Contacts of the helix formed by residues 241 - 255 (chain C) in PDB entry 4BGG
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 ASP 241 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C ARG 5.6 0.2 - - - +
219C TYR* 4.2 22.9 - - + +
237C PHE* 3.7 14.0 - - + -
238C SER* 3.0 14.6 + - - +
240C ARG* 1.3 80.4 - - + +
242C GLU* 1.3 62.8 + - - +
243C LYS 3.3 2.2 - - - -
244C SER* 3.1 24.7 + - - +
245C TRP 3.3 8.0 + - - -
373C ASN* 6.0 1.3 - - - -
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Residues in contact with GLU 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 SER 3.6 2.4 + - - -
239C SER* 4.1 11.7 - - - +
240C ARG 3.6 3.0 + - - -
241C ASP* 1.3 75.9 - - - +
243C LYS* 1.3 62.3 + - - +
245C TRP* 3.2 8.8 + - - +
246C PHE* 3.0 24.1 + - - +
279C LEU* 4.1 27.4 - - + -
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Residues in contact with LYS 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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240C ARG 5.4 0.4 + - - -
241C ASP 3.3 1.0 - - - -
242C GLU* 1.3 78.7 - - - +
244C SER* 1.3 56.0 + - - +
246C PHE* 3.7 7.3 - - - +
247C ARG* 3.0 29.5 + - - +
372C ASN 4.9 4.5 - - - +
373C ASN* 4.0 27.6 + - + +
374C PRO* 4.9 6.5 - - + -
250D GLU* 5.1 8.1 - - - +
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Residues in contact with SER 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LYS* 6.0 0.7 - - - -
237C PHE* 4.0 13.5 - - - -
241C ASP* 3.1 20.5 + - - +
243C LYS* 1.3 73.5 - - - +
245C TRP* 1.3 65.4 + - - +
247C ARG 3.4 0.3 + - - -
248C GLU* 3.0 27.5 + - - +
356C GLY* 3.8 21.6 + - - -
357C LEU* 5.2 1.4 - - - +
373C ASN* 3.0 25.5 + - - +
375C ARG* 4.6 8.3 - - - +
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Residues in contact with TRP 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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237C PHE* 3.6 47.7 - + + -
241C ASP 3.3 3.3 + - - +
242C GLU* 3.2 11.3 + - + +
244C SER* 1.3 79.3 - - - +
246C PHE* 1.3 104.8 + + + +
248C GLU* 3.9 1.3 - - - +
249C THR* 2.9 48.6 + - + -
268C SER* 3.0 29.5 + - - -
269C ASP 4.1 16.2 - - - -
270C MET* 5.2 5.4 - - + -
279C LEU* 3.6 34.8 - - + -
280C TRP 3.1 18.5 + - - +
281C LEU* 4.4 2.0 - - + -
245D TRP* 6.3 3.4 - + - -
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Residues in contact with PHE 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 GLU 3.0 15.0 + - - +
243C LYS* 3.7 6.3 - - - +
245C TRP* 1.3 106.6 - + - +
247C ARG* 1.3 65.0 + - - +
249C THR* 3.8 3.0 - - - -
250C GLU* 3.0 31.7 + - - +
245D TRP* 5.1 3.6 - + - -
246D PHE* 3.6 53.8 - + + -
249D THR* 4.2 19.7 - - + -
250D GLU* 3.9 38.1 - - + +
253D ASN* 6.2 1.8 - - + -
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Residues in contact with ARG 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 LYS 3.0 18.7 + - - +
244C SER 3.9 0.4 - - - +
246C PHE* 1.3 76.0 - - - +
248C GLU* 1.3 63.8 + - - +
250C GLU* 3.4 6.4 + - - +
251C LEU* 3.1 28.9 + - + +
355C LEU 4.7 3.4 - - - +
356C GLY 3.8 20.9 - - - +
358C ALA 5.4 6.7 - - - +
373C ASN* 5.3 0.9 - - - +
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Residues in contact with GLU 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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235C LYS* 4.7 0.9 + - - -
237C PHE* 3.7 20.8 - - + -
244C SER 3.0 14.6 + - - +
245C TRP* 3.9 3.4 - - - +
247C ARG* 1.3 76.2 - - - +
249C THR* 1.3 64.0 + - - +
251C LEU* 3.4 6.0 + - - +
252C TYR* 3.1 50.5 + - + -
281C LEU* 3.7 21.1 - - + +
354C ASP* 3.4 14.8 + - - +
