Contacts of the helix formed by residues 286 - 300 (chain B) in PDB entry 5B2R
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 TYR 286 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 3.6 22.7 - - + -
196B PHE* 3.3 40.6 - + - -
256B PHE* 3.7 26.7 - + - -
279B LEU* 3.5 19.5 - - + +
282B ILE* 3.4 35.0 - - + -
283B GLY* 3.2 12.5 + - - -
284B ASP 3.0 2.0 - - - -
285B GLN* 1.3 83.3 - - + +
287B ALA* 1.3 61.4 + - - +
288B ASP 3.5 1.6 - - - -
289B LEU* 3.8 13.8 + - + -
290B PHE* 3.4 25.4 - + + -
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 5.8 3.6 - - - +
279B LEU* 4.4 14.6 - - + -
284B ASP 3.1 16.0 + - - +
285B GLN 3.2 1.8 - - - -
286B TYR* 1.3 79.1 - - - +
288B ASP* 1.3 66.8 + - - +
289B LEU 3.3 0.3 + - - -
290B PHE* 3.6 2.6 + - - +
291B LEU* 3.0 29.4 + - + +
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Residues in contact with ASP 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B THR* 3.2 28.1 - - + +
195B LEU* 5.5 3.1 - - + -
285B GLN 4.3 6.1 + - - +
286B TYR 3.5 0.4 - - - -
287B ALA* 1.3 81.7 - - - +
289B LEU* 1.3 60.1 + - - +
291B LEU* 3.7 23.6 - - + +
292B ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.6 18.9 - - + +
191B THR* 4.2 2.9 - - - +
192B TYR* 3.6 37.5 - - + +
195B LEU* 3.6 19.5 - - + +
196B PHE* 4.1 12.8 - - + -
237B LEU* 3.9 23.6 - - + -
241B LEU* 3.7 27.8 - - + +
256B PHE* 5.7 0.2 - - + -
286B TYR* 3.8 14.9 + - + +
287B ALA 3.2 1.2 - - - -
288B ASP* 1.3 78.6 - - - +
290B PHE* 1.3 68.0 + - + +
292B ALA 3.6 0.2 + - - -
293B ALA* 3.1 26.2 + - - +
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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
----------------------------------------------------------
241B LEU* 3.7 29.2 - - + -
244B LEU* 5.8 2.2 - - + -
252B PHE* 4.6 3.6 - + - -
256B PHE* 4.6 12.1 - + - -
264B LEU* 3.5 34.1 - - + -
271B TYR* 3.4 22.1 + - - +
275B LEU* 3.5 27.1 - - + -
278B LEU* 3.8 23.1 - - + -
279B LEU* 4.9 0.2 - - + -
282B ILE* 4.5 4.9 - - + -
286B TYR* 3.4 29.8 - - + -
287B ALA 3.6 2.8 + - - +
289B LEU* 1.3 85.4 - - + +
291B LEU* 1.3 58.1 + - - +
293B ALA* 3.7 9.4 - - + +
294B LYS* 3.0 27.4 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 5.9 0.4 - - - +
287B ALA* 3.0 19.8 + - + +
288B ASP* 3.8 25.8 - - - +
289B LEU 3.2 0.4 - - - -
290B PHE* 1.3 75.2 - - - +
292B ALA* 1.3 60.8 + - - +
294B LYS* 3.3 6.9 + - + +
295B ASN* 3.0 43.5 + - - +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 5.2 1.4 - - - +
187B GLN* 4.3 13.0 - - - +
188B LEU* 3.7 37.5 - - + +
191B THR* 3.8 10.1 - - + +
288B ASP 3.0 18.9 + - - +
291B LEU* 1.3 74.5 - - - +
293B ALA* 1.3 64.6 + - - +
295B ASN* 3.8 8.2 - - - +
296B LEU* 3.1 25.1 + - - +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 4.0 14.2 - - + +
241B LEU* 5.4 11.9 - - + +
244B LEU* 5.0 15.0 - - + -
245B SER* 2.8 28.7 + - - +
266B LEU* 4.3 4.0 - - + +
271B TYR* 5.9 0.4 - - - +
289B LEU 3.1 18.5 + - - +
290B PHE* 3.7 12.1 - - + +
291B LEU 3.2 0.4 - - - -
292B ALA* 1.3 78.1 - - - +
