Contacts of the helix formed by residues 224 - 238 (chain C) in PDB entry 4IYM
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 SER 224 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C PHE* 3.8 3.5 - - - -
223C GLY* 1.3 75.1 - - - -
225C THR* 1.3 60.0 + - - +
226C PRO* 3.7 12.8 - - - +
227C ILE* 3.3 23.9 + - - +
228C ALA* 2.9 27.2 + - - +
246C GLY* 4.0 0.7 - - - -
247C GLY* 4.5 5.6 - - - +
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Residues in contact with THR 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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224C SER* 1.3 69.1 - - - +
226C PRO* 1.4 76.6 - - + +
228C ALA* 3.3 3.6 + - - +
229C ARG* 2.9 47.2 + - + +
246C GLY* 3.6 8.0 - - - -
247C GLY* 2.7 31.8 + - - +
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Residues in contact with PRO 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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224C SER* 3.6 15.3 - - - +
225C THR* 1.4 94.5 - - + +
227C ILE* 1.3 68.5 + - + +
229C ARG* 3.4 11.3 + - + +
230C TYR* 3.2 20.8 + - - +
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Residues in contact with ILE 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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207C VAL* 6.1 1.8 - - + -
221C PHE* 3.5 29.8 - - + -
224C SER* 3.3 18.7 + - - +
225C THR 3.3 0.2 - - - -
226C PRO* 1.3 80.0 - - + +
228C ALA* 1.3 55.8 + - - +
230C TYR* 3.2 12.4 + - + +
231C VAL* 2.8 41.5 + - + +
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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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221C PHE* 3.5 25.5 - - + -
224C SER 2.9 18.3 + - - +
225C THR* 3.3 9.8 + - + +
227C ILE* 1.3 76.1 - - - +
229C ARG* 1.3 56.4 + - + +
231C VAL 4.5 0.2 - - - +
232C TYR* 2.9 33.8 + - - +
244C CYS* 3.7 13.8 - - + +
245C PHE 4.2 9.6 - - - +
246C GLY* 4.3 4.0 - - - -
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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* 2.9 36.3 + - + +
226C PRO* 3.6 11.9 - - - +
228C ALA* 1.3 76.4 - - + +
230C TYR* 1.3 59.0 + - - +
232C TYR* 3.8 5.4 - - - +
233C GLY* 3.0 27.0 + - - -
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Residues in contact with TYR 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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204C LYS* 3.4 23.8 + - + -
207C VAL* 5.0 5.2 - - + -
208C ASP* 2.5 34.0 + - - -
211C LEU* 4.0 10.5 - - + -
226C PRO 3.2 10.1 + - - +
227C ILE* 3.2 17.6 + - + +
229C ARG* 1.3 80.2 - - - +
231C VAL* 1.3 67.7 + - + +
233C GLY* 4.1 0.2 - - - -
234C THR* 2.7 61.1 + - + +
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Residues in contact with VAL 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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144C ILE* 4.2 2.5 - - + -
207C VAL* 4.3 17.3 - - + -
211C LEU* 3.9 22.4 - - + +
219C VAL* 4.1 12.3 - - + -
221C PHE* 3.6 45.3 - - + -
227C ILE* 2.8 31.2 + - + +
228C ALA 4.0 2.7 - - - +
230C TYR* 1.3 80.3 - - + +
232C TYR* 1.3 57.4 + - - +
235C ALA* 2.9 33.7 + - + +
242C ALA* 5.8 0.2 - - + -
244C CYS* 3.9 5.6 - - - -
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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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228C ALA 2.9 19.6 + - - +
229C ARG* 3.8 4.7 - - - +
231C VAL* 1.3 78.9 - - - +
233C GLY* 1.3 66.8 + - - +
235C ALA* 3.7 1.9 - - - +
236C ALA* 3.1 30.9 + - + +
242C ALA* 3.8 36.2 - - + +
243C GLN* 4.8 1.3 - - - -
244C CYS* 3.7 19.7 - - + -
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Residues in contact with GLY 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 ARG 3.0 16.1 + - - -
230C TYR* 5.4 0.2 - - - -
232C TYR* 1.3 82.3 - - - +
234C THR* 1.3 51.4 + - - +
236C ALA* 3.2 6.6 + - - +
237C MSE 2.8 39.9 + - - +
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Residues in contact with THR 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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208C ASP* 5.3 0.9 - - - +
211C LEU* 3.9 25.8 - - + -
212C THR* 5.3 5.2 - - + -
230C TYR* 2.7 49.9 + - + +
233C GLY* 1.3 72.1 - - - +
235C ALA* 1.3 66.0 + - - +
237C MSE 3.3 8.4 + - + +
238C ASN* 2.8 42.3 + - - +
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Residues in contact with ALA 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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211C LEU* 4.1 18.9 - - + +
219C VAL* 4.6 6.1 - - + -
231C VAL* 2.9 21.4 + - + +
232C TYR 3.7 3.6 - - - +
234C THR* 1.3 75.8 - - - +
236C ALA* 1.3 57.8 + - - +
238C ASN* 3.1 14.9 + - - +
239C GLY 3.3 0.2 + - - -
240C LYS* 3.0 38.8 + - + +
242C ALA* 3.7 22.2 - - + -
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Residues in contact with ALA 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 TYR* 3.1 26.3 + - + +
233C GLY* 3.6 5.4 - - - +
235C ALA* 1.3 71.1 - - - +
237C MSE 1.3 61.8 + - - +
238C ASN 3.0 4.5 - - - -
239C GLY* 2.9 18.5 + - - -
240C LYS 3.9 12.1 + - - +
242C ALA* 5.9 1.3 - - + -
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Residues in contact with MSE 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 GLY 2.8 21.6 + - - +
234C THR* 3.5 12.3 - - + +
236C ALA* 1.3 76.9 - - - +
238C ASN* 1.3 63.7 + - - +
239C GLY 3.6 0.2 + - - -
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Residues in contact with ASN 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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211C LEU 3.2 27.0 + - - +
212C THR* 3.6 24.5 - - - +
234C THR* 2.8 35.5 + - - +
235C ALA 3.1 7.9 + - - +
236C ALA 3.0 1.4 - - - -
237C MSE 1.3 86.2 - - - +
239C GLY* 1.3 58.8 + - - +
240C LYS* 3.3 17.6 + - + +
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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