Contacts of the helix formed by residues 409 - 426 (chain B) in PDB entry 1YA8
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 409 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B THR* 3.3 7.6 + - - +
408B ASP* 1.3 74.8 - - - +
410B THR* 1.3 64.7 + - - +
411B VAL* 2.6 40.6 + - - +
412B LYS* 3.0 43.5 + - + +
413B LYS* 2.9 25.5 + - - +
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Residues in contact with THR 410 (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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372B GLN* 3.2 33.0 + - + +
373B LEU 2.7 45.2 + - - +
374B ASP* 5.4 3.4 - - + -
408B ASP 3.0 12.0 + - - +
409B ASP* 1.3 72.4 + - - +
411B VAL* 1.3 65.6 + - - +
413B LYS* 3.4 10.1 - - + +
414B LYS 3.4 1.6 + - - -
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLY 4.0 22.4 - - - +
372B GLN* 4.6 5.8 - - + +
409B ASP* 2.6 22.0 + - - +
410B THR* 1.3 76.6 - - - +
412B LYS* 1.3 58.5 - - + +
413B LYS 2.9 2.6 + - - -
414B LYS* 3.2 11.9 + - + +
415B ASP* 2.6 32.1 + - - +
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B THR* 2.9 43.7 - - + +
409B ASP* 3.0 34.5 + - + +
411B VAL* 1.3 77.4 - - + +
413B LYS* 1.3 61.5 + - + +
415B ASP* 3.6 11.3 - - - +
416B LEU* 3.2 32.1 + - + +
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.2 32.8 - - + +
374B ASP* 4.0 11.2 - - - +
375B GLN* 3.8 17.8 + - - +
404B LEU* 2.9 50.3 + - + +
407B THR 3.1 14.9 + - - +
408B ASP* 3.3 27.5 + - - +
409B ASP 2.9 19.1 + - - +
410B THR* 3.4 8.7 - - - +
411B VAL 2.9 1.0 - - - -
412B LYS* 1.3 74.6 - - + +
414B LYS* 1.3 68.6 + - - +
415B ASP 3.1 1.1 - - - -
416B LEU* 2.9 5.1 + - + -
417B PHE* 2.8 20.4 + - - +
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Residues in contact with LYS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 4.0 36.0 + - + +
371B GLY* 3.5 39.0 - - - +
372B GLN* 4.1 6.3 - - - +
373B LEU* 4.1 9.0 - - + +
410B THR 3.4 5.9 + - - +
411B VAL* 3.2 9.5 + - + +
413B LYS* 1.3 76.9 - - - +
415B ASP* 1.3 69.7 + - - +
417B PHE* 3.0 9.8 + - - +
418B LEU* 3.0 40.5 + - + +
4004B SMB 2.9 28.9 + - - -
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Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 2.6 33.2 - - - +
412B LYS* 3.6 10.3 - - - +
413B LYS 3.1 0.2 - - - -
414B LYS* 1.3 87.4 - - - +
416B LEU* 1.3 55.6 + - + +
418B LEU* 3.2 16.2 + - - +
419B ASP* 2.7 32.7 + - - +
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Residues in contact with LEU 416 (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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403B TYR* 3.2 37.6 - - + +
404B LEU* 3.4 21.3 - - + -
406B GLY* 4.9 11.2 - - - +
407B THR 5.5 2.5 - - - +
412B LYS* 3.2 19.7 + - + +
413B LYS* 2.9 6.7 + - + +
415B ASP* 1.3 76.2 - - + +
417B PHE* 1.3 52.8 + - - +
419B ASP* 3.0 19.0 + - + +
420B LEU* 2.7 33.3 + - - +
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Residues in contact with PHE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 3.4 30.1 - + - -
368B LEU* 5.2 3.8 - - + -
373B LEU* 3.9 18.4 - - + -
378B ALA* 3.9 8.7 - - + -
381B LEU* 3.7 22.4 - - + -
382B LEU* 3.7 50.7 - - + -
400B THR* 6.0 1.1 - - + -
404B LEU* 3.4 21.7 - - + +
413B LYS 2.8 11.7 + - - +
414B LYS 3.0 13.7 + - - +
416B LEU* 1.3 77.0 - - - +
418B LEU* 1.3 62.1 + - + +
420B LEU* 2.9 31.4 - - + +
421B ILE* 3.0 20.0 + - + +
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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
----------------------------------------------------------
355B PHE* 3.4 46.8 - - + +
356B GLY* 4.0 21.8 - - - +
360B PRO* 4.7 0.9 - - + -
366B TYR* 5.1 0.2 - - + -
368B LEU* 3.7 24.7 - - + -
414B LYS* 3.0 37.0 + - + +
415B ASP* 3.2 16.4 + - - +
417B PHE* 1.3 82.8 - - + +
419B ASP* 1.3 58.7 + - - +
421B ILE 3.6 0.2 + - - -
422B ALA* 2.8 30.4 + - - +
