Contacts of the helix formed by residues 404 - 428 (chain B) in PDB entry 5YL4
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 ASP 404 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B THR* 5.2 2.2 - - - -
402B GLY 3.9 1.2 + - - +
403B MET* 1.3 75.6 - - - +
405B GLU* 1.3 78.5 + - - +
406B MET* 3.1 28.7 + - + +
407B GLU* 3.2 23.6 + - + +
408B PHE* 3.8 10.1 - - - -
82E VAL* 5.9 0.4 - - - +
85E LYS* 3.4 22.9 + - - +
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.8 9.5 - - + -
392B LYS* 3.1 49.6 + - - +
395B LEU* 3.9 18.0 - - + +
399B THR* 5.1 10.2 - - + +
404B ASP* 1.3 77.6 + - - +
406B MET* 1.3 66.5 + - - +
408B PHE* 3.0 22.5 + - - +
409B THR* 3.0 16.5 + - - +
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Residues in contact with MET 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ASP* 3.1 22.1 + - + +
405B GLU* 1.3 77.4 - - - +
407B GLU* 1.3 56.5 + - - +
409B THR* 3.3 16.7 + - - -
410B GLU* 2.9 52.6 + - - +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.9 13.0 - - - -
106B TYR* 2.4 32.5 + - - -
187B LEU* 4.1 6.0 - - + +
403B MET* 3.6 25.3 - - + +
404B ASP* 3.2 16.3 + - + +
405B GLU 3.2 1.0 - - - -
406B MET* 1.3 78.0 - - - +
408B PHE* 1.3 58.1 + - - +
410B GLU* 3.8 14.7 - - - +
411B ALA* 3.1 26.2 + - - +
78E HIS* 3.0 28.6 + - + +
82E VAL* 4.6 1.6 - - - +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B TYR* 3.7 27.6 - + + -
187B LEU* 4.1 14.4 - - + -
385B PHE* 3.7 26.3 - + + -
389B PHE* 3.3 24.5 - + + -
395B LEU* 3.4 31.9 - - + -
398B TYR* 3.6 34.3 - + + -
399B THR* 6.2 1.6 - - + -
403B MET* 3.6 24.2 - - + -
404B ASP 3.8 14.1 - - - -
405B GLU* 3.0 6.8 + - - +
407B GLU* 1.3 74.8 - - - +
409B THR* 1.3 60.0 + - - +
411B ALA* 3.2 6.4 + - - +
412B GLU* 2.9 30.3 + - - +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.7 15.9 - - + -
405B GLU* 3.0 15.5 + - - +
406B MET* 3.5 18.9 - - - -
408B PHE* 1.3 76.8 - - - +
410B GLU* 1.3 61.3 + - + +
412B GLU* 3.5 15.4 - - - +
413B SER* 3.1 31.7 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B HIS* 5.8 1.8 - - + +
406B MET* 2.9 45.1 + - + +
407B GLU* 3.8 14.3 - - + +
409B THR* 1.3 72.2 - - - +
411B ALA* 1.3 52.9 + - - +
413B SER* 3.0 10.2 + - - -
414B ASN* 2.8 46.0 + - - +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 3.7 26.5 - - + +
187B LEU* 3.9 22.2 - - + -
190B HIS* 4.6 9.6 - - + +
385B PHE* 5.5 0.4 - - + -
407B GLU 3.1 16.0 + - - +
408B PHE* 3.2 4.0 + - - +
410B GLU* 1.3 73.9 - - - +
412B GLU* 1.3 66.8 + - - +
414B ASN* 3.3 11.7 + - - +
415B MET* 3.1 24.6 + - - +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 4.0 10.5 - - - +
382B SER* 4.9 4.6 + - - +
385B PHE* 3.7 27.6 - - + -
386B THR* 3.2 28.6 + - - +
389B PHE* 4.1 15.8 - - - -
408B PHE 2.9 15.7 + - - +
409B THR* 3.5 14.6 - - - +
411B ALA* 1.3 76.2 - - - +
