Contacts of the strand formed by residues 287 - 291 (chain B) in PDB entry 5WWT
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 ILE 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B THR* 3.8 22.0 - - + -
250B THR* 3.7 45.8 - - + +
253B ALA* 3.6 23.3 - - + -
262B VAL* 3.4 8.5 - - + +
264B ALA* 4.7 1.3 - - + -
275B ILE* 4.5 12.6 - - + -
276B LYS* 6.2 0.7 - - - -
279B ALA* 3.8 25.1 - - + +
284B LEU* 3.8 10.6 - - + +
285B ASN 3.2 5.9 - - - +
286B SER* 1.3 78.8 - - - +
288B ARG* 1.3 72.6 + - - +
289B ALA* 4.3 1.7 + - + +
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Residues in contact with ARG 288 (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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261B GLU* 2.5 39.1 + - - +
262B VAL 2.9 9.7 + - - -
263B ILE* 3.5 25.6 - - + +
264B ALA 2.9 25.3 + - - +
285B ASN 5.5 2.2 - - - +
286B SER 4.8 4.5 - - - +
287B ILE* 1.3 79.9 - - - +
289B ALA* 1.3 60.2 + - - +
290B PHE* 3.9 21.5 - - + -
308B GLY* 3.2 38.0 + - - -
309B GLU* 5.5 0.6 - - - +
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Residues in contact with ALA 289 (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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264B ALA* 3.2 9.0 - - + +
272B VAL* 3.8 11.7 - - + -
275B ILE* 3.8 25.8 - - + -
276B LYS* 3.4 46.3 + - + +
287B ILE* 4.2 2.6 + - + +
288B ARG* 1.3 71.8 - - - +
290B PHE* 1.3 75.0 + - - +
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Residues in contact with PHE 290 (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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263B ILE* 4.0 21.3 - - + -
264B ALA 2.9 8.3 + - - -
265B LEU* 3.4 10.4 - - + -
266B ASP 3.0 24.6 + - - -
272B VAL* 3.6 7.3 - - - +
276B LYS* 6.0 0.2 - - - -
288B ARG* 3.9 51.6 - - + -
289B ALA* 1.3 83.6 - - - +
291B CYS* 1.3 64.1 + - - +
292B PHE 3.4 0.5 + - - -
308B GLY 4.5 2.5 - - - -
309B GLU* 4.0 26.5 - - + -
310B PRO* 3.5 39.9 - - + -
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Residues in contact with CYS 291 (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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266B ASP 3.1 6.1 - - - -
267B LYS 3.2 26.7 - - - -
268B ILE 3.9 0.2 - - - -
269B PHE* 3.6 38.1 - - + -
272B VAL* 3.7 13.2 - - + +
290B PHE* 1.3 68.9 - - - +
292B PHE* 1.3 68.0 + - - +
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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