Contacts of the helix formed by residues 223 - 232 (chain C) in PDB entry 5TF6
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 ASP 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C GLU 4.7 4.2 - - - +
221C LEU 2.8 7.5 + - - -
222C LEU* 1.3 76.3 - - - +
224C GLU* 1.3 60.3 + - - +
225C ASN* 3.0 8.5 + - - +
226C LEU* 2.8 37.5 + - - +
227C LEU* 2.9 32.6 + - - +
242C ILE* 4.8 4.0 - - - -
247C LYS* 4.6 7.9 - - - +
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Residues in contact with GLU 224 (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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223C ASP* 1.3 76.1 + - - +
225C ASN* 1.3 57.5 + - - +
227C LEU* 3.2 6.7 + - - +
228C ARG* 2.7 73.0 + - - +
240C ILE* 4.0 39.1 + - + +
242C ILE* 4.9 6.2 - - + +
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Residues in contact with ASN 225 (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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223C ASP* 3.0 6.4 + - - +
224C GLU* 1.3 82.0 - - - +
226C LEU* 1.3 63.5 + - - +
228C ARG* 3.4 16.9 + - - +
229C GLU* 3.1 26.9 + - - +
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Residues in contact with LEU 226 (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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220C GLU 3.8 22.9 - - - +
221C LEU* 3.9 35.2 - - + +
223C ASP* 2.8 31.2 + - - +
225C ASN* 1.3 74.6 - - - +
227C LEU* 1.3 57.4 + - + +
229C GLU* 3.5 5.8 + - - +
230C SER* 2.6 38.9 + - - +
277C LEU* 4.3 10.1 - - + -
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Residues in contact with LEU 227 (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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214C ILE* 4.5 7.0 - - + -
217C LEU* 3.9 33.0 - - + -
221C LEU 3.8 10.8 - - - +
222C LEU* 4.9 0.4 - - - -
223C ASP 2.9 26.0 + - - +
224C GLU* 3.7 3.6 - - - +
226C LEU* 1.3 70.2 - - + +
228C ARG* 1.3 68.4 + - - +
230C SER* 3.4 3.9 + - - -
231C PHE* 3.2 44.1 + - + +
240C ILE* 4.7 9.2 - - + -
242C ILE* 4.0 15.5 - - + -
256C ALA* 3.9 26.5 - - + -
258C MET* 4.2 12.6 - - + -
277C LEU* 4.7 7.9 - - + -
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Residues in contact with ARG 228 (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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224C GLU* 2.7 63.6 + - - +
225C ASN* 3.8 16.9 + - - +
226C LEU 3.4 0.2 - - - -
227C LEU* 1.3 71.6 - - - +
229C GLU* 1.3 53.3 + - - +
231C PHE* 2.8 7.1 + - - -
232C GLU* 2.7 51.6 + - + +
237C ILE* 4.2 26.2 + - + +
238C GLU 6.3 0.2 - - - -
239C LYS* 5.8 2.4 - - - +
240C ILE* 3.8 23.0 - - + +
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Residues in contact with GLU 229 (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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225C ASN 3.1 18.0 + - - +
226C LEU* 3.6 6.7 - - - +
228C ARG* 1.3 76.8 - - - +
230C SER* 1.3 61.8 + - - +
231C PHE 3.3 0.7 + - - -
232C GLU* 3.8 31.4 + - - +
233C GLY 4.8 1.2 + - - -
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Residues in contact with SER 230 (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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226C LEU* 2.6 29.8 + - - +
227C LEU* 3.5 7.7 + - - -
228C ARG 3.3 0.4 - - - -
229C GLU* 1.3 77.9 - - - +
231C PHE* 1.3 70.5 + - - +
233C GLY 5.3 0.8 + - - -
234C PHE* 4.0 10.7 - - - -
272C MET* 4.0 8.6 - - - +
277C LEU* 3.9 27.2 - - - +
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Residues in contact with PHE 231 (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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212C ILE* 4.1 22.9 - - + -
214C ILE* 3.7 26.7 - - + -
227C LEU* 3.2 32.7 + - + +
228C ARG 2.8 3.4 + - - +
230C SER* 1.3 84.9 - - - +
232C GLU* 1.3 65.1 + - - +
233C GLY 3.1 3.8 - - - -
234C PHE* 3.0 41.0 + + - +
237C ILE* 4.0 1.6 - - - -
258C MET* 3.5 28.3 - - + -
260C PHE* 4.0 6.5 - - + -
269C ALA* 4.2 7.0 - - + -
272C MET* 3.7 38.8 - - + -
277C LEU* 5.1 1.8 - - + -
282C ILE* 4.1 14.6 - - + -
284C VAL* 4.3 2.7 - - + -
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Residues in contact with GLU 232 (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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228C ARG* 2.7 35.7 + - + +
229C GLU* 3.8 36.3 - - - +
230C SER 3.8 0.4 - - - -
231C PHE* 1.3 71.1 - - - +
233C GLY* 1.3 65.8 + - - +
234C PHE 3.2 0.2 - - - -
235C GLY* 3.2 20.2 + - - +
237C ILE* 3.7 17.0 - - + +
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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