Contacts of the helix formed by residues 227 - 245 (chain C) in PDB entry 1HYH
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 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C TRP* 3.4 54.7 - - + +
216C ILE* 3.7 35.7 - - + +
217C VAL* 4.4 13.0 - - + -
220C ALA* 3.7 28.7 - - + +
225C ILE* 3.8 4.2 + - + -
226C ASP* 1.3 73.4 + - - +
228C ALA* 1.3 55.9 + - - +
230C ILE* 3.3 13.2 + - + +
231C GLU* 3.0 24.5 + - - +
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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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226C ASP* 3.2 14.6 + - - +
227C LEU* 1.3 77.2 - - - +
229C ALA* 1.3 57.9 + - - +
231C GLU* 3.2 16.3 + - - +
232C GLU* 2.9 24.1 + - - -
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Residues in contact with ALA 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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226C ASP* 3.2 29.4 + - + +
228C ALA* 1.3 76.5 - - - +
230C ILE* 1.3 60.4 + - + +
232C GLU* 3.0 3.5 + - - +
233C GLU* 2.9 29.1 + - - +
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Residues in contact with ILE 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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175C MET* 4.8 2.9 - - + +
178C ALA* 3.7 18.4 - - + +
179C VAL* 3.6 19.5 - - + +
182C ALA* 4.7 10.5 - - + -
206C TRP* 3.5 18.8 - - + -
216C ILE* 4.2 9.9 - - + -
225C ILE* 3.4 38.4 - - + -
226C ASP 3.4 7.6 + - - +
227C LEU* 3.3 26.1 + - + +
229C ALA* 1.3 75.8 - - + +
231C GLU* 1.3 62.7 - - - +
233C GLU* 3.4 8.6 + - - +
234C ALA* 3.3 19.1 + - + +
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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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203C PHE* 4.8 5.0 - - - +
204C VAL* 3.6 41.3 + - + +
206C TRP* 3.5 27.4 + - + -
227C LEU 3.0 9.9 + - - +
228C ALA* 3.4 16.0 - - - +
230C ILE* 1.3 78.6 - - - +
232C GLU* 1.3 59.0 + - - +
234C ALA* 3.5 5.6 + - - +
235C ARG* 3.3 18.2 + - - -
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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 ALA 2.9 13.9 + - - -
229C ALA* 3.0 5.5 + - - +
231C GLU* 1.3 75.7 - - - +
233C GLU* 1.3 49.9 + - - +
235C ARG* 3.3 2.1 + - - +
236C LYS* 2.7 39.0 + - - +
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Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 5.4 4.0 - - - +
177C ARG* 3.3 26.7 + - - +
178C ALA* 4.0 18.8 - - + +
181C GLU* 5.0 8.3 - - + +
229C ALA 2.9 11.4 + - - +
230C ILE* 3.4 11.0 + - - +
232C GLU* 1.3 71.5 - - - +
234C ALA* 1.3 60.0 + - - +
236C LYS* 3.7 11.3 - - - +
237C GLY* 2.9 24.6 + - - -
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Residues in contact with ALA 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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171C ASP 5.4 0.7 - - - +
174C ARG* 3.5 45.6 + - + +
175C MET* 4.1 9.9 - - + +
177C ARG* 3.8 10.2 + - - +
178C ALA* 4.1 1.8 - - + +
230C ILE 3.3 12.7 + - - +
231C GLU* 3.9 6.3 - - - +
232C GLU 3.3 0.4 - - - -
233C GLU* 1.3 74.8 - - - +
235C ARG* 1.3 65.4 + - - +
237C GLY* 3.3 9.5 + - - -
238C GLY 3.5 7.3 + - - -
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Residues in contact with ARG 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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174C ARG* 6.0 0.9 - - - +
231C GLU 3.3 7.5 + - - -
232C GLU 3.3 4.6 + - - -
234C ALA* 1.3 74.6 - - - +
236C LYS* 1.3 65.7 + - - +
237C GLY 3.0 1.2 + - - -
238C GLY* 3.1 12.6 + - - -
239C PHE* 3.5 22.2 + - - -
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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 GLU 2.7 24.3 + - - +
233C GLU* 3.8 13.2 - - - +
235C ARG* 1.3 71.3 - - - +
237C GLY* 1.3 61.3 + - - +
