Contacts of the strand formed by residues 271 - 277 (chain B) in PDB entry 2BTO
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 PHE 271 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B LEU* 3.7 32.3 - - + -
196B LEU* 3.9 19.3 - - + -
197B ARG* 4.0 11.9 - - - -
203B CYS* 3.4 30.3 - - + -
205B ILE* 4.2 8.5 - - + -
270B HIS* 1.3 102.7 - + - +
272B LEU* 1.3 59.6 + - - +
375B ASN* 3.2 15.6 - - - +
376B ASN 4.8 1.2 + - - -
379B ILE* 3.3 30.5 - - + +
383B LEU* 5.3 2.2 - - + -
423B LEU* 3.9 35.0 - - + -
427B TYR* 2.9 24.4 + - + +
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Residues in contact with LEU 272 (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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169B LEU* 5.1 5.4 - - + -
202B ALA* 4.5 15.0 - - + -
203B CYS 2.9 12.3 + - - +
204B LEU* 4.0 17.5 - - + -
205B ILE* 3.1 30.7 + - - +
260B LEU* 4.7 7.4 - - + -
263B LEU* 3.8 38.6 - - + +
264B VAL* 4.7 2.7 - - + -
270B HIS 4.1 10.5 - - - +
271B PHE* 1.3 82.7 - - - +
273B MET* 1.3 67.9 + - - +
373B LEU* 5.1 5.4 - - + -
374B ALA 3.4 9.4 - - - +
375B ASN* 3.8 28.9 - - + +
376B ASN 5.8 0.2 - - - +
379B ILE* 4.3 0.7 - - - +
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Residues in contact with MET 273 (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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204B LEU* 3.7 5.6 - - - -
205B ILE* 3.8 21.8 - - + -
272B LEU* 1.3 78.6 - - - +
274B CYS* 1.3 63.6 + - - +
305B VAL* 4.1 9.9 - - + -
306B PHE 5.9 0.2 - - - -
307B ALA* 3.8 22.2 - - + -
309B CYS* 3.8 14.8 - - - -
311B PRO* 4.2 22.0 - - + -
373B LEU* 3.4 4.3 - - - +
374B ALA* 2.9 35.3 + - + +
376B ASN* 3.6 37.2 - - + +
379B ILE* 4.0 24.2 - - + +
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Residues in contact with CYS 274 (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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204B LEU* 3.9 11.2 - - + +
205B ILE 4.8 2.2 + - - -
206B PHE* 3.7 32.3 - - - -
236B ALA* 4.3 11.2 - - - -
273B MET* 1.3 77.4 - - - +
275B ALA* 1.3 57.1 + - - +
305B VAL* 3.3 4.9 - - - +
306B PHE* 2.7 47.8 + - - +
371B VAL* 4.4 5.8 - - + -
372B LEU* 2.9 13.9 - - - +
373B LEU* 3.7 16.6 - - + -
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Residues in contact with ALA 275 (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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274B CYS* 1.3 76.5 - - - +
276B PHE* 1.3 62.8 + - - +
299B LEU* 3.5 30.1 - - + +
301B ASP 5.6 0.2 - - - +
304B SER* 3.5 22.4 - - - +
305B VAL* 3.9 6.7 - - + -
306B PHE* 4.5 2.0 - - - +
371B VAL* 3.4 8.1 - - - +
372B LEU* 2.8 39.9 + - + +
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Residues in contact with PHE 276 (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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235B GLU* 3.3 55.2 - - + -
236B ALA* 4.2 10.8 - - + -
239B GLY* 5.6 1.1 - - - -
275B ALA* 1.3 75.8 - - - +
277B ALA* 1.3 78.8 + - - +
278B PRO 3.2 25.1 - - - -
279B LEU* 3.4 27.4 - - + +
299B LEU* 4.0 3.7 - - - +
304B SER* 3.7 11.9 + - - -
306B PHE* 3.7 24.0 - + + -
366B HIS* 3.9 7.9 - + - -
369B SER* 3.6 26.7 - - - -
370B MET 3.4 14.1 - - - -
371B VAL* 3.7 17.7 - - + -
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Residues in contact with ALA 277 (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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276B PHE* 1.3 79.8 - - - +
278B PRO* 1.3 70.8 - - + +
279B LEU 4.0 0.4 - - - +
295B MET* 3.6 34.9 - - + +
298B SER* 4.6 7.0 - - - -
299B LEU* 4.1 18.2 - - + +
369B SER* 3.3 3.3 - - - -
370B MET* 2.7 37.7 + - + +
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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