Contacts of the helix formed by residues 237 - 245 (chain C) in PDB entry 4G1U
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 ASN 237 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C GLU 4.5 7.0 + - - +
234C GLU 3.8 14.5 + - - -
235C VAL 2.8 30.0 + - - -
236C LEU* 1.3 74.5 - - - +
238C ALA* 1.3 65.3 + - - +
239C GLU* 3.1 17.7 + - - +
240C THR* 3.2 25.2 + - - -
241C LEU* 3.1 20.1 + - - +
251C VAL* 3.5 8.5 - - + -
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Residues in contact with ALA 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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237C ASN* 1.3 72.7 - - - +
239C GLU* 1.3 56.2 + - - +
241C LEU* 3.8 4.6 - - - +
242C THR* 2.9 38.1 + - - +
249C LEU 5.0 0.8 - - - +
250C GLY* 4.7 6.3 - - - -
251C VAL* 3.3 34.6 - - + +
265C ARG* 5.4 6.5 - - - +
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Residues in contact with GLU 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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237C ASN* 3.1 12.3 + - - +
238C ALA* 1.3 78.9 - - - +
240C THR* 1.3 61.4 + - - +
242C THR* 3.8 4.6 - - - -
243C GLN* 3.0 32.5 + - + +
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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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220C LEU* 3.5 29.5 - - + +
227C VAL 5.4 1.8 - - - +
228C ALA* 4.9 8.5 - - + -
235C VAL* 3.8 19.8 + - - +
237C ASN* 3.2 18.8 + - - -
239C GLU* 1.3 77.8 - - - +
241C LEU* 1.3 62.0 + - + +
243C GLN* 3.3 5.3 + - - -
244C TRP* 3.0 39.2 + - + +
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Residues in contact with LEU 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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208C LEU* 3.6 25.6 - - + -
220C LEU* 5.5 3.1 - - + -
235C VAL 4.9 2.2 - - - +
236C LEU* 4.3 24.0 - - + -
237C ASN 3.1 22.2 + - - +
238C ALA* 3.8 6.3 - - - +
240C THR* 1.3 77.4 - - + +
242C THR* 1.3 58.8 + - - +
245C TYR* 2.8 53.2 + - + +
249C LEU* 4.3 19.7 - - + +
250C GLY 5.3 0.4 - - - +
251C VAL* 4.5 5.2 - - + -
262C ILE* 3.4 39.3 - - + -
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Residues in contact with THR 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 ALA* 2.9 21.9 + - - +
239C GLU* 3.8 4.7 - - - -
241C LEU* 1.3 73.9 - - - +
243C GLN* 1.3 64.2 + - - +
245C TYR 3.3 16.9 - - - +
247C ALA 5.7 2.0 - - - -
249C LEU 4.2 11.8 + - - -
265C ARG* 5.2 2.9 + - - -
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Residues in contact with GLN 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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239C GLU* 3.0 22.4 + - + +
240C THR* 3.4 10.1 - - - +
241C LEU 3.2 0.2 - - - -
242C THR* 1.3 79.1 - - - +
244C TRP* 1.3 92.3 + - + +
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Residues in contact with TRP 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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45C PRO* 3.9 23.5 - - + +
220C LEU* 3.9 15.0 - - + -
222C ALA* 3.5 26.2 - - + -
223C GLN* 3.7 29.4 - - - -
227C VAL* 3.6 37.1 + - + +
240C THR* 3.0 40.6 + - + +
243C GLN* 1.3 102.4 - - + +
245C TYR* 1.3 70.5 + - + +
246C GLN* 4.4 2.9 + - - +
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Residues in contact with TYR 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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43C ILE* 3.9 1.2 - - - +
44C GLY* 2.9 45.8 + - - -
45C PRO* 4.3 10.8 - - + -
206C HIS 5.0 7.6 + - - -
208C LEU* 3.5 39.5 - - + +
220C LEU* 3.8 21.9 - - + +
241C LEU* 2.8 40.4 + - + +
242C THR* 3.3 17.2 - - - +
244C TRP* 1.3 84.1 - - + +
246C GLN* 1.3 64.7 + - - +
247C ALA* 3.5 7.5 + - + +
249C LEU* 4.4 19.3 - - + -
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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