239C PHE* 3.2 15.4 + - + +
240C THR* 3.0 31.7 + - - +
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Residues in contact with GLY 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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64A ILE* 3.8 14.0 - - - +
68A ASP* 5.1 1.8 - - - -
174C ARG* 5.2 0.2 - - - -
177C ARG* 3.8 13.2 - - - -
233C GLU* 2.9 20.5 + - - -
234C ALA 3.3 4.7 + - - -
235C ARG 3.1 0.8 - - - -
236C LYS* 1.3 75.9 - - - +
238C GLY* 1.3 61.4 + - - +
240C THR* 3.3 9.3 + - - -
241C VAL* 3.2 25.1 + - - +
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Residues in contact with GLY 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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174C ARG* 3.8 33.2 - - - +
234C ALA 3.5 5.3 + - - -
235C ARG 3.1 8.1 + - - -
237C GLY* 1.3 73.1 - - - +
239C PHE* 1.3 62.1 + - - +
241C VAL* 3.3 7.0 + - - +
242C LEU* 3.0 34.8 + - - +
248C THR* 4.5 1.0 - - - +
331C SO4 4.7 3.1 - - - -
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Residues in contact with PHE 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 ARG* 3.5 21.4 + - - -
236C LYS* 3.2 15.0 + - + +
238C GLY* 1.3 75.0 - - - +
240C THR* 1.3 56.1 + - - +
242C LEU* 3.7 18.2 - - + +
243C ASN* 2.7 38.3 + - + +
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Residues in contact with THR 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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57A ALA* 5.4 2.7 - - - +
60A LYS* 4.0 33.9 - - + +
61A ALA* 3.9 3.5 - - - +
64A ILE* 4.7 9.0 - - + -
236C LYS* 3.0 23.2 + - - +
237C GLY* 3.3 10.2 + - - -
239C PHE* 1.3 76.0 - - - +
241C VAL* 1.3 58.7 + - - +
243C ASN* 3.8 7.0 - - + +
244C GLY* 2.9 27.0 + - - -
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 3.6 28.0 - - - +
64A ILE* 3.9 17.3 - - + -
65A ASP* 4.0 13.7 - - + +
68A ASP* 4.7 3.4 - - - +
174C ARG* 5.1 1.6 - - - +
237C GLY 3.2 16.5 + - - +
238C GLY* 3.5 8.5 - - - +
239C PHE 3.2 0.2 - - - -
240C THR* 1.3 76.3 - - - +
242C LEU* 1.3 53.4 + - - +
245C LYS* 2.8 48.5 + - + +
247C TYR 3.4 17.7 - - - +
248C THR* 3.5 22.9 - - + -
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Residues in contact with LEU 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 GLY 3.0 23.0 + - - +
239C PHE* 3.7 20.0 - - + +
241C VAL* 1.3 77.4 - - - +
243C ASN* 1.3 57.4 + - - +
246C GLY* 2.7 36.1 + - - +
247C TYR* 3.8 26.9 - - - +
248C THR* 4.1 9.2 - - + +
331C SO4 4.0 22.0 - - - +
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Residues in contact with ASN 243 (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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57A ALA* 4.5 12.4 - - - +
239C PHE 2.7 22.2 + - - +
240C THR* 3.8 6.8 + - - +
242C LEU* 1.3 76.5 - - - +
244C GLY* 1.3 62.6 - - - +
246C GLY 4.8 0.3 + - - -
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Residues in contact with GLY 244 (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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55A ASN* 5.1 2.3 + - - -
57A ALA* 3.5 33.3 - - - +
58A LYS* 3.7 19.1 + - - +
61A ALA* 3.9 5.6 - - - -
240C THR 2.9 13.6 + - - -
243C ASN* 1.3 77.9 - - - +
245C LYS* 1.3 60.8 + - - +
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Residues in contact with LYS 245 (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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58A LYS* 4.6 15.2 - - + +
61A ALA* 3.9 8.3 - - + -
62A ASP* 3.2 27.1 + - - +
65A ASP* 2.3 37.2 + - - +
241C VAL* 2.8 27.8 + - + +
244C GLY* 1.3 76.2 - - - +
246C GLY* 1.3 55.3 + - - +
247C TYR* 3.2 70.6 - - + +
249C SER* 3.4 5.0 + - - +
250C TYR* 3.3 15.4 - - - -
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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