Contacts of the helix formed by residues 421 - 449 (chain C) in PDB entry 2BG9
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C GLY* 1.3 64.6 + - - +
423C ILE* 3.5 9.5 - - - +
424C ASP* 3.7 14.9 + - - +
425C SER* 2.8 24.8 + - - -
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Residues in contact with GLY 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.2 25.3 - - - +
421C SER* 1.3 78.3 - - - +
423C ILE* 1.3 67.2 + - - +
424C ASP 3.1 0.2 - - - -
425C SER* 2.9 25.1 + - - -
426C THR* 3.0 10.0 + - - -
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B VAL* 3.8 14.6 - - + -
406B GLU* 4.3 3.2 - - + +
409B LYS* 3.1 36.3 - - - +
421C SER* 4.7 6.7 - - - +
422C GLY* 1.3 77.2 - - - +
424C ASP* 1.3 61.8 + - - +
426C THR* 3.3 3.5 + - - -
427C ASN* 3.1 27.7 + - - +
376D ILE* 3.6 40.7 - - + +
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Residues in contact with ASP 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C SER* 3.7 17.4 + - - +
422C GLY 3.1 0.2 - - - -
423C ILE* 1.3 82.3 - - - +
425C SER* 1.3 64.4 + - - +
427C ASN* 3.4 3.2 + - - +
428C TYR* 2.9 42.1 + - - +
431C LYS* 4.6 15.6 + - - -
375D ALA* 5.8 3.5 - - - +
376D ILE* 4.0 14.7 - - + +
379D VAL* 5.2 5.2 - - - +
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Residues in contact with SER 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 4.7 3.6 - - - -
421C SER* 2.8 20.7 + - - -
422C GLY* 2.9 16.8 + - - -
424C ASP* 1.3 80.9 - - - +
426C THR* 1.3 49.5 + - - +
428C TYR* 3.3 7.5 + - - +
429C ILE* 2.6 34.3 + - - +
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Residues in contact with THR 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 3.6 6.2 + - - -
409B LYS* 2.6 65.8 - - + +
412B ALA* 5.7 1.1 - - + -
413B GLU* 4.4 8.3 + - + +
422C GLY 3.0 12.5 + - - -
423C ILE 3.6 3.4 - - - -
424C ASP 3.2 0.2 - - - -
425C SER* 1.3 74.3 - - - +
427C ASN* 1.3 63.5 + - - +
429C ILE* 2.4 47.7 - - + +
430C VAL* 3.1 3.3 - - + +
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Residues in contact with ASN 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LYS* 5.0 8.7 - - - +
423C ILE* 3.1 16.1 + - - +
424C ASP* 4.4 3.4 - - - +
426C THR* 1.3 79.5 - - - +
428C TYR* 1.3 61.2 + - - +
430C VAL* 2.9 20.4 + - - +
431C LYS* 2.8 32.5 + - - +
376D ILE* 5.3 13.3 + - - +
379D VAL* 4.0 38.2 - - + +
380D LYS* 5.9 2.6 - - - +
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Residues in contact with TYR 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ASP* 2.9 35.5 + - - +
425C SER* 3.5 8.5 - - - +
427C ASN* 1.3 73.4 - - - +
429C ILE* 1.3 56.7 + - - +
431C LYS* 3.1 32.0 + - + +
432C GLN* 2.7 59.7 + - - +
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Residues in contact with ILE 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ALA* 6.0 2.7 - - + +
413B GLU* 4.5 30.1 - - + +
416B GLU* 4.9 0.9 - - - +
425C SER 2.6 28.1 + - - +
426C THR* 2.4 45.1 - - + +
428C TYR* 1.3 76.4 - - - +
430C VAL* 1.3 65.2 + - + +
432C GLN* 3.0 12.3 - - - +
433C ILE* 2.8 63.2 + - + +
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Residues in contact with VAL 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLU* 5.4 1.8 - - - +
426C THR* 3.1 17.0 - - + +
427C ASN* 3.1 32.1 - - - +
429C ILE* 1.3 85.4 - - + +
431C LYS* 1.3 53.6 + - - +
432C GLN 2.9 1.6 - - - -
433C ILE* 3.0 9.8 + - + +