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Residues in contact with ASP 419 (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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352B LYS 4.9 8.3 - - - +
353B GLN* 5.2 8.8 - - - +
403B TYR* 4.4 5.8 - - + -
415B ASP* 2.7 21.7 + - - +
416B LEU* 3.0 25.3 + - + +
418B LEU* 1.3 75.8 - - - +
420B LEU* 1.3 64.5 + - - +
422B ALA* 3.0 7.5 + - - +
423B ASP* 2.6 40.0 + - - +
540B LYS* 5.7 3.8 + - - +
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LEU* 3.7 34.5 - - + -
389B VAL* 5.2 0.2 - - + -
391B ILE* 4.5 0.2 - - + -
399B ALA* 4.1 10.1 - - + +
400B THR* 5.7 1.6 - - - -
403B TYR* 3.2 45.0 - - + -
404B LEU* 6.3 0.4 - - + -
416B LEU 2.7 12.8 + - - +
417B PHE* 2.9 25.8 - - + +
419B ASP* 1.3 78.2 - - - +
421B ILE* 1.3 65.1 + - + +
423B ASP* 3.2 9.7 + - - +
424B VAL* 3.3 17.7 + - + +
547B TRP* 3.2 30.1 - - + -
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 3.9 28.3 - - + -
366B TYR* 3.3 27.8 - - + +
382B LEU* 4.6 3.6 - - + -
385B SER* 4.5 5.6 - - - +
388B LEU* 5.7 3.4 - - + -
389B VAL* 3.9 26.5 - - + -
417B PHE* 3.0 26.3 + - + +
418B LEU 4.0 4.3 - - - +
420B LEU* 1.3 84.3 - - + +
422B ALA* 1.3 62.9 + - - +
423B ASP 3.0 4.7 - - - -
424B VAL* 3.0 12.8 + - - +
425B MET* 3.0 40.7 + - + +
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Residues in contact with ALA 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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350B ILE* 5.6 0.9 - - - +
352B LYS 5.3 3.1 - - - +
353B GLN* 5.0 3.4 - - - -
354B GLU* 4.1 12.5 - - + +
355B PHE* 3.8 25.5 - - - +
418B LEU 2.8 23.2 + - - +
419B ASP* 3.0 10.1 + - - +
421B ILE* 1.3 73.5 - - - +
423B ASP* 1.3 58.3 + - - +
426B PHE* 3.4 18.9 + - - +
427B GLY* 3.1 18.7 + - - -
540B LYS* 6.0 0.8 - - - +
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Residues in contact with ASP 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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403B TYR* 3.3 27.0 + - - +
419B ASP* 2.6 31.5 + - - +
420B LEU 3.5 5.4 - - - +
422B ALA* 1.3 77.9 - - - +
424B VAL* 1.3 64.4 + - - +
427B GLY* 3.3 4.7 + - - +
428B VAL* 2.8 42.1 + - + +
540B LYS* 2.9 47.2 + - - +
543B GLU* 3.6 6.9 - - + +
547B TRP* 4.4 1.8 - - - +
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B THR* 6.0 0.2 - - - -
388B LEU 4.8 1.3 - - - +
389B VAL* 3.7 45.8 - - + +
391B ILE* 4.5 2.5 - - + -
420B LEU* 3.3 15.9 + - + +
421B ILE 3.0 7.0 + - - +
423B ASP* 1.3 78.2 - - - +
425B MET* 1.3 59.0 + - - +
428B VAL* 4.8 2.5 - - - -
429B PRO* 3.2 23.1 - - - +
547B TRP* 3.9 38.4 - - + -
551B PHE* 4.7 11.9 - - + -
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Residues in contact with MET 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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252B THR* 3.4 37.1 + - + +
254B VAL* 5.6 8.1 - - + -
355B PHE* 3.3 37.5 - - + -
359B ILE* 4.7 4.3 - - + -
388B LEU* 3.9 39.9 - - - +
389B VAL* 4.6 2.7 - - + -
421B ILE* 3.0 26.3 + - + +
424B VAL* 1.3 77.1 - - - +
426B PHE* 1.3 94.7 + - + +
429B PRO* 3.7 5.2 - - - +
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Residues in contact with PHE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B SER* 5.1 3.1 - - - -
247B SER* 3.7 24.2 - - - -
248B GLY* 4.4 4.5 - - - +
249B VAL* 6.3 0.4 - - - -
252B THR* 5.8 3.8 - - + -
350B ILE* 4.3 9.6 - - + -
354B GLU* 3.3 44.0 - - + -
355B PHE 5.0 0.2 - - - -
359B ILE* 3.6 24.7 - - + -
422B ALA* 3.4 6.6 + - - +
425B MET* 1.3 121.7 - - + +
427B GLY* 1.3 71.7 + - - +
429B PRO* 3.6 2.9 - - - +
430B SER* 3.0 28.9 + - - +
468B HIS* 3.8 20.0 - + - -
4002B SMB 5.4 2.0 - - - -
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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
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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