Contacts of the helix formed by residues 225 - 232 (chain C) in PDB entry 5H1C
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 THR 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C SER 4.7 0.2 - - - -
224C ALA* 1.3 86.9 - - + +
226C ALA* 1.3 66.3 + - - +
227C LEU 3.3 2.9 - - - -
228C TYR* 3.0 26.0 + - - +
229C ARG* 3.5 4.3 + - - +
245C LEU* 5.3 6.3 - - + -
265C ILE* 5.3 2.7 - - + -
266C THR 4.1 2.7 + - - +
267C ASN* 4.0 18.4 - - + -
268C GLN* 3.8 22.9 + - - +
287C ILE* 3.5 26.0 - - + +
292C ILE* 3.7 30.3 - - + -
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Residues in contact with ALA 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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163C GLU* 4.0 10.5 - - + +
223C SER* 3.5 29.2 + - - +
224C ALA 3.5 1.2 - - - -
225C THR* 1.3 82.4 + - - +
227C LEU* 1.3 66.1 + - + +
228C TYR 3.3 0.3 + - - -
229C ARG* 3.4 19.2 + - - +
230C THR* 3.7 14.4 + - - +
268C GLN* 3.5 17.3 - - - +
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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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162C THR* 4.3 27.6 - - + +
194C ALA* 4.7 0.7 - - + -
195C PHE* 3.2 34.1 - - - +
196C ASN 3.6 15.9 - - - +
197C THR* 3.6 16.4 - - + -
200C GLN* 3.3 31.9 - - + +
223C SER 4.8 0.9 - - - +
225C THR 3.3 0.6 - - - -
226C ALA* 1.3 80.1 - - + +
228C TYR* 1.3 62.3 + - + +
230C THR* 3.1 10.2 + - - +
231C ASP* 3.0 33.8 + - - +
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Residues in contact with TYR 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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197C THR* 4.2 13.9 + - + -
200C GLN* 3.6 19.0 + - - -
224C ALA 3.0 29.4 - - - -
225C THR* 3.0 13.0 + - - +
227C LEU* 1.3 76.5 - - + +
229C ARG* 1.3 65.3 + - - +
231C ASP 4.1 0.2 - - - -
232C TYR* 3.3 35.9 + + - +
241C ARG* 3.3 42.7 - - + +
244C HIS* 2.7 48.7 + + + -
245C LEU* 3.4 33.3 - - + +
248C PHE* 4.3 8.1 - + - +
287C ILE* 5.5 0.2 - - + -
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Residues in contact with ARG 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 THR 3.5 6.2 + - - +
226C ALA* 3.4 12.9 + - - +
227C LEU 3.2 0.8 - - - -
228C TYR* 1.3 82.8 - - - +
230C THR* 1.3 68.4 + - + +
231C ASP 3.2 0.3 + - - -
232C TYR 3.5 14.9 + - - +
233C SER* 4.1 4.5 + - - -
241C ARG* 5.3 2.0 - - - +
268C GLN* 3.9 20.1 - - - +
269C VAL 2.4 43.9 + - - +
270C VAL* 3.3 2.6 - - - +
287C ILE* 3.3 30.7 - - + +
9D T 3.5 37.4 + - - +
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Residues in contact with THR 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 ALA 3.7 9.5 + - - +
227C LEU* 3.1 19.6 + - - +
229C ARG* 1.3 84.1 - - + +
231C ASP* 1.3 68.5 + - - +
233C SER* 5.0 5.0 + - - -
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Residues in contact with ASP 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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195C PHE 4.9 1.7 - - - +
196C ASN* 4.7 3.3 - - - +
197C THR* 3.1 38.3 + - + +
227C LEU* 3.0 18.8 + - - +
230C THR* 1.3 89.3 + - - +
232C TYR* 1.3 72.2 + - + +
233C SER* 3.5 5.0 + - - -
237C GLU* 5.2 2.1 - - - +
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Residues in contact with TYR 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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197C THR* 3.9 20.9 + - + -
198C ASP* 4.7 2.8 + - - -
228C TYR* 3.3 40.6 + + - +
229C ARG* 3.6 9.4 - - - +
231C ASP* 1.3 85.1 - - + +
233C SER* 1.3 58.9 + - - +
234C GLY 2.8 9.6 + - - -
237C GLU* 4.1 22.7 - - + -
238C LEU* 4.6 0.6 + - - +
240C ALA* 5.1 13.1 + - + +
241C ARG* 3.5 49.0 + - + -
244C HIS* 4.5 16.2 - - + +
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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