413B SER* 1.3 64.7 + - - +
415B MET* 3.4 3.0 + - - +
416B ASN* 3.1 42.9 + - - +
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 3.1 16.6 + - - +
410B GLU* 3.0 12.6 + - - -
412B GLU* 1.3 79.7 + - - +
414B ASN* 1.3 61.6 + - - +
416B ASN* 3.6 6.7 + - - +
417B ASP* 3.1 38.3 + - - +
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Residues in contact with ASN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B HIS* 2.7 57.7 + - + +
193B VAL* 5.7 3.3 - - + +
262B ARG* 4.0 10.0 + - - +
410B GLU* 2.8 35.4 + - - +
411B ALA 3.3 4.7 + - - +
413B SER* 1.3 76.9 - - - +
415B MET* 1.3 57.6 + - - +
417B ASP* 3.5 12.5 + - - +
418B LEU* 3.1 24.4 + - - +
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Residues in contact with MET 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B THR* 3.3 37.0 - - + +
189B VAL* 3.8 38.8 - - + -
190B HIS* 5.9 1.5 - - + +
378B PHE* 4.0 29.6 - - + +
381B ILE* 3.9 8.1 - - + -
382B SER* 3.8 33.4 - - - +
385B PHE* 5.5 0.2 - - + -
411B ALA 3.1 14.7 + - - +
412B GLU* 3.9 3.4 - - - +
414B ASN* 1.3 75.2 - - - +
416B ASN* 1.3 61.6 + - - +
417B ASP 3.2 0.2 - - - -
418B LEU* 3.3 8.0 + - + +
419B VAL* 3.1 27.7 + - + +
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Residues in contact with ASN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B SER* 2.8 29.7 + - - -
386B THR* 5.7 1.0 + - - -
412B GLU* 3.1 32.1 + - - +
413B SER* 4.1 5.3 - - - +
415B MET* 1.3 75.4 - - - +
417B ASP* 1.3 59.9 + - - +
419B VAL* 3.5 11.8 + - - +
420B SER* 2.9 30.6 + - - -
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 3.8 12.7 + - - +
413B SER* 3.1 30.6 + - - +
414B ASN* 3.6 13.1 + - - +
415B MET 3.2 0.2 - - - -
416B ASN* 1.3 74.3 - - - +
418B LEU* 1.3 55.4 + - - +
420B SER* 3.2 9.0 + - - -
421B GLU* 2.8 35.7 + - - +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 4.1 10.3 - - + -
193B VAL* 3.6 27.6 - - + -
262B ARG* 3.5 39.8 - - + +
263B LEU* 4.0 8.7 - - + -
265B PHE* 4.1 2.5 - - + -
378B PHE* 3.7 37.7 - - + -
414B ASN 3.1 14.2 + - - +
415B MET* 3.4 10.3 - - + +
417B ASP* 1.3 73.9 - - - +
419B VAL* 1.3 58.0 + - - +
421B GLU* 3.2 4.9 + - - +
422B TYR* 3.0 47.8 + - + -
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN* 3.8 20.1 - - + +
378B PHE* 3.8 27.8 - - + +
379B LYS* 3.7 34.5 - - + +
382B SER* 5.8 0.2 - - - -
415B MET* 3.1 17.3 + - + +
416B ASN* 3.6 15.3 - - - +
417B ASP 3.2 0.2 - - - -
418B LEU* 1.3 75.9 - - - +
420B SER* 1.3 58.5 + - - +
422B TYR* 3.3 9.9 + - - +
423B GLN* 3.0 26.0 + - + +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ASN 2.9 16.1 + - - -
417B ASP* 3.2 12.1 + - - -
419B VAL* 1.3 73.5 - - - +
421B GLU* 1.3 66.7 + - - +
423B GLN* 3.1 9.7 + - - +
424B GLN* 3.0 22.5 + - - +
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Residues in contact with GLU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B PHE* 4.5 7.6 - - - +