355C LEU* 3.0 36.7 + - + +
356C GLY* 3.7 13.3 + - - +
1000C 844 3.4 12.9 - - - +
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Residues in contact with THR 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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245C TRP* 2.9 39.8 + - + -
246C PHE* 3.8 4.9 - - - -
248C GLU* 1.3 76.7 - - - +
250C GLU* 1.3 57.7 + - - +
252C TYR* 3.1 7.2 + - - +
253C ASN* 2.8 46.0 + - - +
265C PHE* 5.2 2.0 - - - -
268C SER* 2.8 32.9 + - - +
281C LEU* 4.7 4.4 - - - +
245D TRP* 6.2 0.7 - - + -
246D PHE* 4.3 13.7 - - + -
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Residues in contact with GLU 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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246C PHE* 3.0 24.8 + - - +
247C ARG* 3.9 5.3 - - - +
248C GLU 3.4 0.2 - - - -
249C THR* 1.3 74.8 - - - +
251C LEU* 1.3 59.8 + - - +
254C THR* 2.8 42.7 + - - -
255C VAL* 4.7 0.5 - - - +
360C MET* 5.1 10.6 - - - +
243D LYS* 3.2 28.9 - - - +
246D PHE* 3.2 55.0 - - + +
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Residues in contact with LEU 251 (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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247C ARG* 3.1 16.4 + - + +
248C GLU 3.7 7.2 - - - +
250C GLU* 1.3 76.5 - - - +
252C TYR* 1.3 62.8 + - - +
255C VAL* 3.1 38.1 + - + +
256C MET 3.5 2.8 + - - -
257C LEU* 4.0 12.6 - - + +
332C ILE* 4.0 23.3 - - + -
355C LEU* 4.1 24.9 - - + +
358C ALA* 3.6 32.1 - - + +
360C MET* 3.5 38.1 - - + -
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Residues in contact with TYR 252 (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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248C GLU* 3.1 48.1 + - + +
249C THR 3.7 2.9 - - - +
251C LEU* 1.3 80.8 - - + +
253C ASN* 1.3 61.5 + - - +
256C MET* 3.5 18.0 + - - -
257C LEU* 3.9 28.9 + - + +
262C ILE* 4.1 8.2 - - + +
263C LEU* 2.8 40.5 + - - +
264C GLY* 5.3 0.2 - - - -
265C PHE* 3.4 59.0 - + + -
281C LEU* 4.4 9.0 - - + -
283C THR* 5.4 2.0 - - + -
352C ILE 5.1 0.9 + - - -
353C ALA* 5.5 0.2 - - - -
354C ASP 5.4 1.9 + - - -
355C LEU* 4.0 23.1 - - + +
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Residues in contact with ASN 253 (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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249C THR* 2.8 40.4 + - - +
252C TYR* 1.3 74.6 - - - +
254C THR* 1.3 59.0 + - - +
256C MET* 4.4 3.7 + - - +
265C PHE* 3.6 27.3 - - - -
268C SER* 4.6 1.7 - - - -
242D GLU* 5.6 1.6 - - - +
246D PHE* 4.2 17.0 - - + -
279D LEU* 6.3 1.6 - - + -
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Residues in contact with THR 254 (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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250C GLU* 2.8 36.6 + - - -
253C ASN* 1.3 74.2 - - - +
255C VAL* 1.3 69.0 + - - +
256C MET* 5.0 1.3 - - - +
242D GLU* 4.4 14.8 - - - -
243D LYS* 5.0 11.9 - - - -
246D PHE* 4.3 11.9 - - - -
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Residues in contact with VAL 255 (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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250C GLU 5.6 0.2 - - - -
251C LEU* 3.1 34.0 + - + +
254C THR* 1.3 83.0 - - - +
256C MET* 1.3 70.3 + - - +
257C LEU* 4.2 18.4 - - + +
328C GLY 3.7 15.6 - - - +
329C LYS* 4.1 14.7 - - + +
330C PRO* 3.8 33.4 - - + -
332C ILE* 4.7 7.6 - - + -
360C MET* 4.9 5.2 - - - -
243D LYS* 5.5 7.6 - - - +
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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