Contacts of the helix formed by residues 232 - 241 (chain C) in PDB entry 4OMC
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 THR 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230C GLU* 3.3 42.1 + - + +
231C VAL* 1.3 76.5 - - - +
233C ASP* 1.3 65.2 + - - +
234C ALA* 3.3 9.1 + - - +
235C VAL* 3.0 28.2 + - + +
236C GLU* 2.9 23.2 + - - +
453D ASP* 4.0 14.5 + - - +
565D LYS* 6.4 1.8 - - - -
1J 2UC 3.7 10.5 - - - -
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Residues in contact with ASP 233 (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 THR* 1.3 73.8 - - - +
234C ALA* 1.3 57.8 + - - +
236C GLU* 3.2 5.4 + - - +
237C ALA* 2.8 27.5 + - - +
267C ALA* 3.2 32.9 + - + +
268C ARG* 3.6 2.3 + - - +
269C LEU* 2.8 34.1 + - + +
270C ALA* 2.9 29.3 + - - +
530D ASP* 4.6 5.5 - - - +
565D LYS* 6.0 8.5 - - + -
1J 2UC 3.8 14.7 + - - +
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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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232C THR* 3.2 8.1 + - - +
233C ASP* 1.3 81.0 - - - +
235C VAL* 1.3 61.9 + - + +
237C ALA* 3.8 1.7 - - - +
238C ARG* 2.9 35.5 + - - +
269C LEU* 4.2 14.9 - - + +
451D ILE* 4.2 16.2 - - + -
453D ASP* 3.9 31.2 - - + +
567D THR* 4.5 3.1 - - + +
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Residues in contact with VAL 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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175C VAL* 3.7 30.5 - - + +
176C ASN* 4.5 4.7 - - - +
178C GLN* 6.0 0.7 - - - +
226C MET* 3.6 32.5 - - + +
230C GLU 3.6 16.6 - - - +
231C VAL* 4.4 10.3 - - + -
232C THR* 3.0 30.3 + - + +
234C ALA* 1.3 78.2 - - + +
236C GLU* 1.3 62.1 + - - +
238C ARG* 3.4 2.6 + - - +
239C SER* 2.8 27.7 + - - -
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Residues in contact with GLU 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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226C MET* 4.5 3.8 - - + -
231C VAL* 4.0 10.5 - - + +
232C THR 2.9 11.6 + - - +
233C ASP* 3.5 7.0 - - - +
235C VAL* 1.3 78.3 - - - +
237C ALA* 1.3 57.4 + - - +
239C SER* 3.1 6.4 + - - -
240C LEU* 2.8 38.6 + - + +
254C TRP* 3.8 22.7 - - + -
270C ALA* 3.7 15.8 - - + +
308C TYR* 2.6 31.8 + - - -
1J 2UC 2.7 32.6 + - - -
2J ARG* 3.1 19.4 + - - +
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Residues in contact with ALA 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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233C ASP 2.8 20.5 + - - +
234C ALA 3.8 2.0 - - - +
236C GLU* 1.3 73.1 - - - +
238C ARG* 1.3 58.8 + - - +
241C GLY* 2.9 27.4 + - - -
269C LEU* 3.5 37.9 - - + +
270C ALA* 4.3 2.9 - - - +
273C ALA* 3.8 14.8 - - + +
451D ILE* 3.8 17.6 - - + +
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Residues in contact with ARG 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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173C PHE* 4.0 18.6 - - - -
175C VAL* 4.0 31.5 - - + +
178C GLN* 3.8 29.7 + - - +
234C ALA* 2.9 24.6 + - - +
235C VAL* 3.9 3.8 - - - +
237C ALA* 1.3 77.2 - - - +
239C SER* 1.3 60.3 + - - +
241C GLY* 3.8 1.4 - - - -
242C LEU* 3.3 24.4 + - - +
451D ILE* 3.7 41.3 + - + +
453D ASP 6.0 1.6 - - - +
474D CYS* 5.6 4.6 - - - -
477D GLU* 3.8 25.1 + - - -
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Residues in contact with SER 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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152C LEU* 3.9 19.1 - - - +
175C VAL* 3.9 3.6 - - - +
224C VAL* 3.5 23.2 - - - +
226C MET* 3.3 33.1 - - - +
235C VAL 2.8 14.3 + - - -
236C GLU 3.1 8.1 + - - -
238C ARG* 1.3 74.1 - - - +
240C LEU* 1.3 66.1 + - - +
241C GLY 3.1 1.6 - - - -
242C LEU* 3.1 18.4 + - - +
250C TYR* 3.8 8.3 - - - -
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Residues in contact with LEU 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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152C LEU* 3.8 20.6 - - + -
236C GLU* 2.8 29.6 + - + +
239C SER* 1.3 73.7 - - - +
241C GLY* 1.3 56.9 + - - +
244C PRO* 5.3 0.3 - - - +
250C TYR* 3.4 22.3 + - + -
254C TRP* 5.3 2.9 - - + -
270C ALA* 4.2 23.8 - - + +
273C ALA* 3.9 14.3 - - + +
274C PHE* 3.8 28.0 - - + -
277C GLY* 5.9 0.5 - - - -
287C SER* 5.4 0.3 + - - -
289C PHE* 3.7 39.3 - - + -
291C TRP* 3.9 24.9 - - + -
308C TYR* 5.4 0.2 - - + -
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Residues in contact with GLY 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 ALA 2.9 17.8 + - - -
238C ARG* 3.8 4.0 - - - -
240C LEU* 1.3 78.5 - - - +
242C LEU* 1.3 62.5 + - - +
243C ASN 3.3 0.9 + - - -
244C PRO* 3.2 24.7 - - - +
273C ALA* 4.4 8.5 - - - +
479D ASN* 5.3 4.3 - - - +
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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