Contacts of the helix formed by residues 235 - 242 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C VAL* 5.1 3.4 - - + -
102C PHE* 4.5 4.0 - - + -
104C VAL* 3.9 27.4 - - + -
185C ALA 3.6 15.9 - - - +
186C GLU 3.8 0.7 - - - +
188C PHE* 2.9 42.8 + - + +
189C THR 4.5 0.7 - - - +
190C VAL* 4.1 29.4 - - + -
233C PHE 3.7 0.2 + - - -
234C ARG* 1.3 69.1 - - - +
236C GLY* 1.3 69.1 + - - +
238C ILE* 2.8 17.8 + - + +
239C VAL* 3.0 14.2 + - - +
246C PHE* 3.8 14.6 - - + -
322C PHE* 3.6 29.5 - - + -
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Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLU* 2.8 41.8 + - - -
234C ARG* 3.5 0.8 - - - +
235C LEU* 1.3 71.9 - - - +
237C ASP* 1.3 53.7 + - - +
239C VAL* 3.1 2.4 + - - +
240C GLY* 2.7 35.0 + - - -
246C PHE* 4.0 13.2 - - - +
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Residues in contact with ASP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C VAL* 4.6 3.6 - - - +
222C PHE* 3.9 22.8 - - + +
223C SER* 5.6 0.9 - - - -
233C PHE* 6.1 0.4 - - + -
234C ARG* 3.5 29.9 + - + +
235C LEU 3.2 0.8 - - - -
236C GLY* 1.3 75.0 - - - +
238C ILE* 1.3 57.4 + - + +
240C GLY* 4.4 1.1 - - - +
241C GLU* 2.9 33.8 + - - +
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Residues in contact with ILE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PHE* 5.8 0.2 - - + -
190C VAL* 4.2 16.8 - - + -
192C ILE* 5.1 1.6 - - + -
233C PHE* 3.8 23.3 - - + -
234C ARG 3.1 16.2 + - - +
235C LEU* 2.8 13.1 + - + +
237C ASP* 1.3 79.3 - - - +
239C VAL* 1.3 62.0 + - - +
241C GLU 3.7 0.2 + - - -
242C ALA* 3.5 18.5 + - - +
256C MET* 4.1 11.7 - - + -
258C VAL* 4.2 15.0 - - + -
279C PHE* 3.3 44.7 - - + +
322C PHE* 3.7 28.7 - - + -
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C LEU 3.0 8.9 + - - +
236C GLY 3.6 5.4 - - - +
238C ILE* 1.3 73.4 - - - +
240C GLY* 1.3 70.5 + - - +
242C ALA* 3.1 12.0 + - - +
244C GLU* 3.3 31.7 + - + +
246C PHE* 3.4 55.9 - - + +
249C MET* 3.6 13.7 - - + -
256C MET* 4.1 25.8 - - + -
320C ILE* 4.3 5.6 - - + -
322C PHE* 4.8 4.0 - - + -
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Residues in contact with GLY 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLY 2.7 20.1 + - - -
237C ASP* 3.9 1.8 - - - -
239C VAL* 1.3 68.9 - - - +
241C GLU* 1.3 52.1 + - - +
242C ALA 2.6 3.3 + - - -
243C GLU* 2.5 36.0 + - - +
244C GLU 3.7 12.3 - - - +
246C PHE 5.6 0.4 - - - +
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C PHE* 5.4 5.0 - - - -
224C ARG* 2.6 43.4 + - - +
237C ASP* 2.9 23.1 + - - +
238C ILE 3.8 4.7 - - - +
240C GLY* 1.3 69.6 - - - -
242C ALA* 1.3 56.9 + - - +
243C GLU* 3.1 12.5 + - - +
279C PHE* 3.7 28.5 - - + +
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ILE 3.5 3.3 + - - +
239C VAL 3.1 11.2 + - - +
240C GLY 2.6 5.3 + - - -
241C GLU* 1.3 73.8 - - - +
243C GLU* 1.3 71.4 + - - +
244C GLU* 3.4 9.0 - - + +
256C MET* 3.6 29.2 - - + -
279C PHE 3.5 26.8 - - - +
280C ARG* 4.1 4.7 - - - +
281C ARG* 4.2 5.5 + - - +
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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