Contacts of the helix formed by residues 266 - 273 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A HIS* 4.2 12.1 - - + -
218A PHE* 3.6 45.6 - - + -
228A GLY* 3.6 4.4 + - - +
265A ALA* 1.3 74.6 - - - +
267A ASP* 1.3 58.2 + - - +
269A TRP* 3.3 6.9 + - + -
270A ALA* 2.7 35.2 + - + +
280A ILE* 3.8 24.5 - - + -
282A LYS* 4.3 24.7 - - + -
285A VAL* 3.9 25.6 - - + -
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Residues in contact with ASP 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ALA* 4.1 10.5 - - - +
266A LEU* 1.3 77.1 - - - +
268A GLU* 1.3 84.6 + - - +
270A ALA* 4.0 0.2 - - - +
271A GLY* 2.8 28.4 + - - -
277A GLN* 5.5 8.5 - - + +
280A ILE* 3.8 22.4 - - + +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A CYS* 3.5 18.9 - - - +
257A ASP* 4.1 1.3 - - - -
258A LEU* 2.7 43.5 + - + +
259A ASP* 3.2 11.9 + - - +
263A TYR 2.9 3.1 - - - +
264A ILE* 3.7 3.8 - - + -
265A ALA* 2.9 34.9 + - - +
266A LEU 3.3 0.4 - - - -
267A ASP* 1.3 94.6 + - - +
269A TRP* 1.3 54.2 + - - +
271A GLY* 3.9 0.2 - - - -
272A CYS* 2.8 37.2 + - - +
302A CA 2.6 27.8 - - - -
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Residues in contact with TRP 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MET* 5.2 2.2 - - - -
154A LEU* 4.6 4.7 - - + -
214A VAL* 2.8 30.2 + - + +
217A GLN* 3.5 38.6 - - + -
218A PHE* 3.5 28.7 - + + +
221A LEU* 4.2 3.4 - - + -
230A LEU* 3.9 22.2 - - + -
238A LEU* 3.8 17.5 - - + -
253A PHE* 3.3 37.9 - + - -
256A CYS* 5.5 0.2 - - - -
264A ILE* 3.5 14.7 - - + +
265A ALA 2.8 16.9 + - - +
266A LEU* 3.6 7.9 - - + +
268A GLU* 1.3 73.7 - - - +
270A ALA* 1.3 74.3 + - - +
272A CYS* 3.1 14.0 + - - +
273A PHE* 3.2 40.3 + + - -
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 4.2 9.9 - - + -
215A HIS* 5.1 3.4 - - + +
266A LEU* 2.7 23.6 + - + +
269A TRP* 1.3 82.2 - - + +
271A GLY* 1.3 59.2 + - - +
273A PHE* 2.8 21.8 + - - +
274A GLY 3.2 0.2 + - - -
275A ILE* 3.2 27.7 + - + +
280A ILE* 3.6 32.3 - - + -
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Residues in contact with GLY 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ASP 2.8 21.5 + - - -
268A GLU* 3.7 0.7 - - - -
270A ALA* 1.3 73.8 - - - +
272A CYS* 1.3 59.9 + - - +
274A GLY* 3.2 12.4 + - - -
275A ILE 3.7 12.8 - - - -
277A GLN* 6.4 0.2 - - - -
280A ILE* 4.8 1.9 - - - +
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Residues in contact with CYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PRO* 4.5 7.4 - - - +
252A PHE* 3.2 28.3 - - + -
255A THR* 4.6 6.7 - - - -
256A CYS* 2.0 55.0 - - + -
268A GLU 2.8 20.0 + - - +
269A TRP* 3.1 7.8 + - - +
270A ALA 3.1 0.2 + - - -
271A GLY* 1.3 77.8 - - - +
273A PHE* 1.3 62.2 + - + +
274A GLY 3.3 0.8 + - - -
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Residues in contact with PHE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PRO* 4.1 20.4 - - + -
150A MET* 3.4 37.0 - - + -
151A ARG* 2.7 45.8 + - + +
154A LEU* 5.3 2.7 - - + -
203A PHE* 3.6 2.3 - - - -
214A VAL* 4.1 22.9 - - + -
252A PHE* 3.7 28.0 - + - -
253A PHE* 3.8 12.8 - + - -
269A TRP* 3.2 61.8 + + - +
270A ALA 2.8 8.4 + - - +
272A CYS* 1.3 80.3 - - + +
274A GLY* 1.3 56.2 + - - +
275A ILE* 3.3 2.7 + - - +
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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