Contacts of the helix formed by residues 395 - 405 (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 LEU 395 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B ILE* 3.9 9.4 - - + -
392B ALA* 2.7 36.0 + - + +
394B GLU* 1.3 87.4 - - + +
396B ILE* 1.3 67.2 + - - +
397B PRO* 3.0 5.8 - - - -
398B GLU* 3.2 23.4 + - - +
399B ALA* 3.2 9.9 + - - +
550B LEU* 3.4 45.7 - - + +
551B PHE* 4.3 21.5 - - + +
553B LYS* 4.4 21.5 - - + -
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Residues in contact with ILE 396 (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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379B MET* 3.2 44.9 - - + +
382B LEU* 3.9 18.0 - - + +
383B TRP* 3.6 39.0 - - + +
391B ILE* 3.9 15.9 - - + +
392B ALA 2.9 6.6 + - - +
393B LYS* 3.2 32.8 - - + +
395B LEU* 1.3 75.5 - - - +
397B PRO* 1.3 58.8 - - + +
399B ALA* 3.2 3.2 + - - +
400B THR* 2.6 39.7 + - - +
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Residues in contact with PRO 397 (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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379B MET* 4.0 27.4 - - - -
393B LYS 3.3 11.0 - - - +
394B GLU* 4.2 5.6 - - - +
395B LEU 3.3 5.6 - - - +
396B ILE* 1.3 93.2 - - + +
398B GLU* 1.3 68.7 + - + +
400B THR* 2.8 5.1 + - - +
401B GLU* 2.7 27.9 + - - +
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Residues in contact with GLU 398 (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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394B GLU 4.6 6.9 - - - +
395B LEU* 3.2 17.8 + - - +
397B PRO* 1.3 80.1 - - + +
399B ALA* 1.3 60.7 - - - +
401B GLU* 3.8 5.4 - - - +
402B LYS* 3.1 24.6 + - - +
546B PHE* 3.7 8.3 - - + -
550B LEU* 3.0 28.7 - - + +
553B LYS 5.4 2.6 - - - +
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Residues in contact with ALA 399 (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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382B LEU* 4.3 11.7 - - + -
391B ILE* 4.8 2.7 - - + -
395B LEU 3.2 4.7 + - - +
396B ILE* 3.5 9.4 - - - +
397B PRO 3.0 0.6 - - - -
398B GLU* 1.3 77.0 - - - +
400B THR* 1.3 67.0 + - - +
401B GLU 3.1 0.7 + - - -
402B LYS 3.4 8.8 + - - -
403B TYR* 3.4 19.6 + - - +
420B LEU* 4.1 3.0 - - + +
546B PHE* 3.8 12.1 - - - -
547B TRP* 3.7 19.5 - - + -
550B LEU* 3.4 22.2 - - + +
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLN* 3.3 22.8 + - - +
378B ALA* 3.5 29.8 - - + -
379B MET* 3.3 24.8 - - + +
382B LEU* 4.2 9.0 - - - +
396B ILE* 2.6 32.9 + - - +
397B PRO* 2.8 8.0 + - - -
399B ALA* 1.3 71.7 - - - +
401B GLU* 1.3 54.8 + - - -
403B TYR* 5.3 1.3 - - - -
404B LEU* 2.9 36.8 + - + +
417B PHE* 6.0 1.8 - - + -
420B LEU* 5.4 3.1 - - - -
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Residues in contact with GLU 401 (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* 4.1 17.1 + - - +
397B PRO 2.7 19.9 + - - +
398B GLU* 3.8 7.2 - - - +
400B THR* 1.3 69.3 - - - +
402B LYS* 1.3 68.1 + - - +
403B TYR 2.8 4.1 + - - -
405B GLY* 2.9 51.3 + - - +
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Residues in contact with LYS 402 (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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398B GLU 3.1 6.8 + - - +
399B ALA 3.4 2.6 + - - +
401B GLU* 1.3 79.3 - - - +
403B TYR* 1.3 65.6 + - + +
405B GLY 4.9 0.3 + - - -
406B GLY 5.7 0.2 + - - -
542B LYS* 3.2 42.4 + - - +
546B PHE* 3.5 60.6 - - + -
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Residues in contact with TYR 403 (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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399B ALA 3.4 8.6 + - - +
400B THR* 4.2 1.3 - - - +
401B GLU 2.8 2.4 + - - -
402B LYS* 1.3 89.2 - - + +
404B LEU* 1.3 60.8 + - + +
405B GLY 3.1 9.5 + - - -
406B GLY* 3.8 3.8 + - - -
416B LEU* 3.2 42.5 - - + +
419B ASP* 4.0 5.4 - - + -
420B LEU* 3.2 58.8 - - + -
423B ASP* 3.3 27.1 + - - +
543B GLU* 3.8 13.4 - - + +
546B PHE* 4.1 10.3 - + - -
547B TRP* 2.8 34.7 + + - -
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Residues in contact with LEU 404 (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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373B LEU* 4.6 5.4 - - + -
374B ASP 5.1 0.9 - - - +
375B GLN* 2.8 25.3 - - - +
378B ALA* 3.2 35.4 - - + -
400B THR* 2.9 23.3 + - + +
401B GLU 3.9 0.2 - - - -
403B TYR* 1.3 74.2 - - + +
405B GLY* 1.3 59.0 + - - +
406B GLY 3.3 2.4 + - - -
407B THR 3.9 1.4 - - - +
413B LYS* 2.9 64.5 + - + +
416B LEU* 3.4 14.8 - - + -
417B PHE* 3.4 30.5 - - + +
420B LEU* 6.2 0.7 - - + -
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Residues in contact with GLY 405 (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* 4.0 2.0 - - - -
401B GLU* 2.9 39.2 + - - +
402B LYS 5.5 0.2 - - - -
403B TYR 3.1 1.2 - - - -
404B LEU* 1.3 78.6 - - - +
406B GLY* 1.3 70.0 + - - +
407B THR 4.4 1.9 - - - +
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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
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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