Contacts of the helix formed by residues 425 - 430 (chain B) in PDB entry 2YA4
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 LYS 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B TRP* 3.4 56.0 - - + +
395B ILE* 3.7 27.7 - - + +
424B GLY* 1.3 69.5 - - - -
426B GLY* 1.3 64.9 + - - +
427B ILE 3.2 0.5 + - - -
428B PHE* 2.8 36.2 + - + +
429B GLY* 3.7 10.1 - - - +
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Residues in contact with GLY 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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357B ASP 3.8 17.9 - - - -
358B TRP* 3.4 5.2 - - - +
399B VAL* 4.3 6.1 - - - -
421B PHE* 3.8 29.3 - - - +
422B PRO 5.3 1.1 + - - +
424B GLY 2.8 14.2 + - - -
425B LYS* 1.3 68.9 - - - +
427B ILE* 1.3 58.7 + - - -
429B GLY* 2.8 22.5 + - - -
430B MET 3.8 2.9 + - - -
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Residues in contact with ILE 427 (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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357B ASP* 4.8 2.0 + - + -
358B TRP* 5.6 2.2 - - + -
421B PHE* 3.6 23.0 - - + -
425B LYS 3.2 0.6 + - - +
426B GLY* 1.3 71.7 - - - -
428B PHE* 1.3 88.7 + - + +
429B GLY 3.1 0.4 - - - -
430B MET* 3.3 34.1 + - - +
550B PHE* 3.6 39.0 - - + -
582B HIS* 4.1 14.4 + - + +
583B LEU* 3.9 29.8 - - + -
1780B EDO 3.9 24.0 + - - +
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Residues in contact with PHE 428 (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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358B TRP* 3.7 36.3 - + - -
425B LYS* 2.8 30.9 + - + +
427B ILE* 1.3 88.5 - - + +
429B GLY* 1.3 58.3 + - - +
430B MET 3.4 5.2 + - - +
582B HIS* 5.7 3.4 - + - -
583B LEU* 3.9 27.6 - - + -
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Residues in contact with GLY 429 (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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423B GLU 5.5 2.1 - - - +
424B GLY* 4.8 6.7 - - - -
425B LYS* 3.5 17.0 + - - -
426B GLY 2.8 12.8 + - - -
428B PHE* 1.3 77.3 - - - +
430B MET* 1.3 65.5 + - - +
517B LYS* 3.4 27.0 - - - +
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Residues in contact with MET 430 (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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421B PHE* 4.3 3.8 - - + -
426B GLY 3.8 0.8 + - - -
427B ILE* 3.3 38.4 + - - +
428B PHE 3.4 5.4 - - - +
429B GLY* 1.3 80.4 - - - +
431B SER* 1.3 68.4 + - - +
432B SER* 3.6 1.9 + - - -
517B LYS 3.4 8.1 - - - +
518B ASP* 3.9 26.7 - - - +
519B SER* 3.7 27.4 - - - +
549B LYS* 3.4 54.4 + - + +
550B PHE* 4.4 4.9 - - - -
582B HIS* 4.7 3.1 - - - -
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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