Contacts of the strand formed by residues 5430 - 5433 (chain b) in PDB entry 2AXT
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 PHE5430 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5052b LEU* 3.8 17.9 - - + -
5307b GLU 4.6 1.8 - - - -
5310b ALA* 3.6 8.5 - - + -
5311b PHE* 3.2 59.0 - + + -
5314b TYR* 4.5 8.9 - + + -
5337b ALA* 4.9 2.0 - - + -
5339b ALA 3.5 17.9 - - - -
5340b TRP* 3.9 17.9 - + + -
5341b LYS* 3.4 15.0 - - - +
5428b GLU* 3.3 34.2 + - + -
5429b ILE* 1.3 82.4 - - - +
5431b GLU* 1.3 60.3 + - - +
5432b PHE* 4.0 34.1 + - + -
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Residues in contact with GLU5431 (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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84O ASN* 6.0 1.7 - - - +
5337b ALA* 4.0 0.3 - - - -
5338b GLN* 2.7 47.5 + - + +
5339b ALA* 2.8 19.4 + - - +
5341b LYS* 3.9 22.7 + - + +
5405b GLU* 2.8 27.0 - - - +
5430b PHE* 1.3 72.8 - - - +
5432b PHE* 1.3 62.4 + - - +
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Residues in contact with PHE5432 (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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5057b ARG* 4.2 3.8 - - - -
5311b PHE* 4.5 2.2 - + - -
5314b TYR* 3.2 33.9 - + - -
5334b ASP* 3.3 34.5 - - + +
5335b GLY* 3.8 10.5 - - - -
5336b ILE 3.5 1.8 - - - +
5337b ALA* 3.5 35.9 - - + -
5338b GLN* 4.1 2.7 - - - -
5430b PHE* 4.0 31.2 - - + -
5431b GLU* 1.3 80.2 - - - +
5433b ASP* 1.3 60.7 + - - +
5434b THR* 3.7 6.7 + - + +
5202o GLN* 3.1 28.9 - - - -
5204o LYS* 4.0 18.9 + - - +
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Residues in contact with ASP5433 (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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5335b GLY* 3.6 0.7 - - - -
5336b ILE* 2.8 48.8 + - + +
5338b GLN* 3.7 23.9 + - + +
5432b PHE* 1.3 70.7 - - - +
5434b THR* 1.3 63.3 + - - +
5435b GLU* 3.0 13.9 + - - +
5436b THR* 2.3 35.8 + - - -
5437b LEU* 5.5 0.9 + - - +
5439b SER* 4.7 0.5 + - - -
5204o LYS* 5.4 0.2 - - - +
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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