Contacts of the helix formed by residues 230 - 248 (chain C) in PDB entry 3SF4
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 230 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ARG* 4.0 5.9 + - - -
225C ALA* 3.0 16.4 + - - +
228C PHE* 3.0 14.4 - - + +
229C GLY* 1.3 72.1 - - - +
231C LYS* 1.3 62.6 + - - +
232C ALA* 3.5 10.9 + - - +
233C ALA* 3.3 32.2 + - + +
234C GLU* 3.1 23.2 + - - +
236C ARG* 4.7 3.0 + - - -
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLY* 3.1 15.9 + - - +
230C ASP* 1.3 68.7 + - - +
232C ALA* 1.3 67.0 + - - +
234C GLU* 3.1 32.2 + - - +
235C ARG* 2.9 24.4 + - - +
264C LEU* 3.6 23.3 - - + +
267C GLN* 4.6 10.7 - - - +
268C LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ASP* 3.3 10.0 + - - +
231C LYS* 1.3 77.7 - - - +
233C ALA* 1.3 63.2 + - - +
235C ARG* 3.2 8.6 + - - +
236C ARG* 3.0 40.7 + - - +
268C LEU* 4.6 8.6 - - + +
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Residues in contact with ALA 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ARG* 2.8 40.2 - - - +
225C ALA* 3.6 10.2 - - + +
230C ASP* 3.3 23.5 + - - +
232C ALA* 1.3 79.6 - - - +
234C GLU* 1.3 56.9 + - - +
236C ARG* 3.1 18.4 + - - +
237C ALA* 2.9 29.6 + - - +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 3.5 16.1 - - + +
225C ALA* 3.6 12.7 - - + +
226C LYS* 3.0 33.9 + - + +
229C GLY 5.9 0.5 - - - -
230C ASP 3.1 12.8 + - - +
231C LYS* 3.1 43.5 + - - +
233C ALA* 1.3 76.0 - - - +
235C ARG* 1.3 58.7 + - - +
237C ALA* 3.4 3.0 + - - +
238C TYR* 3.0 54.3 + - + -
264C LEU* 3.7 11.7 - - + +
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Residues in contact with ARG 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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231C LYS 2.9 12.6 + - - +
232C ALA* 3.5 9.5 + - - +
234C GLU* 1.3 74.2 - - - +
236C ARG* 1.3 74.2 + - - +
238C TYR* 3.3 5.2 + - - +
239C SER* 2.8 56.0 + - - -
261C THR* 4.1 14.8 - - - +
264C LEU* 3.3 28.7 - - + +
265C ALA* 4.4 3.8 - - - +
268C LEU* 4.2 14.4 - - + +
273C VAL* 3.7 41.9 - - - +
276C GLN* 4.3 6.1 - - - +
40F GLU* 3.2 27.6 + - - +
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Residues in contact with ARG 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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221C ARG* 3.7 1.0 - - + +
230C ASP* 4.7 3.0 + - - -
232C ALA* 3.0 34.4 + - - +
233C ALA* 3.1 28.6 + - - +
235C ARG* 1.3 84.5 - - - +
237C ALA* 1.3 63.7 + - - +
239C SER* 3.3 2.9 + - - -
240C ASN* 3.0 30.8 + - - +
40F GLU* 3.9 37.2 - - + +
41F CYS 3.5 20.9 + - - -
42F GLU* 3.0 43.5 + - - +
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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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218C HIS* 3.9 10.2 - - - +
221C ARG* 4.0 10.9 - - + +
222C LEU* 3.8 39.3 - - + +
233C ALA 2.9 15.4 + - - +
234C GLU 3.7 4.7 - - - +
236C ARG* 1.3 79.4 - - - +
238C TYR* 1.3 56.8 + - - +
240C ASN* 3.5 7.2 + - - +
241C LEU* 2.9 36.9 + - + +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LEU* 3.5 25.9 - - + +
226C LYS* 2.8 27.2 + - - -
234C GLU* 3.0 43.1 + - + +
235C ARG* 3.7 2.2 - - - +
236C ARG 3.2 0.4 - - - -
237C ALA* 1.3 77.0 - - - +
239C SER* 1.3 61.2 + - - +
241C LEU* 3.4 2.5 + - + +
242C GLY* 3.0 18.2 + - - -
257C TYR* 3.6 33.7 - + - +
260C LYS* 3.7 45.2 + - + +
261C THR* 3.0 21.9 - - + +
264C LEU* 4.1 12.1 - - + -
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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
----------------------------------------------------------
235C ARG* 2.8 33.7 + - - -
236C ARG 3.7 5.4 - - - -
238C TYR* 1.3 76.2 - - - +
240C ASN* 1.3 64.6 + - - +
242C GLY* 3.1 3.1 + - - -
243C ASN* 3.0 32.7 + - - +
258C TYR* 4.0 8.2 - - - -
261C THR* 3.1 21.3 + - - +
273C VAL* 5.3 0.3 - - - +
276C GLN* 4.7 7.5 + - - -
277C SER* 5.4 0.5 + - - -
40F GLU* 4.1 11.7 - - - -
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Residues in contact with ASN 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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199C GLY* 5.9 0.4 - - - -