434C LYS* 2.4 37.5 + - - +
379D VAL* 6.1 1.6 - - + -
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Residues in contact with LYS 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C ASP* 4.6 11.2 + - - -
427C ASN 2.8 22.2 + - - +
428C TYR* 3.7 36.8 - - + +
430C VAL* 1.3 73.3 - - - +
432C GLN* 1.3 58.4 + - - +
434C LYS* 2.8 35.8 - - + +
435C GLU* 3.0 17.6 + - - +
379D VAL* 3.5 20.5 - - + +
382D ILE* 3.3 38.1 - - + +
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Residues in contact with GLN 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C TYR* 2.7 35.9 + - - +
429C ILE* 3.0 18.1 - - - +
431C LYS* 1.3 73.8 - - - +
433C ILE* 1.3 65.0 + - + +
434C LYS 2.9 0.9 - - - -
435C GLU* 4.1 4.4 + - - +
436C LYS* 3.0 44.5 + - + +
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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
----------------------------------------------------------
413B GLU* 6.4 0.7 - - - -
416B GLU* 2.6 60.6 - - + +
420B GLU* 5.9 0.7 - - - +
429C ILE* 2.8 44.9 + - + +
430C VAL* 3.0 9.4 + - + +
432C GLN* 1.3 74.2 - - + +
434C LYS* 1.3 64.7 + - - +
436C LYS* 3.7 20.2 - - - +
437C ASN* 3.4 29.1 + - + +
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Residues in contact with LYS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C VAL 2.4 27.3 + - - +
431C LYS* 2.8 22.0 - - + +
432C GLN 2.9 0.4 - - - -
433C ILE* 1.3 72.8 - - - +
435C GLU* 1.3 108.8 + - + +
437C ASN* 3.5 1.2 + - - +
438C ALA* 3.4 19.8 + - + +
441C GLU* 4.3 3.5 - - - +
382D ILE* 6.1 4.9 - - + +
386D MET* 3.5 37.7 - - + -
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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
----------------------------------------------------------
428C TYR* 6.6 0.2 - - - -
431C LYS* 3.0 15.7 + - - +
432C GLN* 4.2 4.0 + - - +
434C LYS* 1.3 125.0 + - + +
436C LYS* 1.3 55.7 + - - +
438C ALA* 2.7 33.6 + - - +
439C TYR* 3.0 24.3 + - + -
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Residues in contact with LYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B GLU* 5.7 0.6 + - - -
420B GLU* 5.8 2.2 + - - -
432C GLN* 3.0 38.2 + - + +
433C ILE* 3.7 20.8 - - - +
435C GLU* 1.3 75.4 - - - +
437C ASN* 1.3 69.1 + - - +
439C TYR* 3.0 30.0 + - - +
440C ASP* 3.5 5.9 + - - +
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B GLU* 4.6 20.6 + - - +
433C ILE* 3.4 24.5 + - + +
434C LYS 4.6 0.4 - - - +
436C LYS* 1.3 85.5 - - - +
438C ALA* 1.3 54.6 + - - +
439C TYR 3.0 1.3 - - - -
440C ASP* 2.8 29.1 + - - +
441C GLU* 2.6 48.2 + - + +
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LYS* 3.4 13.6 + - + +
435C GLU* 2.7 22.8 + - - +
437C ASN* 1.3 78.5 - - - +
439C TYR* 1.3 65.0 + - + +
441C GLU* 2.8 22.9 + - - +
442C GLU* 3.1 26.3 + - - +
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Residues in contact with TYR 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C GLU* 3.0 41.5 + - + -
436C LYS* 3.0 15.0 + - - +
437C ASN 3.0 0.2 - - - -
438C ALA* 1.3 79.6 - - + +
440C ASP* 1.3 50.9 + - - +
442C GLU* 3.4 4.5 + - - +
443C VAL* 2.7 44.6 + - + +
446C TRP* 5.2 0.7 + - - -
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Residues in contact with ASP 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LYS 3.5 3.1 + - - +
437C ASN* 2.8 46.8 + - - +
439C TYR* 1.3 77.1 - - - +
441C GLU* 1.3 58.4 + - + +
