Contacts of the helix formed by residues 235 - 242 (chain B) in PDB entry 3I5D
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B VAL* 5.1 3.1 - - + -
102B PHE* 4.5 4.5 - - + -
104B VAL* 3.9 31.2 - - + -
185B ALA 3.7 16.4 - - - +
188B PHE* 2.9 39.8 + - + +
189B THR 4.5 1.1 - - - +
190B VAL* 4.1 29.2 - - + +
234B ARG* 1.3 69.6 - - - +
236B GLY* 1.3 64.4 + - - +
238B ILE* 2.8 19.0 + - + +
239B VAL* 3.0 14.6 + - - +
246B PHE* 3.9 14.8 - - + -
322B PHE* 3.6 29.8 - - + -
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Residues in contact with GLY 236 (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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186B GLU* 2.9 40.1 + - - -
234B ARG* 3.4 6.2 - - - +
235B LEU* 1.3 72.8 - - - +
237B ASP* 1.3 51.8 + - - +
239B VAL* 3.1 2.9 + - - +
240B GLY* 2.7 34.1 + - - -
246B PHE* 4.0 12.2 - - - +
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Residues in contact with ASP 237 (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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221B VAL* 4.6 2.9 - - - +
222B PHE* 3.9 22.8 - - + +
223B SER* 5.6 1.0 - - - -
233B PHE* 6.1 0.7 - - + -
234B ARG* 3.0 53.4 + - + +
236B GLY* 1.3 75.0 - - - +
238B ILE* 1.3 59.5 + - + +
240B GLY* 4.4 1.1 - - - +
241B GLU* 2.9 33.5 + - - +
279B PHE* 6.0 0.2 - - - -
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Residues in contact with ILE 238 (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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102B PHE* 5.8 0.2 - - + -
190B VAL* 4.2 16.2 - - + -
192B ILE* 5.1 1.8 - - + -
233B PHE* 3.8 25.4 - - + -
234B ARG 3.0 14.4 + - - +
235B LEU* 2.8 13.2 + - + +
237B ASP* 1.3 80.2 - - - +
239B VAL* 1.3 62.0 + - - +
241B GLU* 3.8 0.2 - - - +
242B ALA* 3.5 17.8 + - - +
256B MET* 4.1 11.4 - - + -
258B VAL* 4.2 14.6 - - + -
279B PHE* 3.3 44.0 - - + +
322B PHE* 3.7 29.8 - - + -
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Residues in contact with VAL 239 (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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235B LEU 3.0 9.8 + - - +
236B GLY 3.6 5.2 - - - +
238B ILE* 1.3 72.0 - - - +
240B GLY* 1.3 71.1 + - - +
242B ALA* 3.1 12.0 + - - +
244B GLU* 3.3 31.4 + - + +
246B PHE* 3.5 55.4 - - + +
249B MET* 3.6 13.0 - - + -
256B MET* 4.1 25.8 - - + -
320B ILE* 4.3 5.8 - - + -
322B PHE* 4.8 4.0 - - + -
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Residues in contact with GLY 240 (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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236B GLY 2.7 20.0 + - - -
237B ASP* 3.9 2.0 - - - -
239B VAL* 1.3 72.1 - - - +
241B GLU* 1.3 52.5 - - - +
242B ALA 2.6 0.3 + - - -
243B GLU* 2.4 35.7 + - - -
244B GLU 3.5 11.8 + - - -
246B PHE 6.1 0.2 - - - -
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Residues in contact with GLU 241 (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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222B PHE* 5.4 4.8 - - - -
224B ARG* 2.6 42.2 + - - +
237B ASP 2.9 22.8 + - - +
238B ILE 3.8 4.7 - - - +
240B GLY* 1.3 69.8 - - - +
242B ALA* 1.3 56.4 + - - +
243B GLU* 3.1 12.5 + - - +
279B PHE* 3.7 28.3 - - + +
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Residues in contact with ALA 242 (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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238B ILE 3.5 4.2 + - - +
239B VAL 3.1 10.7 + - - +
240B GLY 2.6 5.4 + - - -
241B GLU* 1.3 74.2 - - - +
243B GLU* 1.3 70.5 + - - +
244B GLU* 3.7 9.0 - - + +
256B MET* 3.6 28.9 - - + -
279B PHE 3.5 24.6 - - - +
280B ARG* 4.0 5.2 - - - +
281B ARG* 4.1 5.7 + - - +
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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