Contacts of the strand formed by residues 5427 - 5430 (chain b) in PDB entry 3A0B
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 PHE5427 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5049b LEU* 3.4 28.9 - - + -
5304b GLU* 4.1 5.2 - - - -
5307b ALA* 3.6 9.4 - - + -
5308b PHE* 3.0 50.7 - + + -
5311b TYR* 4.7 6.3 - + + -
5334b ALA* 5.4 1.3 - - + -
5336b ALA* 2.9 25.4 - - - +
5337b TRP* 3.5 34.3 - + + -
5338b LYS* 4.5 7.9 + - - +
5425b GLU* 3.4 18.6 + - + -
5426b ILE* 1.3 84.3 - - - +
5428b GLU* 1.3 58.6 + - - +
5429b PHE* 3.0 36.1 + - + -
5202o GLN* 5.3 0.3 + - - -
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Residues in contact with GLU5428 (chain b).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5335b GLN* 2.5 49.4 + - + +
5336b ALA* 2.7 25.4 + - + +
5338b LYS* 4.0 28.6 - - + +
5402b GLU* 3.7 18.6 - - - +
5427b PHE* 1.3 67.5 - - - +
5429b PHE* 1.3 62.0 + - - +
5204o LYS* 5.0 6.1 - - - +
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Residues in contact with PHE5429 (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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5054b ARG* 4.2 4.0 - - - -
5308b PHE* 4.6 5.8 - + - -
5311b TYR* 3.3 29.8 - + - -
5331b ASP* 3.0 59.0 - - + +
5332b GLY* 3.2 19.3 - - - -
5333b ILE 3.6 3.1 - - - -
5334b ALA* 4.4 6.3 - - + -
5335b GLN* 4.5 0.4 - - - -
5427b PHE* 3.0 43.9 + - + -
5428b GLU* 1.3 77.8 - - - +
5430b ASP* 1.3 58.5 + - - +
5431b THR* 3.3 3.3 + - + -
5202o GLN* 4.4 13.5 - - + +
5204o LYS* 2.5 39.7 + - - +
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Residues in contact with ASP5430 (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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5333b ILE* 2.9 33.6 + - + +
5335b GLN* 3.3 36.9 + - + +
5429b PHE* 1.3 69.3 - - - +
5431b THR* 1.3 57.6 + - - +
5432b GLU* 3.0 5.8 + - - +
5433b THR* 2.3 50.1 + - - -
5434b LEU* 5.2 1.7 - - - +
5204o LYS* 4.8 0.9 - - - +
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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