Contacts of the strand formed by residues 254 - 259 (chain B) in PDB entry 5E9W
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 SER 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ASN* 3.1 15.0 + - - -
222B LYS* 3.4 21.8 - - - +
223B LEU 2.9 25.0 + - - -
240B TYR* 3.6 4.5 - - - -
244B LYS* 5.6 1.8 - - - +
251B TYR* 5.3 0.4 + - - -
252B ILE 3.6 1.2 + - - -
253B PHE* 1.3 77.3 - - - +
255B ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 255 (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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212B LEU* 6.1 0.2 - - + -
222B LYS* 5.5 2.2 - - - -
223B LEU* 3.2 11.7 - - + +
225B CYS* 5.6 0.4 - - - -
240B TYR* 3.7 32.2 + - + -
253B PHE* 4.1 8.1 - - + -
254B SER* 1.3 76.4 - - - +
256B GLU* 1.3 62.8 + - - +
257B PHE* 3.7 28.7 - - + -
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Residues in contact with GLU 256 (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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222B LYS* 3.0 28.1 + - - +
223B LEU 2.9 9.2 + - - +
224B VAL* 3.4 11.2 - - + +
225B CYS* 2.8 27.5 + - - +
255B ALA* 1.3 75.8 - - - +
257B PHE* 1.3 69.6 + - - +
258B ILE* 3.8 20.8 - - + +
270B LYS 3.8 2.3 - - - +
271B PHE* 3.5 9.6 - - - +
272B ARG* 2.7 45.0 + - - +
273B ASP 5.1 0.5 + - - -
276B MET* 4.8 1.6 - - - +
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Residues in contact with PHE 257 (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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212B LEU* 5.2 0.7 - - + -
225B CYS* 3.4 26.0 - - + -
233B VAL* 3.9 20.5 - - + +
236B CYS* 4.0 14.8 - - - -
237B GLN* 3.5 61.0 - - + +
240B TYR* 3.6 36.1 - + + -
241B GLU* 5.7 0.9 - - - -
255B ALA* 3.7 26.7 - - + -
256B GLU* 1.3 77.6 - - - +
258B ILE* 1.3 65.8 + - - +
259B THR 4.3 0.5 + - - -
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Residues in contact with ILE 258 (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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224B VAL* 3.9 14.1 - - + -
225B CYS 2.9 9.5 + - - +
226B THR* 2.6 45.8 + - - +
227B ASP 3.2 3.6 + - - -
233B VAL* 4.0 5.6 - - - +
256B GLU* 3.8 22.0 - - + +
257B PHE* 1.3 80.2 - - - +
259B THR* 1.3 61.7 + - - +
260B ALA* 4.2 2.7 - - + -
267B LEU* 4.6 5.2 - - + +
270B LYS* 3.7 46.2 - - + +
271B PHE* 3.6 32.3 - - + -
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Residues in contact with THR 259 (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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227B ASP 3.4 6.5 - - - +
228B ILE 3.8 20.4 - - - +
230B ASP* 2.6 40.2 + - + +
233B VAL* 3.5 19.2 - - - +
257B PHE 4.3 0.6 + - - -
258B ILE* 1.3 75.1 - - - +
260B ALA* 1.3 68.1 + - - +
270B LYS* 4.0 10.2 - - - +
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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