Contacts of the helix formed by residues 234 - 242 (chain C) in PDB entry 5UHE
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 VAL 234 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C PHE* 3.8 33.4 - - + -
222C VAL* 3.1 42.1 + - + +
223C GLY* 4.7 0.7 - - - +
224C VAL* 4.3 9.2 - - + -
232C GLN 3.6 0.2 + - - -
233C PRO* 1.3 70.3 - - - +
235C THR* 1.3 67.3 + - - +
236C VAL 3.2 0.9 - - - -
237C LEU* 3.1 14.7 + - + +
238C LEU* 3.4 13.1 + - + +
258C MET* 3.9 26.5 - - + -
261C THR* 4.2 6.4 - - + +
342C ILE* 4.3 21.3 - - + -
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Residues in contact with THR 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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233C PRO* 4.1 5.7 - - - +
234C VAL* 1.3 78.2 - - + +
236C VAL* 1.3 60.7 + - - +
237C LEU 3.1 2.2 - - - -
238C LEU* 3.5 8.2 - - + +
239C LYS* 2.9 35.9 + - - +
248C ILE* 3.9 19.1 - - + -
258C MET* 4.5 6.7 - - + -
261C THR* 4.1 11.1 + - + +
262C LEU* 3.7 41.7 - - + +
265C ASP* 3.6 26.0 + - - +
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Residues in contact with VAL 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 GLN* 3.5 15.3 - - + +
233C PRO* 3.3 40.6 - - + +
234C VAL 3.2 0.4 - - - -
235C THR* 1.3 77.4 + - - +
237C LEU* 1.3 61.7 + - - +
239C LYS* 5.0 1.8 - - - -
240C ALA* 3.3 21.1 + - - +
265C ASP* 4.0 15.5 - - - +
266C ASN* 5.6 2.7 - - + +
267C THR* 5.7 4.0 - - - +
273C ALA* 3.4 16.9 - - + +
276C ASP* 3.4 27.4 - - + +
277C ILE* 3.9 14.1 - - + -
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Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C LEU* 5.0 8.1 - - + -
214C PHE* 3.8 33.9 - - + -
224C VAL* 4.5 17.5 - - + -
226C ILE* 5.1 9.9 - - + -
233C PRO 4.1 0.2 + - - -
234C VAL* 3.1 12.9 + - + +
235C THR 3.1 0.4 - - - -
236C VAL* 1.3 79.8 - - - +
238C LEU* 1.3 60.7 + - + +
240C ALA* 3.2 2.3 + - - +
241C LEU* 3.1 46.5 + - + +
277C ILE* 3.9 21.7 - - + +
296C LEU* 4.5 13.0 - - + -
338C VAL* 4.8 8.7 - - + -
342C ILE* 6.1 1.1 - - + -
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Residues in contact with LEU 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 VAL* 3.4 13.4 + - + +
235C THR* 3.1 14.6 + - + +
237C LEU* 1.3 80.7 - - + +
239C LYS* 1.3 58.2 + - - +
240C ALA 3.1 1.0 + - - -
241C LEU* 3.6 11.4 + - + -
242C GLY 3.6 2.9 + - - -
243C TRP* 3.1 53.7 + - + +
248C ILE* 4.2 30.7 - - + -
252C PHE* 3.9 28.5 - - + -
258C MET* 4.8 6.3 - - + -
338C VAL* 5.9 0.4 - - + -
339C VAL* 4.7 10.1 - - + -
342C ILE* 4.4 22.2 - - + -
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Residues in contact with LYS 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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235C THR 2.9 17.9 + - - +
236C VAL* 5.5 1.3 - - - -
238C LEU* 1.3 75.7 - - - +
240C ALA* 1.3 60.3 + - - +
242C GLY* 4.0 3.1 + - - -
243C TRP 3.9 10.1 - - - +
245C SER* 3.2 22.7 + - - +
248C ILE* 3.9 12.1 - - + -
262C LEU* 3.6 27.8 + - - +
265C ASP* 2.3 36.3 + - - +
267C THR 4.2 2.5 - - - +
268C VAL* 3.3 34.8 - - + +
269C GLY 4.3 6.7 - - - +
270C THR* 3.3 30.1 + - - +
273C ALA* 3.7 15.3 - - + -
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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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236C VAL 3.3 18.6 + - - +
237C LEU 3.4 7.0 - - - +
238C LEU 3.1 0.6 - - - -
239C LYS* 1.3 79.2 - - - +
241C LEU* 1.3 64.4 + - - +
242C GLY 3.3 0.8 + - - -
270C THR* 4.4 3.8 - - - +
273C ALA* 3.8 10.1 - - + -
274C LEU* 3.3 41.6 - - + +
277C ILE* 3.6 20.6 - - + -
293C GLN* 5.2 3.1 + - - +
296C LEU* 4.0 5.7 - - + +
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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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237C LEU* 3.1 33.4 + - + +
238C LEU* 3.6 13.0 + - + +
240C ALA* 1.3 78.8 - - - +
242C GLY* 1.3 56.8 + - - +
243C TRP* 3.7 33.7 - - + +
270C THR* 5.3 0.4 - - - +
293C GLN* 5.3 6.2 + - - -
296C LEU* 5.2 7.9 - - + -
301C PHE* 4.7 17.7 - - + -
335C GLU* 4.4 33.6 - - + +
338C VAL* 4.8 20.6 - - + -
339C VAL* 5.3 1.8 - - + -
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Residues in contact with GLY 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 LEU 3.6 1.6 + - - -
239C LYS 4.0 2.2 + - - -
240C ALA 3.3 2.8 - - - -
241C LEU* 1.3 79.1 - - - +
243C TRP* 1.3 66.8 + - - +
244C THR* 3.5 7.4 + - - +
247C GLN* 5.0 0.3 - - - +
270C THR* 4.4 22.2 + - - -
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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