Contacts of the strand formed by residues 281 - 286 (chain A) in PDB entry 1BPO
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A PRO* 3.8 32.9 - - + +
255A GLU* 4.0 11.4 + - - +
256A ALA* 4.2 14.3 + - + +
259A ASP* 3.4 20.2 - - - -
275A LEU 4.3 0.2 - - - -
276A ILE* 3.2 8.9 - - - +
277A THR* 3.0 40.9 + - + +
279A TYR* 3.8 12.3 - - + -
280A GLY* 1.3 80.2 - - - +
282A ILE* 1.3 58.5 + - - +
283A HIS* 4.3 9.9 - + - +
295A MET* 6.3 1.3 - - + -
296A ASN* 3.4 19.1 - - - -
297A ARG* 3.6 41.1 + - + +
298A ILE* 5.1 0.2 - - - -
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Residues in contact with ILE 282 (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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7A ILE* 5.2 0.4 - - + -
274A PHE* 4.6 8.7 - - + -
275A LEU 3.2 5.2 - - - +
276A ILE* 3.5 31.2 - - + -
281A TYR* 1.3 74.3 - - - +
283A HIS* 1.3 73.1 + - - +
284A LEU* 4.4 9.6 - - + -
294A TYR* 3.9 9.9 - - + +
295A MET* 3.2 4.0 - - - +
296A ASN* 2.8 43.7 + - + +
298A ILE* 3.7 29.8 - - + -
315A ILE* 4.1 17.9 - - + -
327A VAL* 4.2 22.4 - - + -
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Residues in contact with HIS 283 (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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250A VAL* 4.3 7.9 - - + -
251A PHE 3.5 25.1 + - - -
273A VAL 3.4 0.6 - - - +
274A PHE* 3.4 5.0 - - - -
275A LEU* 2.8 47.8 + - + +
277A THR* 3.6 25.8 - - + +
281A TYR* 4.3 8.3 - + - +
282A ILE* 1.3 84.7 - - - +
284A LEU* 1.3 66.0 + - - +
285A TYR* 3.1 39.2 + + + -
294A TYR 3.2 8.5 - - - +
295A MET* 3.0 28.5 - - + +
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Residues in contact with LEU 284 (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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7A ILE* 3.9 24.9 - - + -
272A VAL* 3.6 22.4 - - + -
273A VAL 3.3 4.0 - - - -
274A PHE* 3.1 35.9 - - + -
282A ILE* 4.4 9.9 - - + -
283A HIS* 1.3 79.4 - - - +
285A TYR* 1.3 56.2 + - - +
292A CYS* 3.7 4.9 - - - -
293A ILE* 2.8 36.4 + - + -
294A TYR* 2.8 28.5 + - + +
327A VAL* 4.8 1.3 - - + -
329A VAL* 3.8 21.1 - - + -
334A ILE* 4.7 11.9 - - + -
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Residues in contact with TYR 285 (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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228A LEU* 3.7 27.1 - - + -
248A VAL* 4.2 13.5 - - + -
249A ASP 4.2 1.7 + - - -
250A VAL* 3.2 27.8 - - + +
251A PHE 4.3 0.7 + - - -
272A VAL* 3.2 6.2 - - - -
273A VAL* 2.7 55.9 + - + -
275A LEU* 4.0 19.1 - - + -
283A HIS* 3.1 43.3 + - + -
284A LEU* 1.3 75.6 - - - +
286A ASP* 1.3 63.3 + - - +
290A GLY 3.7 13.5 - - - +
291A THR 3.2 4.9 - - - +
292A CYS* 3.4 35.1 - - + -
293A ILE* 4.2 4.3 - - - +
295A MET* 4.9 0.3 - - - -
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Residues in contact with ASP 286 (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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230A ILE* 4.0 0.9 - - - +
271A ASP 4.0 2.9 - - - -
272A VAL* 5.0 0.2 - - - -
285A TYR* 1.3 70.9 - - - +
287A LEU* 1.3 60.7 + - - +
288A GLU* 3.3 5.8 + - - +
289A THR* 2.8 42.7 + - - +
290A GLY* 2.6 33.6 + - - -
291A THR* 2.7 20.1 + - - +
293A ILE* 3.9 17.4 - - + +
347A LEU* 3.7 14.7 - - + +
351A MET* 4.4 3.8 - - + -
354A ARG* 3.1 29.9 + - - -
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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