Contacts of the helix formed by residues 408 - 431 (chain F) in PDB entry 4XLN
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 408 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402F GLY* 4.9 0.9 - - - -
406F GLY 5.5 0.7 - - - +
407F VAL* 1.3 78.6 - - - +
409F ARG* 1.3 67.4 + - - +
410F GLU 4.2 2.5 - - - -
411F ARG* 3.1 21.8 + - - +
412F ILE* 3.3 9.9 + - - +
2O T 2.6 57.4 + - + +
3O T 4.0 27.8 - - + +
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Residues in contact with ARG 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398F LEU* 3.6 38.8 + - + +
399F GLU* 3.3 32.5 + - - +
407F VAL 4.0 0.4 + - - -
408F THR* 1.3 74.3 - - - +
410F GLU* 1.3 74.5 + - + +
412F ILE* 3.2 5.1 + - - +
413F ARG* 3.0 23.0 + - - +
3O T 6.1 1.3 - - + -
4O G 4.5 7.6 + - - -
5O A 3.6 21.4 - - - +
6O C 5.1 2.4 - - - +
42P T 3.2 29.1 + - - +
43P G 3.2 35.5 + - - -
44P T 3.8 21.0 + - - +
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Residues in contact with GLU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F THR* 3.2 1.0 + - - +
409F ARG* 1.3 84.0 - - - +
411F ARG* 1.3 62.5 + - - +
413F ARG* 2.4 44.5 + - - +
414F GLN* 2.9 26.7 + - - +
2O T 4.0 15.3 - - + +
3O T 3.9 25.6 - - + +
4O G 4.1 0.4 - - - +
44P T 3.2 19.6 - - - +
45P C 2.8 32.5 + - - +
46P A 3.9 15.4 + - - +
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Residues in contact with ARG 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F ARG* 2.9 22.8 - - - +
407F VAL* 3.8 11.0 - - + -
408F THR* 3.1 13.7 + - - +
410F GLU* 1.3 79.2 - - - +
412F ILE* 1.3 57.7 + - - +
414F GLN* 3.3 10.6 + - - +
415F ILE* 2.9 62.8 + - + +
1O C 3.2 68.7 + - - +
2O T 3.6 21.0 - - - +
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Residues in contact with ILE 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL* 4.0 14.6 - - + -
398F LEU* 3.8 13.5 - - + +
401F VAL* 3.6 40.6 - - + +
402F GLY* 3.6 23.3 - - - +
405F PHE* 4.3 3.4 - - + -
407F VAL* 3.6 25.1 - - + -
408F THR 3.3 2.4 + - - +
409F ARG 3.2 8.3 + - - +
411F ARG* 1.3 77.6 - - - +
413F ARG* 1.3 64.1 + - - +
415F ILE* 3.2 16.8 + - + +
416F GLU* 2.9 40.2 + - - +
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Residues in contact with ARG 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398F LEU* 4.1 12.1 - - + +
409F ARG 3.0 13.0 + - - +
410F GLU* 2.4 40.6 + - - +
412F ILE* 1.3 78.4 - - - +
414F GLN* 1.3 87.5 + - - +
416F GLU* 3.2 13.0 - - - +
417F ASN* 2.8 42.8 + - - +
44P T 3.8 52.8 + - - +
45P C 3.4 30.6 + - - +
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Residues in contact with GLN 414 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410F GLU* 2.9 16.9 + - - +
411F ARG* 3.8 10.6 + - - +
413F ARG* 1.3 98.5 - - - +
415F ILE* 1.3 56.3 + - - +
417F ASN* 3.7 8.4 - - - +
418F LYS* 2.9 33.1 + - - +
421F ARG* 5.3 0.2 + - - -
1O C 3.3 40.0 + - - +
2O T 3.5 21.1 + - - +
47P A 4.5 8.3 - - - +
48P G 5.5 0.4 + - - -
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Residues in contact with ILE 415 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379F ARG* 3.7 25.8 - - + +
380F GLU* 3.6 34.8 - - + +
383F VAL* 4.3 11.4 - - + -
407F VAL* 5.1 0.4 - - + -
411F ARG* 2.9 64.8 + - + +
412F ILE* 3.3 23.1 - - + +
414F GLN* 1.3 77.0 - - - +
416F GLU* 1.3 59.6 + - - +
418F LYS* 3.4 4.5 + - - +
419F ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 416 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL* 4.5 6.3 - - + -
384F LEU* 3.7 25.8 - - + +
387F ARG* 3.1 48.0 + - + +
388F LYS* 5.1 7.3 + - - -
398F LEU* 3.2 22.0 - - - +
412F ILE* 2.9 18.1 + - - +
413F ARG* 3.2 17.7 - - - +
415F ILE* 1.3 74.7 - - - +
417F ASN* 1.3 66.3 + - - +
419F ALA* 4.0 0.3 - - - +
420F LEU* 2.9 30.1 + - - +
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Residues in contact with ASN 417 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413F ARG* 2.8 45.6 + - - +
414F GLN* 3.7 7.7 - - - +
416F GLU* 1.3 82.1 - - - +
418F LYS* 1.3 63.9 + - - +
420F LEU* 3.1 8.3 + - - +
421F ARG* 3.0 49.5 + - - +
44P T 5.5 3.2 + - - -
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Residues in contact with LYS 418 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380F GLU* 5.2 2.9 - - - +
414F GLN 2.9 17.9 + - - +
415F ILE* 3.7 4.9 - - - +
417F ASN* 1.3 73.6 - - - +
419F ALA* 1.3 58.4 + - - +
421F ARG* 3.2 24.2 + - + +
422F LYS* 2.9 51.2 + - + +
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Residues in contact with ALA 419 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376F LEU* 3.8 7.0 - - + +
380F GLU* 3.5 42.3 + - + +