294B LYS* 1.3 60.9 + - - +
296B LEU 3.7 0.2 + - - -
297B SER* 3.2 12.8 + - - -
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Residues in contact with LYS 294 (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 LEU* 4.0 30.9 - - + +
271B TYR* 5.1 2.5 - - + +
290B PHE 3.0 17.9 + - - +
291B LEU* 3.6 9.0 - - + +
292B ALA 3.2 0.4 - - - -
293B ALA* 1.3 75.5 - - - +
295B ASN* 1.3 65.1 + - - +
297B SER* 3.2 14.0 + - - -
298B ASP* 3.4 16.1 + - - +
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Residues in contact with ASN 295 (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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184B LEU* 3.3 32.5 - - + +
187B GLN* 4.1 16.1 + - - +
291B LEU* 3.0 36.1 + - - +
292B ALA* 3.3 8.5 + - - +
294B LYS* 1.3 74.6 - - - +
296B LEU* 1.3 65.0 + - - +
298B ASP* 3.3 24.2 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.8 23.4 - - + +
185B PHE* 3.4 51.1 - - + +
188B LEU* 4.4 13.5 - - + -
212B LEU* 4.8 14.4 - - + -
242B ILE* 6.2 0.7 - - + -
245B SER* 3.9 24.0 - - - +
292B ALA 3.1 15.6 + - - +
295B ASN* 1.3 77.1 - - - +
297B SER* 1.3 62.0 + - - +
298B ASP 3.2 0.9 + - - -
299B ALA* 3.5 11.1 + - - +
300B ILE* 3.6 19.8 + - + +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU 4.4 0.7 + - - -
245B SER* 3.6 24.8 + - - +
266B LEU* 3.6 24.9 - - - +
293B ALA 3.2 15.2 + - - -
294B LYS 3.4 11.2 - - - -
295B ASN 3.2 1.2 - - - -
296B LEU* 1.3 78.3 - - - +
298B ASP* 1.3 62.2 + - - +
299B ALA 3.5 0.2 - - - -
300B ILE* 3.8 1.9 - - - -
301B LEU* 3.1 29.5 + - - +
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Residues in contact with ASP 298 (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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176B PRO* 6.2 0.2 - - - +
177B ASP 5.6 1.4 + - - -
294B LYS 3.6 15.2 - - - +
295B ASN* 3.3 16.6 + - - +
296B LEU 3.2 0.8 - - - -
297B SER* 1.3 81.3 - - - +
299B ALA* 1.3 62.0 + - - +
300B ILE 3.4 0.7 + - - -
301B LEU* 3.5 19.0 + - - +
302B LEU* 4.5 6.2 - - - +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ASP* 3.2 29.6 - - + +
178B ASN* 4.3 21.8 + - - -
184B LEU* 4.0 23.3 - - + -
295B ASN 4.0 1.2 + - - -
296B LEU 3.5 4.0 + - - +
297B SER 3.5 0.2 - - - -
298B ASP* 1.3 80.0 - - - +
300B ILE* 1.3 58.7 + - + +
301B LEU 3.5 0.2 - - - -
302B LEU* 4.0 12.4 - - - +
303B SER* 5.6 0.3 - - - -
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Residues in contact with ILE 300 (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* 6.2 4.3 - - + -
213B SER* 6.2 1.1 - - - -
245B SER 5.5 4.8 - - - +
296B LEU* 3.6 21.6 + - + +
297B SER* 3.8 3.4 - - - +
298B ASP 3.3 0.2 - - - -
299B ALA* 1.3 78.2 - - + +
301B LEU* 1.3 64.6 + - - +
302B LEU 3.4 2.9 - - - -
303B SER* 3.4 27.6 + - - +
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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
------------------------------------------------------------
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