Contacts of the helix formed by residues 237 - 247 (chain C) in PDB entry 3EU9
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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198C ALA 2.9 27.4 + - - +
201C THR 2.7 30.9 + - - +
202C HIS* 3.4 33.6 + - + +
232C ALA* 2.8 15.7 + - + +
235C ALA* 3.1 2.0 - - + -
236C GLY* 1.3 72.8 - - - +
238C THR* 1.3 62.1 + - - +
239C THR* 3.8 3.6 + - - -
240C VAL* 3.3 25.6 + - - +
241C ILE* 3.1 26.1 + - - +
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Residues in contact with THR 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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53B ILE* 3.1 52.2 - - + +
54B ASP* 5.4 1.4 + - - -
236C GLY 3.2 7.9 + - - +
237C ASN* 1.3 68.8 - - - +
239C THR* 1.3 71.7 + - - +
241C ILE* 3.2 18.1 + - - +
242C SER* 3.4 10.2 + - - -
270C ASN* 4.5 4.3 - - - +
272C TRP* 3.6 17.5 - - + -
273C MET* 3.9 23.3 - - + -
452C SO4 4.6 2.0 - - - +
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Residues in contact with THR 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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202C HIS* 4.7 7.0 + - - +
203C SER* 3.8 10.0 - - - +
204C VAL* 3.8 42.0 - - + +
237C ASN* 3.3 8.4 + - - -
238C THR* 1.3 83.3 + - - +
240C VAL* 1.3 63.0 + - - +
242C SER* 3.7 9.3 + - - -
243C LEU* 3.6 15.9 + - + +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ALA* 3.9 20.6 - - + -
201C THR 3.6 9.4 - - - +
203C SER 3.7 12.6 - - - +
207C THR* 3.3 28.7 - - + +
232C ALA* 4.0 3.4 - - + -
237C ASN* 3.3 31.7 + - - +
238C THR 3.2 0.4 - - - -
239C THR* 1.3 77.9 - - - +
241C ILE* 1.3 67.4 + - - +
243C LEU* 3.1 8.5 + - + +
244C LEU* 2.9 46.0 + - + +
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Residues in contact with ILE 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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229C LEU* 4.2 14.3 - - + +
232C ALA* 3.8 14.6 - - + -
233C VAL* 4.0 16.2 - - + -
237C ASN 3.1 16.4 + - - +
238C THR* 3.2 12.3 + - - +
240C VAL* 1.3 78.1 - - - +
242C SER* 1.3 62.1 + - - +
244C LEU* 3.3 2.2 + - - +
245C LEU* 2.9 50.0 + - + +
272C TRP* 4.1 12.3 - - + -
273C MET* 3.7 43.3 - - + -
277C LEU* 3.8 15.3 - - + -
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Residues in contact with SER 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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323A SO4 4.0 15.5 + - - -
238C THR 3.4 5.0 + - - -
239C THR* 4.0 7.7 + - - -
240C VAL 3.3 0.2 - - - -
241C ILE* 1.3 78.3 - - - +
243C LEU* 1.3 65.7 + - - +
245C LEU* 3.4 8.2 + - - +
246C GLU* 3.0 24.7 + - - +
272C TRP* 3.4 28.2 - - - -
276C HIS* 4.8 3.2 - - - -
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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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203C SER 4.8 0.2 - - - +
204C VAL* 3.4 47.3 - - + +
207C THR* 3.8 17.5 - - + -
208C ARG* 4.1 14.8 - - + +
211C LEU* 3.7 16.1 - - + +
239C THR* 3.6 15.2 + - + +
240C VAL* 3.1 9.5 + - - +
242C SER* 1.3 79.5 - - - +
244C LEU* 1.3 62.3 + - - +
246C GLU* 3.3 8.4 + - + +
247C ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 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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194C LEU* 4.0 34.5 - - + -
198C ALA* 4.4 0.4 - - + -
207C THR* 4.4 7.4 - - + -
211C LEU* 4.3 10.3 - - + -
217C VAL* 4.3 6.1 - - + +
228C ALA* 3.7 12.6 - - + +
229C LEU* 3.6 36.3 - - + +
232C ALA* 4.2 4.3 - - + -
240C VAL* 2.9 36.6 + - + +
241C ILE 3.7 3.4 - - - +
243C LEU* 1.3 73.7 - - - +
245C LEU* 1.3 66.6 + - - +
247C ALA* 3.1 12.3 + - - +
248C GLY 3.3 0.5 + - - -
249C ALA* 2.9 31.9 + - + +
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Residues in contact with LEU 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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229C LEU* 4.1 19.3 - - + -
241C ILE* 2.9 40.5 + - + +
242C SER* 3.8 6.7 - - - +
244C LEU* 1.3 75.7 - - - +
246C GLU* 1.3 64.6 + - - +
248C GLY* 3.0 15.1 + - - -
249C ALA* 3.9 7.3 + - + +
251C VAL* 3.8 18.4 - - + -
276C HIS* 3.8 35.2 - - + +
277C LEU* 3.9 5.8 - - + -
280C ALA* 3.7 26.1 - - + +
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Residues in contact with GLU 246 (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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104A ASP* 5.0 13.7 - - - +
242C SER 3.0 18.3 + - - +
243C LEU* 3.6 7.9 - - + +
245C LEU* 1.3 76.9 - - - +
247C ALA* 1.3 56.4 + - - +
248C GLY 3.2 3.3 + - - -
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Residues in contact with ALA 247 (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* 3.9 31.6 - - + -
217C VAL* 3.8 17.6 - - + +
243C LEU 3.1 15.1 + - - +
244C LEU 3.1 7.3 + - - +
246C GLU* 1.3 75.3 - - - +
248C GLY* 1.3 59.1 + - - +
249C ALA 3.6 0.2 - - - -
450C GOL 4.8 4.5 + - - -
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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