Contacts of the helix formed by residues 270 - 283 (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 THR 270 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268B LYS* 3.2 11.7 - - + +
269B ASP* 1.3 79.5 - - + +
271B TYR* 1.3 64.4 + - - +
272B ASP 3.4 1.1 - - - -
273B ASP* 3.2 10.9 + - - +
274B ASP* 2.5 52.4 + - - +
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Residues in contact with TYR 271 (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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244B LEU* 6.2 1.1 - - + -
264B LEU* 4.1 33.0 - - + -
265B GLN 3.4 32.7 + - - +
266B LEU* 3.6 38.9 - - + +
268B LYS* 3.4 10.6 + - - +
269B ASP 3.2 3.2 - - - -
270B THR* 1.3 77.4 + - - +
272B ASP* 1.3 73.3 + - - +
274B ASP* 3.3 4.6 + - - -
275B LEU* 2.8 56.8 + - + +
290B PHE* 3.4 38.2 + - - +
293B ALA* 5.9 0.3 - - - +
294B LYS* 5.5 2.2 - - + -
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Residues in contact with ASP 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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269B ASP 4.4 1.9 + - - +
270B THR 3.4 0.6 - - - -
271B TYR* 1.3 96.5 - - - +
273B ASP* 1.3 56.2 + - - +
275B LEU* 4.2 5.7 - - - +
276B ASP* 3.0 34.0 + - - +
650B GLN* 5.8 6.1 - - - +
653B ARG* 4.1 28.2 + - - +
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Residues in contact with ASP 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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269B ASP 5.3 0.2 + - - -
270B THR* 3.2 13.3 + - - +
271B TYR 3.1 0.6 - - - -
272B ASP* 1.3 79.0 - - - +
274B ASP* 1.3 56.6 + - - +
276B ASP* 3.2 7.7 + - - +
277B ASN* 2.7 33.5 + - - +
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Residues in contact with ASP 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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263B LYS 4.1 21.1 - - - +
264B LEU* 4.9 8.0 - - + -
265B GLN 5.8 0.3 + - - -
270B THR* 2.5 43.4 + - - +
271B TYR* 4.0 5.0 + - - +
273B ASP* 1.3 76.3 - - - +
275B LEU* 1.3 54.0 - - - +
277B ASN* 3.0 9.9 + - - +
278B LEU* 2.7 37.4 + - - +
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Residues in contact with LEU 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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264B LEU* 4.7 8.1 - - + +
271B TYR* 2.8 56.3 + - + +
272B ASP* 4.2 6.7 - - - +
274B ASP* 1.3 73.7 - - - +
276B ASP* 1.3 60.8 + - - +
278B LEU* 4.4 5.8 - - + +
279B LEU* 2.9 43.8 + - + +
286B TYR 5.2 0.2 - - - +
287B ALA* 5.8 3.1 - - - +
290B PHE* 3.5 49.4 - - + -
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Residues in contact with ASP 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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272B ASP* 3.0 24.1 + - - +
273B ASP* 3.4 8.8 - - - +
274B ASP 3.2 0.2 - - - -
275B LEU* 1.3 79.1 - - - +
277B ASN* 1.3 63.9 + - - +
279B LEU* 4.1 7.5 - - - +
280B ALA* 3.1 24.1 + - - +
599B LYS* 3.7 30.6 + - - +
650B GLN* 5.7 2.6 + - - -
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Residues in contact with ASN 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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262B ALA* 4.8 10.9 - - - +
273B ASP 2.7 18.3 + - - +
274B ASP* 3.0 14.7 + - - +
276B ASP* 1.3 75.3 - - - +
278B LEU* 1.3 64.7 + - - +
280B ALA* 3.4 12.3 + - - +
281B GLN* 3.5 29.1 + - - +
599B LYS* 6.3 0.4 - - - +
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Residues in contact with LEU 278 (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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252B PHE* 4.9 8.5 - - + -
256B PHE* 4.4 12.3 - - + -
258B LEU* 3.7 28.9 - - + -
262B ALA* 4.1 18.4 - - + +
264B LEU* 4.1 15.9 - - + -
274B ASP 2.7 19.8 + - - +
275B LEU* 3.9 7.0 - - + +
277B ASN* 1.3 77.5 - - - +
279B LEU* 1.3 58.6 + - - +
281B GLN* 2.9 10.9 + - - +
282B ILE* 2.9 46.9 + - + +
290B PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 279 (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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275B LEU* 2.9 33.9 + - + +
276B ASP* 4.1 8.3 - - - +
278B LEU* 1.3 76.0 - - - +
280B ALA* 1.3 57.5 + - - +
282B ILE* 3.8 8.1 - - + -
283B GLY* 2.6 52.0 + - - +
284B ASP* 3.7 25.9 + - + +
286B TYR* 3.5 33.2 - - + +
287B ALA* 4.4 12.3 - - + -
290B PHE* 4.9 0.4 - - + -
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Residues in contact with ALA 280 (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 ASP 3.1 19.2 + - - +
277B ASN* 3.6 8.5 - - - +
278B LEU 3.2 0.4 - - - -
279B LEU* 1.3 75.8 - - - +
281B GLN* 1.3 61.2 + - + +
283B GLY* 4.8 0.7 + - - -
599B LYS* 6.0 4.9 - - - -
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Residues in contact with GLN 281 (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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258B LEU* 3.7 37.8 - - + +
259B ALA* 5.2 4.4 - - - +
260B GLU* 5.3 9.9 + - - +
262B ALA* 5.0 2.9 - - - +
277B ASN* 3.5 27.6 + - - +
278B LEU* 2.9 11.8 + - - +
280B ALA* 1.3 82.4 - - + +
282B ILE* 1.3 67.5 + - + +
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Residues in contact with ILE 282 (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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256B PHE* 3.5 61.9 - - + -
258B LEU* 4.5 4.0 - - + -
278B LEU* 2.9 42.3 + - + +
279B LEU* 3.8 10.3 - - + -
281B GLN* 1.3 83.7 - - + +
283B GLY* 1.3 61.8 + - - +
286B TYR* 3.4 42.2 - - + -
290B PHE* 4.5 2.7 - - + -
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Residues in contact with GLY 283 (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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279B LEU* 2.6 32.7 + - - +
280B ALA 4.6 1.1 - - - -
281B GLN 3.6 1.2 - - - -
282B ILE* 1.3 74.1 - - - +
284B ASP* 1.3 65.6 + - - -
285B GLN* 3.1 6.4 + - - -
286B TYR* 3.2 15.9 + - - -
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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