203C ASN* 3.3 17.5 + - - +
206C TYR* 5.0 2.7 - - - -
218C HIS* 3.3 36.4 + - + +
236C ARG* 3.0 24.5 + - - +
237C ALA* 3.9 1.9 - - - +
239C SER* 1.3 76.3 - - - +
241C LEU* 1.3 63.2 + - - +
243C ASN* 3.4 10.4 + - - +
244C ALA* 3.0 24.6 + - - +
38F MET 5.1 0.2 - - - +
39F THR* 4.0 3.6 - - - -
40F GLU* 3.1 49.7 + - - +
42F GLU* 5.9 0.2 + - - -
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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
----------------------------------------------------------
215C VAL* 3.5 45.8 - - + +
218C HIS* 3.6 22.0 - - + +
219C GLU* 4.1 8.5 - - + +
222C LEU* 4.5 15.7 - - + -
237C ALA 2.9 29.2 + - - +
238C TYR* 3.7 4.5 - - - +
240C ASN* 1.3 76.2 - - - +
242C GLY* 1.3 65.1 + - - +
244C ALA* 3.2 5.2 + - - +
245C TYR* 3.0 33.0 + - + -
257C TYR* 3.6 38.4 - - + +
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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 TYR 3.0 13.5 + - - -
239C SER 3.1 3.1 + - - -
241C LEU* 1.3 79.2 - - - +
243C ASN* 1.3 62.6 + - - +
245C TYR 3.1 0.7 + - - -
246C ILE* 3.0 24.8 + - - +
254C ALA* 3.6 12.0 - - - +
257C TYR* 3.9 13.8 - - - +
258C TYR* 3.5 20.9 - - - -
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Residues in contact with ASN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TYR* 3.5 25.0 + - + +
239C SER* 3.0 24.6 + - - -
240C ASN* 3.6 14.0 + - - +
242C GLY* 1.3 74.4 - - - +
244C ALA* 1.3 65.1 + - - +
246C ILE* 3.1 12.2 + - - +
247C PHE* 3.3 18.2 + - - -
258C TYR* 2.7 34.2 + - - -
280C SER* 5.3 0.2 + - - -
35F LEU* 3.3 25.0 - - + +
38F MET* 4.3 21.8 + - - +
39F THR* 5.5 0.4 - - - +
40F GLU* 5.7 2.4 - - - +
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Residues in contact with ALA 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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206C TYR* 3.7 18.5 - - + -
211C PHE* 4.0 15.2 - - + +
214C ALA* 4.3 9.0 - - + -
215C VAL* 3.6 22.7 - - + +
218C HIS* 5.3 0.7 - - + -
240C ASN 3.0 18.0 + - - +
241C LEU* 3.6 4.9 - - - +
243C ASN* 1.3 75.7 - - - +
245C TYR* 1.3 64.4 + - - +
247C PHE* 3.1 14.6 + - - +
248C LEU* 3.2 16.7 + - - +
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Residues in contact with TYR 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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212C ARG* 3.7 14.0 + - - -
215C VAL* 3.2 36.9 - - + +
219C GLU* 4.0 6.8 + - - -
241C LEU* 3.0 27.4 + - + -
242C GLY 3.1 6.0 + - - +
244C ALA* 1.3 73.3 - - - +
246C ILE* 1.3 68.0 + - - +
248C LEU* 3.0 17.7 + - + +
250C GLU* 3.1 62.5 + - + +
253C THR* 3.7 24.2 - - + +
254C ALA* 3.9 8.5 - - + -
257C TYR* 3.5 30.9 + + - -
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Residues in contact with ILE 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 GLY 3.0 12.5 + - - +
243C ASN 3.1 7.8 + - - +
245C TYR* 1.3 75.0 - - - +
247C PHE* 1.3 61.2 + - + +
249C GLY* 3.1 13.9 + - - -
251C PHE* 3.4 25.4 - - + -
254C ALA* 3.6 13.7 - - + -
258C TYR* 3.4 26.0 - - + +
284C THR* 3.4 33.7 - - + +
287C LEU* 4.5 5.2 - - + -
31F TRP* 3.9 15.9 - - + -
32F MET* 3.9 26.2 - - + +
35F LEU* 4.1 15.7 - - + -
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Residues in contact with PHE 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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206C TYR* 3.2 30.3 - + - -
211C PHE* 3.5 42.3 - + + -
243C ASN 3.3 18.7 + - - -
244C ALA 3.1 6.6 + - - +
246C ILE* 1.3 73.6 - - + +
248C LEU* 1.3 58.7 + - - +
249C GLY 3.1 5.5 + - - -
32F MET* 3.5 47.8 - - + -
35F LEU* 4.0 16.2 - - + -
36F LYS* 3.6 37.9 - - + -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 3.5 45.5 - - + +
212C ARG* 3.5 47.6 - - + +
215C VAL* 4.2 6.3 - - + -
244C ALA 3.2 6.9 + - - +
245C TYR* 3.0 22.7 + - + +
247C PHE* 1.3 77.1 - - - +
249C GLY* 1.3 58.6 + - - +
250C GLU* 3.2 21.6 + - - +
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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
------------------------------------------------------------
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