Contacts of the helix formed by residues 227 - 239 (chain C) in PDB entry 2NRA
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 VAL 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170C TYR* 3.8 39.8 - - + +
202C LEU* 3.9 17.5 - - + -
217C TYR* 3.5 37.9 - - + -
223C PHE* 2.7 34.9 + - + +
226C ASP* 1.3 84.4 - - - +
228C LEU* 1.3 68.2 + - + +
229C ASN 3.4 0.9 - - - -
230C LYS* 3.6 0.9 + - - +
231C ALA* 2.9 28.4 + - + +
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Residues in contact with LEU 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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174C LEU* 5.2 7.9 - - + -
198C LEU* 3.8 21.3 - - + -
202C LEU* 4.2 12.8 - - + -
220C PHE* 4.7 2.7 - - + -
223C PHE* 3.3 34.2 + - + -
224C LYS* 3.2 18.9 + - - +
227C VAL* 1.3 78.9 - - + +
229C ASN* 1.3 58.2 + - - +
231C ALA* 3.3 3.1 - - + +
232C ILE* 2.8 37.9 + - + +
246C PHE* 3.7 34.8 - - + -
259C LEU* 3.9 17.3 - - + -
261C PHE* 4.4 9.2 - - + -
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Residues in contact with ASN 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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6A T 5.1 7.3 + - - -
224C LYS* 2.9 43.9 + - - +
225C ARG* 3.5 21.3 + - - +
228C LEU* 1.3 69.2 - - - +
230C LYS* 1.3 69.2 + - - +
232C ILE* 2.8 8.9 + - - +
233C ALA* 2.7 25.9 + - - +
246C PHE* 4.2 11.3 - - - -
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Residues in contact with LYS 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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34B G 5.0 12.3 - - + +
35B C 4.1 29.7 + - - +
36B T 4.2 19.4 - - - +
225C ARG 3.7 11.6 + - - +
226C ASP* 3.6 33.5 + - - +
227C VAL 3.6 0.9 + - - +
228C LEU 3.6 0.2 - - - -
229C ASN* 1.3 77.1 - - + +
231C ALA* 1.3 66.5 + - - +
233C ALA* 3.2 18.5 - - - +
234C GLU* 3.2 9.8 + - - +
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Residues in contact with ALA 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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170C TYR* 4.7 7.0 - - + -
171C SER* 4.1 27.7 + - - +
174C LEU* 4.0 17.3 - - + -
202C LEU* 6.3 0.7 - - + -
227C VAL* 2.9 23.4 + - + +
228C LEU* 3.3 6.1 - - + +
229C ASN 2.9 0.4 + - - -
230C LYS* 1.3 76.3 - - - +
232C ILE* 1.3 66.3 + - - +
234C GLU* 2.9 15.9 + - - +
235C ILE* 3.0 16.8 + - - +
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Residues in contact with ILE 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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174C LEU* 4.0 16.6 - - + -
228C LEU* 2.8 28.8 + - + +
229C ASN* 2.8 6.6 + - - +
231C ALA* 1.3 71.0 - - - +
233C ALA* 1.3 65.1 + - - +
235C ILE* 3.2 7.6 + - - +
236C LYS* 3.1 36.3 + - + +
244C VAL* 3.6 38.4 - - + +
246C PHE* 3.5 38.6 - - + -
261C PHE* 4.6 8.3 - - + -
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Residues in contact with ALA 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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229C ASN 2.7 14.3 + - - +
230C LYS* 3.2 16.2 - - - +
232C ILE* 1.3 75.7 - - - +
234C GLU* 1.3 57.4 + - + +
236C LYS* 3.4 9.3 + - - +
237C LYS* 3.0 28.1 + - - +
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Residues in contact with GLU 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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34B G 4.5 12.1 + - - +
166C LEU* 2.4 38.7 - - + +
167C SER* 3.3 4.5 + - - -
168C SER* 3.5 12.0 - - - -
171C SER* 2.8 28.1 + - - +
230C LYS 3.8 6.7 - - - +
231C ALA 2.9 7.4 + - - +
233C ALA* 1.3 73.6 - - + +
235C ILE* 1.3 67.4 + - - +
237C LYS* 3.5 10.3 - - + +
238C LYS* 2.8 51.9 + - + +
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Residues in contact with ILE 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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166C LEU* 4.7 5.8 - - + -
171C SER* 3.8 13.7 - - - +
174C LEU* 3.7 28.5 - - + -
175C TYR* 3.7 34.1 - - + +
178C ILE* 4.3 7.4 - - + -
231C ALA 3.0 14.0 + - - +
232C ILE* 3.7 8.5 - - - +
234C GLU* 1.3 76.6 - - - +
236C LYS* 1.3 66.7 + - - +
238C LYS 2.8 12.6 + - - -
239C THR* 2.6 39.1 + - + +
241C ILE* 3.7 28.3 - - + +
244C VAL* 4.4 6.5 - - + -
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Residues in contact with LYS 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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232C ILE* 3.1 29.3 + - + +
233C ALA* 3.5 10.8 - - - +
235C ILE* 1.3 81.3 - - - +
237C LYS* 1.3 60.3 - - - +
238C LYS 3.5 0.2 + - - -
239C THR 4.1 9.5 - - - +
241C ILE 3.8 13.0 - - - +
242C SER* 3.7 23.2 - - - +
243C PHE* 5.1 8.1 - - - +
244C VAL* 4.3 25.7 + - + +
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Residues in contact with LYS 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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233C ALA 3.0 16.6 + - - +
234C GLU* 3.5 11.0 - - + +
235C ILE 3.0 0.8 - - - -
236C LYS* 1.3 76.9 - - - +
238C LYS* 1.3 85.4 + - + +
239C THR 3.8 0.4 - - - -
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Residues in contact with LYS 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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16A G 4.7 3.2 + - - -
34B G 5.7 1.0 + - - -
162C ALA* 4.3 10.6 - - - -
165C ARG* 2.8 50.5 + - + +
166C LEU* 4.1 9.4 - - + -
167C SER* 3.4 12.3 + - - -
234C GLU* 2.8 42.2 + - + +
235C ILE 2.8 2.8 + - - -
237C LYS* 1.3 107.1 - - + +
239C THR* 1.3 63.8 + - - +
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Residues in contact with THR 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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162C ALA* 3.9 18.4 - - + -
166C LEU* 4.2 21.5 - - + -
175C TYR* 4.3 11.2 - - + -
235C ILE* 2.6 41.5 + - + +
236C LYS 4.1 9.7 - - - +
237C LYS 3.8 0.6 - - - -
238C LYS* 1.3 85.3 - - - +
240C GLU* 1.3 68.0 + - - +
241C ILE* 3.3 14.3 + - - +
242C SER* 5.5 0.2 - - - -
266C ASP* 5.5 0.7 - - - +
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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