.2 - - - +
438M ALA* 1.3 55.1 + - - +
439M TYR 3.0 1.3 - - - -
440M ASP* 2.8 28.7 + - - +
441M GLU* 2.6 48.3 + - + +
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Residues in contact with ALA 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434M LYS* 3.4 12.4 + - - +
435M GLU* 2.7 22.6 + - - +
437M ASN* 1.3 78.9 - - - +
439M TYR* 1.3 65.4 + - + +
441M GLU* 2.8 23.4 + - - +
442M GLU* 3.1 26.7 + - - +
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Residues in contact with TYR 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M GLU* 3.0 41.1 + - + -
436M LYS* 3.0 14.5 + - - +
437M ASN 3.0 0.2 - - - -
438M ALA* 1.3 80.1 - - + +
440M ASP* 1.3 50.1 + - - +
442M GLU* 3.4 4.4 + - - +
443M VAL* 2.7 44.0 + - + +
446M TRP* 5.2 0.7 + - - -
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Residues in contact with ASP 440 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436M LYS 3.5 3.4 + - - +
437M ASN* 2.8 46.9 + - - +
439M TYR* 1.3 76.9 - - - +
441M GLU* 1.3 59.8 + - + +
443M VAL* 2.7 36.0 + - - +
444M GLY* 3.3 3.6 + - - -
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Residues in contact with GLU 441 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434M LYS 4.3 3.5 - - - +
437M ASN* 2.6 43.6 + - + +
438M ALA* 2.8 26.2 + - - +
440M ASP* 1.3 73.9 - - + +
442M GLU* 1.3 59.9 - - + +
444M GLY* 3.5 8.7 + - - -
445M ASN* 3.7 14.9 + - - -
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Residues in contact with GLU 442 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438M ALA 3.1 15.6 + - - +
439M TYR* 3.9 4.9 - - - +
440M ASP 3.1 0.8 - - - -
441M GLU* 1.3 76.8 - - + +
443M VAL* 1.3 63.0 + - - +
444M GLY 2.8 6.9 + - - -
445M ASN* 3.1 17.1 + - - +
446M TRP* 2.9 79.9 + - + +
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Residues in contact with VAL 443 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318M SER* 4.4 11.7 - - - +
439M TYR* 2.7 34.5 + - + +
440M ASP* 2.7 21.4 + - - +
442M GLU* 1.3 71.2 - - - +
444M GLY* 1.3 56.5 + - - +
446M TRP* 3.2 30.6 - - + +
447M ASN* 2.9 22.0 + - - +
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Residues in contact with GLY 444 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318M SER* 4.0 17.7 - - - -
319M THR* 3.5 8.6 + - - -
440M ASP 3.3 6.4 + - - -
441M GLU 3.5 7.1 + - - -
442M GLU 2.8 1.6 - - - -
443M VAL* 1.3 78.3 - - - +
445M ASN* 1.3 57.1 + - - -
446M TRP 3.0 4.7 - - - -
447M ASN* 3.0 8.5 + - - +
448M LEU* 3.0 22.1 + - - -
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Residues in contact with ASN 445 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M GLU 3.7 11.1 + - - +
442M GLU* 3.1 23.1 + - + +
444M GLY* 1.3 73.5 - - - +
446M TRP* 1.3 67.4 + - + +
448M LEU* 2.7 53.6 - - + +
449M VAL 4.1 2.1 + - - -
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Residues in contact with TRP 446 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439M TYR 5.2 0.4 + - - -
442M GLU* 2.9 47.1 + - + +
443M VAL* 3.2 40.1 - - + +
445M ASN* 1.3 81.7 - - + +
447M ASN* 1.3 62.0 + - - +
449M VAL* 4.2 8.0 + - - +
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Residues in contact with ASN 447 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316M THR* 2.5 34.6 + - + -
317M PRO* 2.9 24.7 - - - +
318M SER* 2.7 36.0 + - - -
319M THR 3.8 3.8 - - - +
443M VAL* 2.9 20.2 + - - +
444M GLY 3.3 5.8 - - - +
446M TRP* 1.3 79.5 - - - +
448M LEU* 1.3 53.9 + - - +
449M VAL* 2.3 38.3 - - - +
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Residues in contact with LEU 448 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315M ARG* 3.7 12.5 + - - -
319M THR* 2.9 36.2 + - + +
444M GLY 3.0 8.6 + - - +
445M ASN* 2.7 57.9 - - + +
447M ASN* 1.3 72.7 - - - +
449M VAL* 1.3 76.3 + - - +
450M GLY* 4.6 3.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 449 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315M ARG* 4.2 10.0 + - - +
316M THR* 3.9 10.8 - - + +
445M ASN 4.1 3.6 + - - -
446M TRP 4.2 6.3 + - - +
447M ASN* 2.3 36.4 + - - +
448M LEU* 1.3 80.6 - - - +
450M GLY* 1.3 56.5 + - - +
451M GLN 3.7 0.4 - - - -
452M THR* 2.7 54.1 - - + +
453M ILE* 4.9 0.9 - - - +
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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