Contacts of the helix formed by residues 236 - 245 (chain C) in PDB entry 1TYG
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 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C SER* 2.7 14.0 + - - +
235C ASP* 1.3 79.5 + - - +
237C VAL* 1.3 66.7 + - - +
238C VAL* 3.1 24.4 + - - +
239C LEU* 2.9 31.4 + - + +
240C ALA* 3.1 10.4 + - - +
269C ASN* 4.4 2.7 - - - +
273C ILE* 5.1 0.2 - - - -
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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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235C ASP 2.8 9.8 + - - +
236C ASP* 1.3 71.8 + - - +
238C VAL* 1.3 69.1 + - + +
240C ALA* 3.3 8.5 - - - +
241C ARG* 6.3 0.2 - - - +
269C ASN* 3.1 33.8 - - - +
272C PHE* 3.3 32.3 - - + -
273C ILE* 4.3 8.5 - - - +
276C GLN* 3.0 44.8 + - - +
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Residues in contact with VAL 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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236C ASP* 3.1 11.9 + - - +
237C VAL* 1.3 77.4 - - + +
239C LEU* 1.3 58.3 - - - +
240C ALA 3.0 2.2 - - - -
241C ARG* 2.7 47.8 + - + +
242C LYS* 2.8 39.3 + - + +
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Residues in contact with LEU 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 PRO* 6.1 2.0 - - + -
212C PRO* 4.0 38.4 - - + +
215C THR* 6.4 0.2 - - - -
216C LEU* 4.0 26.5 - - + -
233C THR* 3.1 24.7 - - - +
234C SER* 3.9 16.2 - - - +
236C ASP* 2.9 29.2 + - + +
238C VAL* 1.3 73.2 - - - +
240C ALA* 1.3 64.3 + - - +
242C LYS* 4.0 7.0 - - + -
243C LEU* 3.3 24.9 + - + +
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Residues in contact with ALA 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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233C THR* 4.6 8.7 - - + +
236C ASP 3.1 6.5 + - - +
237C VAL 3.3 12.8 - - - +
238C VAL 3.0 0.4 - - - -
239C LEU* 1.3 80.5 - - - +
241C ARG* 1.3 67.0 + - - +
243C LEU 3.1 0.3 + - - -
244C GLU* 3.1 18.3 + - - +
251C ILE* 3.2 31.8 - - + +
253C PRO* 6.0 0.4 - - + -
273C ILE* 3.9 28.7 - - + -
276C GLN* 4.1 5.2 - - - +
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Residues in contact with ARG 241 (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 VAL* 2.7 32.3 + - + +
240C ALA* 1.3 74.9 - - - +
242C LYS* 1.3 57.4 + - - +
244C GLU* 2.8 22.0 + - + +
245C GLU* 2.6 71.7 + - + +
276C GLN* 3.2 39.6 + - - +
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Residues in contact with LYS 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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216C LEU* 3.9 22.0 - - + -
238C VAL* 2.8 40.7 + - + +
239C LEU* 4.0 7.9 - - + +
241C ARG* 1.3 76.4 - - + +
243C LEU* 1.3 63.1 + - - +
245C GLU* 3.2 33.8 + - - +
246C LEU* 3.2 24.3 - - + +
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Residues in contact with LEU 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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215C THR* 3.9 7.0 - - + +
216C LEU* 3.6 39.7 - - + +
219C SER* 3.8 23.6 - - - +
231C PRO* 3.6 26.0 - - + -
233C THR* 3.5 32.5 - - - +
239C LEU* 3.3 11.5 + - + +
240C ALA 3.1 2.5 + - - +
242C LYS* 1.3 77.5 - - - +
244C GLU* 1.3 61.4 + - - +
246C LEU* 3.4 21.8 + - + +
248C VAL* 3.5 18.3 - - + +
251C ILE* 3.4 19.7 - - + -
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Residues in contact with GLU 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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240C ALA 3.1 6.0 + - - +
241C ARG* 2.8 38.5 + - + +
243C LEU* 1.3 71.8 - - - +
245C GLU* 1.3 59.2 + - + +
246C LEU 3.0 9.8 + - - -
247C GLY* 3.2 12.3 + - - -
248C VAL* 3.6 16.6 + - + +
251C ILE* 4.4 9.9 - - + -
276C GLN* 3.9 7.3 + - - +
277C ALA* 3.3 28.5 + - - +
278C LYS* 3.3 31.3 + - - +
279C VAL* 3.3 27.1 - - + +
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Residues in contact with GLU 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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241C ARG* 2.6 63.5 + - + +
242C LYS* 3.2 30.7 + - - +
244C GLU* 1.3 73.2 - - + +
246C LEU* 1.3 58.6 + - + +
247C GLY 3.6 1.6 + - - -
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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