Contacts of the helix formed by residues 226 - 236 (chain C) in PDB entry 5MR5
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 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159C ASN* 5.0 5.7 + - - +
224C CYS* 3.6 0.5 - - - +
225C GLN* 1.3 83.5 - - + +
227C GLN* 1.3 63.5 + - - +
228C ALA* 3.2 10.6 + - - +
229C CYS* 2.9 29.2 + - - +
230C ALA* 3.1 21.0 + - - +
314C PRO* 3.8 7.9 - - - +
407C SO4 3.2 21.3 - - - +
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Residues in contact with GLN 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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226C ASP* 1.3 71.8 - - - +
228C ALA* 1.3 61.0 + - - +
231C GLU* 2.8 34.8 + - + +
312C SER* 2.8 46.0 + - - +
313C SER* 4.7 0.6 - - - +
314C PRO* 3.6 15.6 - - - +
407C SO4 2.5 32.4 + - - +
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Residues in contact with ALA 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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159C ASN* 4.7 7.4 + - - +
226C ASP* 3.2 11.0 + - - +
227C GLN* 1.3 79.3 - - - +
229C CYS* 1.3 62.2 + - - +
231C GLU* 3.9 4.2 - - - +
232C ARG* 3.1 23.2 + - - +
407C SO4 5.3 0.4 + - - -
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Residues in contact with CYS 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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159C ASN* 3.6 38.2 - - + +
161C CYS* 3.4 16.7 - - - -
223C SER 3.4 6.3 - - - -
224C CYS* 2.1 59.8 - - + -
225C GLN 4.8 0.7 - - - +
226C ASP* 2.9 18.0 + - - +
228C ALA* 1.3 77.1 - - - +
230C ALA* 1.3 56.1 + - - +
232C ARG* 3.2 6.9 + - - +
233C ARG* 3.0 23.7 + - - +
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Residues in contact with ALA 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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224C CYS* 3.4 6.9 - - + -
226C ASP 3.1 15.6 + - - +
227C GLN 3.9 1.1 - - - +
229C CYS* 1.3 73.6 - - - +
231C GLU* 1.3 60.5 + - - +
233C ARG* 3.4 13.1 + - - +
234C ARG* 2.9 28.6 + - - +
309C TYR* 5.8 0.3 - - - +
311C ASP 4.6 0.5 - - - +
312C SER* 3.1 35.4 - - - +
313C SER 3.7 12.1 - - - +
314C PRO* 3.8 8.3 - - + -
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Residues in contact with GLU 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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181A SER* 2.9 36.6 + - - +
227C GLN* 2.8 19.3 + - + +
228C ALA* 3.9 5.2 - - - +
230C ALA* 1.3 74.1 - - - +
232C ARG* 1.3 66.5 + - - +
234C ARG* 2.9 43.3 + - - +
235C GLN* 2.9 29.6 + - - +
312C SER* 3.6 18.1 + - - -
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Residues in contact with ARG 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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121A SER* 4.6 1.0 + - - -
122A ASP* 5.4 1.8 - - - +
123A GLU* 2.7 30.9 + - - +
177A LEU* 3.1 54.0 + - + +
178A ASP 4.9 3.6 + - - -
183A TYR* 4.9 0.7 + - - -
159C ASN* 4.5 5.3 - - - +
161C CYS* 3.7 35.9 - - + +
162C LEU* 3.4 28.9 - - - +
165C ALA* 3.9 9.5 - - - +
178C ARG* 4.1 3.4 - - - +
228C ALA 3.1 14.2 + - - +
229C CYS* 3.4 9.9 - - - +
231C GLU* 1.3 75.6 - - - +
233C ARG* 1.3 63.2 + - - +
235C GLN* 3.0 14.0 + - - +
236C THR* 3.2 11.9 + - - +
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Residues in contact with ARG 233 (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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161C CYS* 3.9 10.3 - - - -
219C MET 4.3 1.8 - - - +
220C LEU* 3.6 11.1 - - - +
221C PHE 4.6 0.8 + - - -
222C CYS* 2.8 44.0 + - - +
223C SER* 4.2 1.6 - - - +
224C CYS* 3.7 21.4 - - - +
229C CYS 3.0 12.5 + - - +
230C ALA* 3.5 17.5 + - - +
232C ARG* 1.3 75.8 - - - +
234C ARG* 1.3 62.4 + - - +
236C THR* 2.7 26.9 + - - -
308C ASN* 4.9 0.9 - - - +
309C TYR* 3.6 46.2 - - + -
313C SER 3.4 16.0 + - - -
314C PRO 3.1 21.4 + - - -
317C ILE* 3.7 27.9 - - - +
352C ILE* 5.7 0.2 - - - +
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Residues in contact with ARG 234 (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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230C ALA 2.9 21.0 + - - +
231C GLU* 2.9 40.8 + - - +
233C ARG* 1.3 74.2 - - - +
235C GLN* 1.3 72.6 + - - +
236C THR 3.5 0.5 + - - -
237C ILE 4.4 0.7 + - - -
239C PRO* 3.3 31.5 - - - +
243C TYR* 5.9 1.0 - - - -
244C GLU* 4.1 15.4 + - - -
308C ASN* 3.0 28.5 + - - +
309C TYR* 3.6 31.2 + - + +
310C VAL 4.4 3.4 + - - -
311C ASP* 3.6 36.1 - - - +
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Residues in contact with GLN 235 (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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177A LEU* 4.1 14.2 - - + +
181A SER* 2.9 45.0 + - - +
183A TYR* 2.7 36.0 + - + +
231C GLU* 2.9 22.6 + - - +
232C ARG 3.0 7.1 + - - +
234C ARG* 1.3 87.9 + - - +
236C THR* 1.3 59.8 + - - +
237C ILE 3.3 2.7 - - - -
238C LEU* 2.8 18.7 + - - +
239C PRO* 3.3 20.2 - - - +
240C SER* 4.7 7.9 + - - -
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Residues in contact with THR 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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183A TYR* 3.6 8.3 + - - -
181C TYR* 2.6 41.1 + - + +
207C PHE* 5.6 1.6 - - + -
208C PHE* 5.2 7.0 - - + -
216C THR 5.7 0.2 - - - +
219C MET* 3.5 41.2 + - + +
220C LEU* 4.2 24.3 - - + +
232C ARG* 3.2 5.9 + - - +
233C ARG* 2.7 26.5 + - - -
234C ARG 3.3 0.6 - - - -
235C GLN* 1.3 77.5 - - - +
237C ILE* 1.3 59.4 + - + +
308C ASN* 6.0 0.2 - - - -
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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