Contacts of the helix formed by residues 238 - 250 (chain C) in PDB entry 2X7O
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 GLU 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215C ARG 3.4 11.3 - - - +
216C PHE* 3.3 27.8 - - + -
217C GLY* 3.3 21.5 + - - -
234C PHE* 4.1 6.3 - - + -
235C SER* 3.2 39.6 + - - +
237C ARG* 1.4 81.2 - - + +
239C GLU* 1.3 60.9 + - - +
240C ARG* 3.4 3.1 - - - +
241C SER* 3.7 15.8 + - - +
242C TRP* 3.5 19.6 + - - +
276C LEU* 4.2 0.2 - - - +
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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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236C SER 3.9 16.8 + - - +
237C ARG 3.3 6.1 + - - +
238C GLU* 1.3 74.7 - - - +
240C ARG* 1.4 61.9 + - + +
242C TRP* 3.6 4.5 + - - +
243C PHE* 3.1 21.8 + - - +
276C LEU* 3.8 18.2 - - + -
173D GLU* 4.1 15.2 - - + +
174D GLY* 3.4 40.7 + - - +
225D ARG* 4.6 10.0 + - - -
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Residues in contact with ARG 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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237C ARG 5.0 0.2 + - - -
238C GLU* 3.4 1.2 - - - +
239C GLU* 1.4 79.0 - - + +
241C SER* 1.4 59.9 + - - +
243C PHE* 3.5 1.3 + - - +
244C ARG* 3.0 45.2 + - + +
174D GLY* 4.1 13.0 - - - -
176D THR* 3.5 37.6 + - - +
179D ASP* 5.3 1.3 - - - -
225D ARG 5.8 1.6 + - - -
227D GLU* 5.7 5.2 + - - +
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Residues in contact with SER 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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216C PHE* 3.3 55.3 - - - -
234C PHE* 4.0 9.2 - - - -
238C GLU* 3.7 14.8 + - - +
239C GLU 3.4 0.2 - - - -
240C ARG* 1.4 78.4 - - - +
242C TRP* 1.3 60.1 + - - +
244C ARG* 4.9 2.7 - - - -
245C GLU* 3.6 24.6 + - - +
353C GLY* 4.3 11.2 - - - -
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Residues in contact with TRP 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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234C PHE* 3.5 39.4 - + + -
238C GLU 3.5 7.2 + - - +
239C GLU 3.8 7.6 - - - +
240C ARG 3.3 0.4 - - - -
241C SER* 1.3 78.8 - - - +
243C PHE* 1.4 77.0 + + - +
245C GLU* 3.7 1.0 + - - +
246C ALA* 3.2 30.3 + - + +
265C ALA* 4.4 8.3 - - + -
266C ASP 3.8 28.5 - - - -
267C ASN* 3.7 20.6 - - + -
276C LEU* 3.6 38.4 - - + -
277C TRP 2.9 25.2 + - - +
278C LEU* 3.6 18.6 - - + +
172D SER* 5.3 4.0 - - - -
173D GLU* 3.4 28.0 - - + -
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Residues in contact with PHE 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 3.1 19.0 + - - +
240C ARG* 4.0 2.2 - - - +
242C TRP* 1.4 83.5 - + - +
244C ARG* 1.4 60.3 + - + +
246C ALA* 3.4 5.6 + - + +
247C GLU* 2.9 62.0 + - + +
172D SER* 3.8 11.0 - - - -
173D GLU 3.8 11.7 - - - +
174D GLY* 3.6 22.7 - - - +
175D THR* 3.3 36.8 - - + -
179D ASP* 3.6 30.3 - - + -
183D ASP* 5.6 3.1 - - - -
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Residues in contact with ARG 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 ARG* 3.0 34.0 + - + +
241C SER* 4.4 2.2 - - - +
243C PHE* 1.4 78.1 - - + +
245C GLU* 1.3 61.4 + - - +
247C GLU* 4.1 4.3 - - - +
248C ILE* 3.2 52.1 + - - +
332C ARG* 5.8 0.7 - - - +
352C LEU 4.3 0.4 - - - -
353C GLY 3.5 23.6 + - - +
354C LEU* 5.5 0.9 - - - +
