Contacts of the helix formed by residues 266 - 273 (chain B) in PDB entry 1BMO
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 LEU 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B HIS* 4.2 12.8 - - + +
218B PHE* 3.6 46.1 - - + -
228B GLY* 3.6 5.3 + - - +
265B ALA* 1.3 74.4 - - - +
267B ASP* 1.3 58.5 + - - +
269B TRP* 3.3 6.8 + - + +
270B ALA* 2.8 35.2 + - + +
280B ILE* 3.9 23.1 - - + -
282B LYS* 4.3 25.4 - - + -
285B VAL* 3.9 25.1 - - + -
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Residues in contact with ASP 267 (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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265B ALA* 4.2 9.9 - - - +
266B LEU* 1.3 77.8 - - - +
268B GLU* 1.3 83.0 + - - +
271B GLY* 2.9 28.1 + - - -
277B GLN* 5.5 9.0 - - + +
280B ILE* 3.9 22.6 - - + +
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Residues in contact with GLU 268 (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 CYS* 3.4 19.4 - - - +
257B ASP* 4.1 1.6 - - - -
258B LEU* 2.7 41.9 + - + +
259B ASP* 3.3 11.5 + - - +
263B TYR 2.9 3.0 - - - +
264B ILE* 3.7 4.0 - - + -
265B ALA* 2.9 34.6 + - + +
267B ASP* 1.3 93.5 + - - +
269B TRP* 1.3 54.3 + - - +
271B GLY* 3.7 0.6 - - - -
272B CYS* 2.8 37.1 + - - +
302B CA 2.6 27.2 - - - -
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Residues in contact with TRP 269 (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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150B MET* 5.1 2.0 - - - -
154B LEU* 4.6 4.7 - - + -
214B VAL* 2.8 31.3 + - + +
217B GLN* 3.5 38.4 - - + -
218B PHE* 3.5 28.5 - + + +
221B LEU* 4.3 2.7 - - + -
230B LEU* 3.9 22.4 - - + -
238B LEU* 3.8 17.5 - - + -
253B PHE* 3.3 38.4 - + - -
256B CYS* 5.2 0.4 - - - -
264B ILE* 3.5 14.5 - - + +
265B ALA 2.8 18.4 + - - +
266B LEU* 3.6 7.6 - - + +
268B GLU* 1.3 72.1 - - - +
270B ALA* 1.3 74.7 + - - +
272B CYS* 3.1 12.8 + - - +
273B PHE* 3.2 40.5 + + - -
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Residues in contact with ALA 270 (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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214B VAL* 4.2 9.2 - - + -
215B HIS* 5.1 2.9 - - + +
266B LEU* 2.8 23.6 + - + +
269B TRP* 1.3 80.9 - - + +
271B GLY* 1.3 55.7 + - - +
273B PHE* 2.8 25.8 + - - +
275B ILE* 3.2 28.0 + - + +
280B ILE* 3.6 33.7 - - + -
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Residues in contact with GLY 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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267B ASP 2.9 21.0 + - - -
268B GLU 3.7 0.4 - - - -
270B ALA* 1.3 74.4 - - - +
272B CYS* 1.3 61.5 + - - +
274B GLY* 3.2 11.7 + - - -
275B ILE 3.8 12.7 + - - -
277B GLN* 6.4 0.2 - - - -
280B ILE* 4.8 1.3 - - - +
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Residues in contact with CYS 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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147B PRO* 4.5 7.3 - - - +
252B PHE* 3.1 30.0 - - + -
255B THR* 4.7 5.8 - - - -
256B CYS* 2.0 54.3 - - + -
268B GLU 2.8 23.2 + - - +
269B TRP* 3.3 7.4 - - - +
270B ALA 3.1 0.2 - - - -
271B GLY* 1.3 74.6 - - - +
273B PHE* 1.3 62.0 + - + +
274B GLY 3.3 1.2 + - - -
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Residues in contact with PHE 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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147B PRO* 4.1 20.2 - - + -
150B MET* 3.4 42.0 - - + -
151B ARG* 2.6 46.2 + - + +
154B LEU* 5.3 3.4 - - + -
203B PHE* 3.6 2.3 - - - -
214B VAL* 4.2 22.9 - - + -
252B PHE* 3.7 24.7 - + - -
253B PHE* 3.9 9.2 - + - -
269B TRP* 3.2 61.2 + + - -
270B ALA 2.8 7.9 + - - +
272B CYS* 1.3 80.8 - - + +
274B GLY* 1.3 57.4 + - - +
275B ILE* 3.3 3.1 + - - +
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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