443C VAL* 2.7 37.1 + - - +
444C GLY* 3.3 3.6 + - - -
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Residues in contact with GLU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LYS 4.3 3.3 - - - +
437C ASN* 2.6 43.3 + - + +
438C ALA* 2.8 25.6 + - - +
440C ASP* 1.3 74.2 - - + +
442C GLU* 1.3 59.2 - - + +
444C GLY* 3.5 8.8 + - - -
445C ASN* 3.7 14.6 + - - -
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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
----------------------------------------------------------
438C ALA 3.1 15.1 + - - +
439C TYR* 3.9 4.9 - - - +
440C ASP 3.1 1.0 - - - -
441C GLU* 1.3 75.3 - - + +
443C VAL* 1.3 62.7 + - - +
444C GLY 2.8 6.7 + - - -
445C ASN* 3.1 17.6 + - - +
446C TRP* 2.9 78.4 + - + +
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Residues in contact with VAL 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C SER* 4.4 12.3 - - - +
439C TYR* 2.7 34.9 + - + +
440C ASP* 2.7 20.5 + - - +
442C GLU* 1.3 71.2 - - - +
444C GLY* 1.3 55.2 - - - +
446C TRP* 3.2 31.3 - - + +
447C ASN* 2.9 22.0 + - - +
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Residues in contact with GLY 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C SER* 4.0 18.6 - - - -
319C THR* 3.5 9.0 + - - -
440C ASP 3.3 6.0 + - - -
441C GLU 3.5 5.6 + - - -
442C GLU 2.8 1.6 - - - -
443C VAL* 1.3 77.8 - - - +
445C ASN* 1.3 57.1 + - - -
446C TRP 3.0 4.3 - - - -
447C ASN* 3.0 8.8 + - - +
448C LEU* 3.0 21.2 + - - -
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Residues in contact with ASN 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C GLU 3.7 11.6 + - - +
442C GLU* 3.1 22.6 + - + +
444C GLY* 1.3 73.6 - - - +
446C TRP* 1.3 67.9 + - + +
448C LEU* 2.7 54.8 + - + +
449C VAL 4.1 1.9 + - - -
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Residues in contact with TRP 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C TYR 5.2 0.6 + - - -
442C GLU* 2.9 47.2 + - + +
443C VAL* 3.2 41.3 - - + +
444C GLY 3.0 0.2 - - - -
445C ASN* 1.3 81.3 - - + +
447C ASN* 1.3 63.3 + - - +
449C VAL* 4.2 7.3 + - - +
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Residues in contact with ASN 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C THR* 2.5 33.6 + - + -
317C PRO* 2.9 25.1 - - - +
318C SER* 2.7 36.0 + - - -
319C THR 3.8 4.0 - - - +
443C VAL* 2.9 18.7 + - - +
444C GLY 3.0 6.9 + - - +
446C TRP* 1.3 78.5 - - - +
448C LEU* 1.3 54.7 + - - +
449C VAL* 2.3 37.6 - - - +
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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
----------------------------------------------------------
315C ARG* 3.7 12.1 + - - -
319C THR* 2.9 36.6 + - + +
444C GLY 3.0 9.1 + - - +
445C ASN* 2.7 56.5 - - + +
447C ASN* 1.3 72.8 - - - +
449C VAL* 1.3 76.0 + - - +
450C GLY* 4.6 2.9 - - - +
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Residues in contact with VAL 449 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C ARG* 4.2 10.1 + - - +
316C THR* 3.9 10.3 - - + +
445C ASN 4.1 3.6 + - - -
446C TRP 4.2 6.1 + - - +
447C ASN* 2.3 37.4 + - - +
448C LEU* 1.3 80.9 - - - +
450C GLY* 1.3 56.3 + - - +
451C GLN 3.7 0.4 - - - -
452C THR* 2.7 53.7 - - + +
453C ILE* 4.3 1.0 + - - +
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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