Contacts of the strand formed by residues 275 - 283 (chain A) in PDB entry 3R9X
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 VAL 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A MET* 3.5 5.1 - - - +
231A LEU* 3.3 13.2 - - + +
233A ILE* 3.6 25.4 - - + -
264A ARG* 3.5 14.2 - - + +
267A LEU* 4.1 12.1 - - + -
268A GLU* 3.2 33.7 + - + +
271A LEU* 4.6 10.5 - - + -
273A ARG 3.3 17.9 - - - +
274A PRO* 1.3 73.7 - - - +
276A TYR* 1.3 70.3 + - - +
277A LEU* 3.9 8.3 - - + +
1537C U 3.1 24.6 + - - +
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Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 3.8 16.7 - - + -
231A LEU 2.9 9.7 + - - -
232A VAL* 3.3 16.1 - - + +
233A ILE 3.0 25.1 + - - +
275A VAL* 1.3 75.0 - - - +
277A LEU* 1.3 59.5 + - - +
278A GLU* 4.2 24.2 + - + +
1537C U 3.4 46.5 + + + -
1538C C 3.6 43.5 - + + +
1539C C 3.8 27.1 + + - -
1540C U 4.5 3.3 + - - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 6.3 1.1 - - + -
198A VAL* 4.2 12.8 - - + -
218A ILE* 5.4 2.7 - - + -
233A ILE* 3.4 34.5 - - + +
235A GLY 5.5 0.4 - - - +
260A GLY* 3.7 26.0 - - - +
263A ALA* 3.7 21.1 - - + -
264A ARG* 3.7 14.6 - - + +
267A LEU* 4.4 6.3 - - + -
275A VAL* 3.9 5.3 - - + -
276A TYR* 1.3 71.8 - - - +
278A GLU* 1.3 60.3 + - - +
279A LEU* 3.9 26.8 + - + +
1536C C 4.0 7.3 + - - +
1537C U 2.9 40.7 + - - +
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Residues in contact with GLU 278 (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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232A VAL* 5.6 2.5 - - + -
233A ILE 2.8 14.2 + - - +
234A LYS* 3.4 23.8 - - + +
235A GLY 2.8 28.2 + - - +
276A TYR* 3.6 23.1 + - + -
277A LEU* 1.3 72.8 - - - +
279A LEU* 1.3 60.6 + - - +
280A TRP* 3.4 30.0 + - + +
1535C C 5.8 0.7 - - - +
1537C U 4.9 2.2 - - - -
1539C C 4.3 9.7 + - - -
1540C U 4.3 7.1 + - - +
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Residues in contact with LEU 279 (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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198A VAL* 4.1 25.8 - - + -
216A VAL* 5.5 1.8 - - + -
218A ILE* 5.8 1.1 - - + -
235A GLY* 3.2 19.5 - - - +
236A GLU 5.4 0.4 - - - -
237A ILE* 4.5 18.4 - - + -
256A LEU* 3.9 28.6 - - + +
259A ILE* 4.7 1.6 - - + -
260A GLY* 3.9 26.5 - - - +
277A LEU* 3.9 29.2 + - + +
278A GLU* 1.3 80.3 - - - +
280A TRP* 1.3 65.9 + - - +
1534C A 4.0 2.1 - - - -
1535C C 2.9 31.2 + - - +
1536C C 5.7 0.2 - - - +
1537C U 5.5 0.4 + - - -
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Residues in contact with TRP 280 (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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234A LYS* 3.2 27.4 - - - +
235A GLY 3.1 8.1 + - - -
236A GLU* 3.4 12.3 - - + +
237A ILE* 3.3 17.1 + - - -
278A GLU* 3.4 31.4 + - + +
279A LEU* 1.3 83.7 + - - +
281A VAL* 1.3 64.9 + - - +
282A LYS* 3.4 2.8 + - - +
1534C A 3.1 63.9 - + + +
1535C C 3.6 17.5 - + - -
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Residues in contact with VAL 281 (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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237A ILE* 3.5 22.0 - - + +
239A VAL* 4.5 6.3 - - + -
245A LYS* 3.5 36.9 + - + +
248A ILE* 3.9 22.9 - - + -
249A ILE* 3.7 22.4 - - + -
256A LEU* 4.2 11.9 - - + -
280A TRP* 1.3 71.1 - - - +
282A LYS* 1.3 63.9 + - - +
1534C A 3.0 37.5 + - + +
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Residues in contact with LYS 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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236A GLU* 3.4 28.3 - - - +
237A ILE 2.9 18.5 + - - +
238A ILE* 4.3 11.4 - - + -
239A VAL* 3.3 20.4 + - - +
245A LYS* 5.6 0.9 - - - +
280A TRP 3.4 5.3 + - - +
281A VAL* 1.3 75.1 - - - +
283A VAL* 1.3 78.2 + - - +
284A VAL* 4.2 19.3 - - + +
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Residues in contact with VAL 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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239A VAL* 3.5 23.3 - - + +
240A ASP 4.2 0.9 - - - -
241A ARG* 4.0 25.8 - - - +
242A GLU* 3.9 19.7 - - + +
245A LYS* 3.7 29.8 - - + +
282A LYS* 1.3 94.3 + - - +
284A VAL* 1.3 67.7 + - - +
285A PRO* 3.6 21.4 - - + +
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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