Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 3FUX
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 PRO 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLY 3.5 7.4 - - - +
232A TYR* 1.4 84.9 - - + +
234A LYS* 1.3 64.8 + - - +
235A ALA* 3.4 2.7 - - + +
236A ARG* 3.2 26.9 + - + +
237A VAL* 3.0 21.7 + - + +
267A LEU* 6.0 1.8 - - + -
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Residues in contact with LYS 234 (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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224A LEU* 3.8 28.0 - - + -
225A ASN* 4.3 13.2 - - - +
228A ALA* 4.2 22.2 - - + +
232A TYR 3.2 6.3 + - - -
233A PRO* 1.3 71.5 - - - +
235A ALA* 1.3 58.2 + - - +
237A VAL* 3.0 4.8 + - - +
238A GLU* 2.8 54.9 + - - +
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Residues in contact with ALA 235 (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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233A PRO* 3.4 1.9 - - + -
234A LYS* 1.3 78.0 - - - +
236A ARG* 1.3 57.6 + - + +
238A GLU* 3.4 16.1 + - - +
239A GLU* 3.0 30.1 + - - +
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Residues in contact with ARG 236 (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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233A PRO* 3.2 30.1 + - + +
235A ALA* 1.3 74.5 - - + +
237A VAL* 1.3 65.8 + - - +
239A GLU* 3.6 5.1 + - - +
240A ALA* 3.2 24.6 + - - +
266A GLY 2.6 30.9 + - - +
267A LEU* 3.1 34.4 + - + +
268A GLU 3.9 8.9 - - - +
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Residues in contact with VAL 237 (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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224A LEU* 3.7 21.8 - - + -
227A LEU* 3.8 29.6 - - + -
228A ALA 5.2 1.1 - - - +
232A TYR* 3.8 23.6 - - + +
233A PRO 3.0 16.8 + - - +
234A LYS* 3.6 5.6 - - - +
236A ARG* 1.3 73.8 - - - +
238A GLU* 1.3 65.7 + - - +
240A ALA* 3.2 2.1 + - - +
241A LEU* 3.0 38.1 + - + +
263A LEU* 4.8 3.8 - - + -
267A LEU* 3.7 21.3 - - + -
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Residues in contact with GLU 238 (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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224A LEU* 3.6 25.6 - - + +
234A LYS* 2.8 45.9 + - - +
235A ALA* 3.6 17.4 - - - +
237A VAL* 1.3 73.0 - - - +
239A GLU* 1.3 57.2 + - - +
241A LEU* 3.4 7.5 + - - +
242A ARG* 3.1 28.2 + - - +
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Residues in contact with GLU 239 (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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235A ALA 3.0 17.4 + - - +
236A ARG* 4.0 6.1 - - - +
238A GLU* 1.3 75.0 - - - +
240A ALA* 1.3 59.0 + - - +
242A ARG* 3.0 44.0 + - - +
243A ALA* 2.9 28.9 + - + +
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Residues in contact with ALA 240 (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 ARG 3.2 16.2 + - - +
237A VAL 3.7 1.8 - - - +
239A GLU* 1.3 76.7 - - - +
241A LEU* 1.3 63.7 + - - +
243A ALA* 3.3 6.5 + - - +
244A LEU* 3.3 28.1 + - - +
262A ARG 5.8 0.2 - - - +
263A LEU* 3.6 24.7 - - + -
266A GLY* 4.4 22.0 - - - +
267A LEU* 4.3 9.4 - - + -
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Residues in contact with LEU 241 (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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223A LEU* 3.9 20.0 - - + -
224A LEU* 4.3 24.7 - - + +
237A VAL* 3.0 34.2 + - + +
238A GLU* 3.7 7.9 - - - +
240A ALA* 1.3 75.3 - - - +
242A ARG* 1.3 64.0 + - - +
244A LEU* 3.1 9.9 + - - +
246A LEU* 3.1 54.7 + - + +
247A PRO 5.1 1.8 - - - +
248A PRO* 4.5 14.8 - - + +
250A VAL* 4.2 10.5 - - + -
263A LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 242 (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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238A GLU 3.1 16.6 + - - +
239A GLU* 3.0 38.4 + - - +
241A LEU* 1.3 78.1 - - - +
243A ALA* 1.4 78.7 + - - +
245A GLY* 3.0 18.8 + - - +
246A LEU 4.6 6.3 + - - -
78C LEU* 5.3 11.5 - - + +
79C ARG* 4.6 21.0 - - - +
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Residues in contact with ALA 243 (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 GLU* 2.9 22.9 + - + +
240A ALA* 3.7 8.3 - - - +
241A LEU 3.2 0.4 - - - -
242A ARG* 1.4 97.2 - - - +
244A LEU* 1.3 63.5 + - + +
245A GLY 3.2 0.8 + - - -
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Residues in contact with LEU 244 (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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240A ALA* 3.3 13.2 + - + +
241A LEU 3.1 8.5 + - - +
242A ARG 3.1 0.6 - - - -
243A ALA* 1.3 82.0 - - + +
245A GLY* 1.3 60.1 + - - +
246A LEU* 3.5 27.6 + - + +
259A ALA* 4.0 11.4 - - + +
262A ARG* 3.6 32.8 - - + +
263A LEU* 3.8 34.3 - - + +
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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