261B PRO* 5.6 1.4 - - - +
262B ARG* 2.6 46.5 + - - +
263B LEU* 3.8 27.1 - - + +
417B ASP 2.8 15.4 + - - +
418B LEU 3.5 5.6 - - - +
420B SER* 1.3 76.7 - - - +
422B TYR* 1.3 60.9 + - - +
424B GLN* 3.2 28.8 - - - +
425B TYR* 3.2 31.4 + - + +
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Residues in contact with TYR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B LEU* 3.6 42.3 - - + +
265B PHE* 3.5 34.1 + - - +
311B LEU* 5.2 1.1 - - + -
370B ASN* 4.8 6.5 - - - -
371B SER 4.2 6.1 - - - -
372B THR* 3.8 41.7 - - + +
374B ILE* 3.4 24.1 - - + +
375B GLN* 4.0 15.9 - - + -
378B PHE* 4.1 7.6 - + - -
418B LEU* 3.0 46.0 + - + -
419B VAL* 3.6 7.2 - - - +
421B GLU* 1.3 75.3 - - - +
423B GLN* 1.3 62.2 + - - +
424B GLN 3.4 0.2 + - - -
425B TYR* 3.4 2.1 + - - -
426B GLN* 3.2 22.2 + - - +
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Residues in contact with GLN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B GLN* 3.4 26.6 + - - +
379B LYS* 5.1 3.1 + - - -
419B VAL* 3.0 15.4 + - + +
420B SER* 3.1 13.2 + - - +
422B TYR* 1.3 74.2 - - - +
424B GLN* 1.3 66.7 + - - +
426B GLN* 3.5 21.1 + - - +
427B ASP* 3.2 44.2 + - - +
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B SER 3.0 11.2 + - - +
421B GLU* 3.2 20.6 - - - +
423B GLN* 1.3 78.3 - - - +
425B TYR* 1.3 89.4 + - + +
427B ASP* 3.4 4.2 + - - +
428B ALA* 3.2 25.1 + - + +
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Residues in contact with TYR 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A LYS* 4.6 12.8 + - + -
260B PHE* 3.4 38.1 - + - +
263B LEU* 3.5 31.0 - - + -
309B ARG* 4.2 5.2 + - - -
311B LEU* 4.5 4.0 - - + -
342B VAL* 4.6 4.9 - - - +
344B TRP* 3.7 40.2 - + + -
372B THR* 4.3 12.2 - - + +
421B GLU* 3.2 37.8 + - + +
422B TYR* 3.4 6.0 + - - +
423B GLN 3.4 0.4 - - - -
424B GLN* 1.3 97.6 + - - +
426B GLN* 1.3 63.6 + - - +
427B ASP 3.3 1.2 + - - -
428B ALA* 3.6 16.8 + - + +
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B HIS 3.0 24.0 + - - +
308B GLY* 3.4 15.8 - - - -
309B ARG* 3.4 24.0 + - + +
372B THR* 3.2 28.4 + - - +
373B ALA* 4.2 0.7 + - - -
375B GLN* 2.8 28.3 + - - +
422B TYR 3.2 15.0 + - - +
423B GLN* 3.6 26.1 + - - +
425B TYR* 1.3 78.5 - - - +
427B ASP* 1.3 61.0 + - - +
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ARG* 5.1 0.2 - - - -
423B GLN* 3.2 33.1 + - - +
424B GLN* 3.4 8.3 + - - +
426B GLN* 1.3 82.0 + - - +
428B ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS* 4.0 25.3 + - + +
309B ARG* 3.6 18.1 + - - -
343B GLU* 4.6 7.4 - - - +
344B TRP* 3.6 28.3 - - + +
424B GLN* 3.2 16.9 + - + +
425B TYR* 3.6 16.7 + - + +
426B GLN 3.6 1.0 - - - -
427B ASP* 1.3 81.3 - - - +
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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