355C ALA 3.0 29.1 + - - -
356C VAL* 4.2 0.8 - - - +
357C ARG* 4.5 1.6 - - - +
366C ASP* 2.8 38.8 + - - +
367C ILE* 3.6 23.9 - - - +
179D ASP* 3.9 21.5 + - - +
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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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232C LYS* 3.5 23.4 + - - +
234C PHE* 3.7 11.1 - - - -
241C SER 3.6 12.4 + - - +
242C TRP 4.1 0.7 - - - +
243C PHE 3.3 0.4 - - - -
244C ARG* 1.3 77.2 - - - +
246C ALA* 1.4 58.6 + - - +
248C ILE* 3.4 2.6 + - - +
249C TYR* 2.9 56.9 + - + -
260C LEU* 5.7 1.6 - - - +
278C LEU* 3.8 23.1 - - + +
351C ASP* 3.5 23.3 + - - +
352C LEU 3.5 20.0 - - - +
353C GLY* 3.5 21.0 + - - +
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Residues in contact with ALA 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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242C TRP* 3.2 27.4 + - + +
243C PHE* 3.8 9.2 - - + +
245C GLU* 1.4 76.4 - - - +
247C GLU* 1.4 55.8 + - - +
249C TYR* 4.1 3.5 - - - +
250C GLN* 3.2 41.3 + - - +
262C PHE* 4.9 3.1 - - - -
265C ALA* 4.1 15.0 - - + -
278C LEU* 4.0 18.3 - - + +
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Residues in contact with GLU 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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243C PHE* 2.9 51.7 + - + +
244C ARG* 4.1 5.2 - - - +
246C ALA* 1.4 73.9 - - - +
248C ILE* 1.3 64.6 + - + +
250C GLN* 5.0 1.1 - - - -
251C THR* 2.8 43.4 + - - +
252C VAL* 3.9 7.1 - - - +
357C ARG* 3.6 32.0 + - - +
179D ASP* 6.0 1.8 - - + +
182D TYR* 6.0 0.5 - - - -
183D ASP* 4.1 19.2 - - - +
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Residues in contact with ILE 248 (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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244C ARG* 3.2 46.7 + - - +
245C GLU 4.0 2.2 - - - +
247C GLU* 1.3 76.2 - - + +
249C TYR* 1.3 60.8 + - - +
252C VAL* 3.4 16.6 - - + +
254C LEU* 3.3 18.1 - - + +
329C ILE* 4.6 17.7 - - + -
352C LEU* 3.4 51.8 - - + +
355C ALA* 3.8 15.5 - - + +
357C ARG* 4.0 25.1 - - + +
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Residues in contact with TYR 249 (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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192C GLY* 5.3 3.5 + - - -
245C GLU* 2.9 54.0 + - + +
246C ALA 4.3 1.6 - - - +
248C ILE* 1.3 76.6 - - - +
250C GLN* 1.4 61.8 + - - +
254C LEU* 3.9 17.6 - - + +
259C ILE* 4.6 7.9 - - + -
260C LEU* 3.4 49.9 - - + +
262C PHE* 3.6 53.7 - + + +
278C LEU* 5.0 2.9 - - + -
349C ILE 4.0 0.5 + - - -
350C ALA* 3.7 3.3 - - - -
351C ASP 3.7 14.6 + - - -
352C LEU* 3.6 26.7 - - + +
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Residues in contact with GLN 250 (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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191C SER* 4.4 17.4 - - - -
192C GLY* 4.6 11.5 + - - +
195C LEU* 4.6 11.4 - - - +
198C GLN* 2.9 36.7 + - - +
246C ALA* 3.2 25.5 + - - +
247C GLU* 4.5 1.3 - - - +
248C ILE 3.4 0.8 - - - -
249C TYR* 1.4 77.0 - - - +
251C THR* 1.4 60.0 + - + +
252C VAL 2.8 18.1 + - - -
253C MET* 3.8 8.0 + - - -
262C PHE* 3.6 18.6 - - + -
265C ALA* 4.0 17.8 + - - +
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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