384F LEU* 3.7 19.3 - - + -
415F ILE 2.9 17.9 + - - +
418F LYS* 1.3 75.1 - - - +
420F LEU* 1.3 62.6 + - - +
422F LYS* 3.2 4.8 + - - +
423F LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 4.6 5.4 - - + -
776C SER* 3.2 40.6 - - - +
777C ILE* 3.4 42.9 - - + +
384F LEU* 4.6 4.9 - - + +
416F GLU 2.9 21.2 + - - +
417F ASN* 3.1 8.7 + - - +
419F ALA* 1.3 76.4 - - - +
421F ARG* 1.3 66.4 + - + +
423F LEU* 3.1 13.0 + - + +
424F LYS* 2.9 23.3 + - + +
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Residues in contact with ARG 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F ASN* 3.0 36.0 + - - +
418F LYS* 3.7 36.1 - - + +
420F LEU* 1.3 84.2 - - + +
422F LYS* 1.3 57.5 + - - +
424F LYS* 3.0 28.7 + - + +
425F TYR* 3.0 13.7 + - - +
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Residues in contact with LYS 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375F LYS 6.0 1.8 - - - -
376F LEU* 4.1 14.8 - - + +
377F SER* 6.1 1.2 - - - +
380F GLU* 4.1 21.0 + - - +
418F LYS* 2.9 43.9 + - + +
419F ALA 3.2 5.1 + - - +
421F ARG* 1.3 77.3 - - + +
423F LEU* 1.3 59.6 + - - +
425F TYR* 3.6 11.1 + - - +
426F HIS* 3.6 21.8 - - - -
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Residues in contact with LEU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773C LEU* 5.5 1.3 - - + -
777C ILE* 3.7 32.5 - - + -
372F ALA* 3.2 33.9 - - + +
373F LEU* 4.6 5.6 - - + -
375F LYS* 4.5 4.0 - - + -
376F LEU* 3.6 22.7 - - + -
384F LEU* 3.6 29.4 - - + -
419F ALA 2.9 14.9 + - - +
420F LEU* 3.1 8.9 + - - +
422F LYS* 1.3 73.6 - - - +
424F LYS* 1.3 65.4 + - - +
425F TYR 3.0 2.2 - - - -
426F HIS* 3.0 8.3 + - - +
427F GLU* 3.0 25.0 + - - +
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Residues in contact with LYS 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C ILE* 3.9 28.8 + - + +
778C PHE* 5.3 17.7 + - + -
420F LEU* 2.9 9.0 + - + +
421F ARG* 3.0 27.4 + - + +
423F LEU* 1.3 76.9 - - - +
425F TYR* 1.3 59.3 + - - +
427F GLU* 4.1 6.2 - - + +
428F SER* 3.4 23.3 + - - -
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Residues in contact with TYR 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F ARG 3.0 9.8 + - - +
422F LYS* 3.7 11.7 - - - +
423F LEU 3.0 0.4 - - - -
424F LYS* 1.3 77.8 - - - +
426F HIS* 1.3 79.1 + + - +
428F SER* 2.8 23.6 + - - -
429F ARG* 3.1 52.2 + - + +
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Residues in contact with HIS 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372F ALA* 6.1 1.3 - - + -
375F LYS* 3.3 55.6 + - + +
422F LYS 3.6 14.8 - - - -
423F LEU* 3.0 6.2 + - - +
425F TYR* 1.3 91.3 - + - +
427F GLU* 1.3 61.1 + - - +
429F ARG* 3.0 28.5 + - - +
430F THR* 2.9 36.5 + - + +
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Residues in contact with GLU 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777C ILE* 4.7 9.2 - - + -
778C PHE* 3.7 28.5 - - + -
372F ALA* 5.6 1.0 - - - +
423F LEU* 3.0 17.9 + - + +
424F LYS* 4.4 6.3 - - + +
425F TYR 3.3 0.2 - - - -
426F HIS* 1.3 77.7 - - - +
428F SER* 1.3 62.5 + - - +
430F THR* 3.8 8.1 + - - -
431F ARG* 3.0 18.5 + - - -
432F LYS* 4.9 0.2 - - - +
433F LEU* 3.0 36.9 + - + +
434F ARG* 2.5 39.4 + - + +
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Residues in contact with SER 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424F LYS* 3.4 18.2 + - - -
425F TYR* 2.8 25.3 + - - -
427F GLU* 1.3 78.0 - - - +
429F ARG* 1.3 62.2 + - - +
434F ARG* 2.6 31.8 + - - +
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Residues in contact with ARG 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425F TYR* 3.1 61.9 + - + +
426F HIS* 3.0 24.9 + - - +
428F SER* 1.3 83.3 + - - +
430F THR* 1.3 70.8 + - + +
431F ARG* 3.4 4.0 + - - +
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Residues in contact with THR 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D PRO* 4.5 7.8 - - - +
375F LYS* 5.0 12.3 - - - +
426F HIS* 2.9 24.8 + - + +
427F GLU* 3.8 11.1 + - - -
429F ARG* 1.3 78.4 - - + +
431F ARG* 1.3 68.5 + - - +
432F LYS* 3.0 33.3 + - + +
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Residues in contact with ARG 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D PRO* 3.9 15.8 - - + +
672D ALA* 5.8 0.7 - - - +
427F GLU* 3.0 22.1 + - - -
428F SER 5.0 0.2 - - - +
429F ARG 3.3 4.9 - - - +
430F THR* 1.3 78.3 + - - +
432F LYS* 1.3 62.4 + - - +
433F LEU 3.6 1.3 - - - -
434F ARG* 3.5 53.4 + - + +
435F ASP* 4.9 1.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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