Contacts of the helix formed by residues 229 - 239 (chain C) in PDB entry 1YI8
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 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C GLY 3.5 3.7 + - - -
228C ASP* 1.3 76.8 - - - +
230C ALA* 1.3 59.1 + - - +
231C ASP* 3.2 16.8 + - - +
232C GLU* 3.0 26.1 + - - +
233C VAL* 2.8 26.9 + - - +
307C ARG* 3.9 5.4 - - - +
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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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229C SER* 1.3 74.1 - - - +
231C ASP* 1.3 55.9 + - - +
233C VAL* 3.6 2.1 + - - +
234C ALA* 3.0 27.2 + - - +
300C ASN* 3.4 28.5 + - - +
307C ARG* 3.3 31.4 - - - +
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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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229C SER* 3.1 11.1 + - - +
230C ALA* 1.3 75.2 - - - +
232C GLU* 1.3 78.5 + - - +
234C ALA* 2.8 19.3 + - - +
235C ARG* 2.3 60.2 + - - +
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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 ASP* 4.1 16.8 - - + +
229C SER* 3.0 21.6 + - - +
231C ASP* 1.3 89.4 - - - +
233C VAL* 1.3 64.2 + - - +
235C ARG* 2.9 35.1 + - - +
236C LYS* 2.8 51.4 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 3.9 19.5 - - + -
228C ASP* 3.8 11.4 - - + +
229C SER 2.8 18.9 + - - +
230C ALA* 3.7 5.6 - - - +
232C GLU* 1.3 72.2 - - - +
234C ALA* 1.3 64.4 + - - +
236C LYS* 3.4 5.8 + - - +
237C VAL* 3.1 26.2 + - + +
296C ILE* 5.8 1.3 - - - -
299C LEU* 4.3 22.4 - - + -
300C ASN* 4.1 13.2 - - - +
303C LEU* 3.8 21.8 - - + -
307C ARG* 3.1 25.6 - - - +
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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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230C ALA 3.0 14.3 + - - +
231C ASP* 2.8 15.5 + - - +
233C VAL* 1.3 79.6 - - - +
235C ARG* 1.3 53.3 + - + +
237C VAL* 3.2 2.8 + - - +
238C MET* 2.7 34.8 + - + +
293C LYS* 5.3 5.2 - - - +
296C ILE* 3.6 32.6 - - + +
300C ASN* 5.1 0.2 + - - -
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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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231C ASP* 2.3 50.1 + - - +
232C GLU* 2.9 29.0 + - - +
234C ALA* 1.3 71.7 - - + +
236C LYS* 1.3 62.5 + - + +
238C MET* 3.0 20.5 + - - +
239C GLY* 3.3 9.9 + - - -
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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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210C LEU* 4.0 13.7 - - + +
223C ALA 2.6 31.1 + - - +
224C ILE* 3.7 20.4 - - + -
225C ALA* 4.2 2.0 - - - +
228C ASP* 2.6 32.8 + - - +
232C GLU* 2.8 41.4 + - - +
233C VAL 3.9 3.4 - - - +
235C ARG* 1.3 74.8 - - + +
237C VAL* 1.3 63.3 + - - +
238C MET 3.3 0.2 + - - -
239C GLY* 3.3 9.9 + - - -
240C MET* 3.5 14.3 + - - +
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Residues in contact with VAL 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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210C LEU* 5.2 0.2 - - - -
224C ILE* 4.4 7.4 - - + -
233C VAL* 3.1 22.6 + - + +
234C ALA 3.6 3.6 - - - +
236C LYS* 1.3 76.0 - - - +
238C MET* 1.3 62.8 + - - +
240C MET* 3.3 27.5 - - - +
292C LYS* 3.4 25.8 - - + +
295C LEU* 3.7 22.0 - - + -
296C ILE* 3.5 28.3 - - + -
299C LEU* 3.7 30.1 - - + -
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Residues in contact with MET 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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234C ALA* 2.7 27.4 - - - +
235C ARG* 3.0 11.6 + - - +
237C VAL* 1.3 77.5 - - - +
239C GLY* 1.3 54.7 + - - +
240C MET 3.2 0.4 - - - -
289C VAL* 5.1 7.9 - - + +
292C LYS* 2.5 48.0 + - + +
293C LYS* 4.3 22.2 - - + +
296C ILE* 3.5 27.1 - - + -
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Residues in contact with GLY 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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210C LEU* 5.6 1.4 - - - +
211C ASP* 5.8 1.6 - - - +
235C ARG 3.3 8.6 + - - -
236C LYS 3.3 6.0 + - - -
237C VAL 3.3 0.2 - - - -
238C MET* 1.3 76.4 - - - +
240C MET* 1.3 64.1 + - - +
241C TYR 3.7 1.0 + - - -
292C LYS* 4.1 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