Contacts of the helix formed by residues 229 - 245 (chain C) in PDB entry 5E9W
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 ALA 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLN* 3.4 31.2 - - + +
227C ASP* 2.8 14.0 + - - +
228C ILE* 1.3 78.8 - - + +
230C ASP* 1.3 60.1 + - - +
231C VAL 3.3 1.3 - - - -
232C SER* 3.1 12.6 + - - +
233C VAL* 3.0 29.9 + - - +
501C SAH 4.0 9.9 - - - +
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Residues in contact with ASP 230 (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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192A ARG 3.7 6.0 - - - +
193A GLN* 2.9 21.4 + - - +
195A LYS* 3.5 31.2 - - - +
228C ILE 3.5 1.6 + - - -
229C ALA* 1.3 73.1 - - - +
231C VAL* 1.3 59.0 + - - +
233C VAL* 3.3 1.3 + - - +
234C LYS* 2.9 63.1 + - - +
259C THR* 2.5 37.1 + - + +
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLU* 4.9 9.9 - - + +
192A ARG* 4.1 28.9 - - + +
193A GLN* 3.4 26.9 - - + +
229C ALA 3.3 0.6 - - - -
230C ASP* 1.3 78.7 - - - +
232C SER* 1.3 58.5 + - - +
234C LYS* 3.5 7.3 + - + +
235C GLN* 2.9 49.1 + - + +
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Residues in contact with SER 232 (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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193A GLN* 4.0 7.2 + - - +
207C GLY* 3.4 28.0 - - - +
208C LYS* 3.8 25.3 - - - +
227C ASP* 4.7 2.0 - - - -
229C ALA* 3.1 24.4 + - - +
231C VAL* 1.3 76.3 - - - +
233C VAL* 1.3 54.6 + - - +
235C GLN* 3.1 3.9 + - - +
236C CYS* 2.7 35.9 + - - +
501C SAH 4.8 3.0 + - - -
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C CYS* 4.9 3.1 - - - -
207C GLY 4.4 1.6 - - - -
225C CYS 4.7 2.5 - - - +
226C THR 4.7 0.4 - - - -
227C ASP* 3.5 39.3 - - + +
229C ALA 3.0 14.8 + - - +
230C ASP* 3.3 6.0 + - - +
232C SER* 1.3 74.1 - - - +
234C LYS* 1.3 61.2 + - + +
236C CYS* 3.1 8.1 + - - +
237C GLN* 2.9 27.6 + - - +
257C PHE* 3.9 27.3 - - + -
258C ILE 4.0 12.6 - - - +
259C THR* 3.8 20.2 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 5.6 0.8 - - - +
230C ASP* 2.9 48.7 + - - +
231C VAL* 3.9 6.5 - - + +
233C VAL* 1.3 78.9 - - + +
235C GLN* 1.3 58.9 + - + +
237C GLN* 3.4 17.6 + - - +
238C GLN* 3.0 26.9 + - - +
259C THR* 5.0 0.6 + - - -
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Residues in contact with GLN 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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208C LYS* 3.1 41.2 + - + +
231C VAL* 2.9 38.8 + - + +
232C SER* 3.1 5.6 + - - +
234C LYS* 1.3 75.9 - - + +
236C CYS* 1.3 64.1 + - - +
238C GLN* 3.3 7.2 + - - +
239C ARG* 3.0 24.8 + - - +
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Residues in contact with CYS 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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206C CYS* 4.1 6.1 - - - -
207C GLY 3.4 12.3 - - - +
208C LYS 3.5 12.0 + - - -
209C GLY* 3.6 22.0 - - - -
212C LEU* 3.6 7.5 - - - +
225C CYS* 3.9 22.2 - - - -
232C SER 2.7 17.8 + - - +
233C VAL* 3.1 11.4 + - - +
235C GLN* 1.3 73.2 - - - +
237C GLN* 1.3 57.2 + - - +
239C ARG* 3.3 4.3 + - - +
240C TYR* 3.0 24.4 + - - +
257C PHE* 3.7 18.4 - - + -
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Residues in contact with GLN 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 2.9 14.2 + - - +
234C LYS* 3.6 19.4 - - - +
235C GLN 3.3 0.2 - - - -
236C CYS* 1.3 73.6 - - - +
238C GLN* 1.3 61.0 + - - +
240C TYR* 3.1 3.5 + - - +
241C GLU* 2.9 42.3 + - + +
257C PHE* 3.5 46.0 - - + +
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Residues in contact with GLN 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 LYS 3.0 16.5 + - - +
235C GLN* 3.3 8.0 + - - +
237C GLN* 1.3 75.6 - - - +
239C ARG* 1.3 58.3 + - - +
241C GLU* 3.1 11.7 + - - +
242C ASP* 2.7 68.2 + - - +
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Residues in contact with ARG 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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208C LYS* 3.3 31.6 + - - +
209C GLY 3.6 29.5 + - - -
210C GLY* 3.9 8.7 - - - +
212C LEU* 3.7 10.5 - - + -
213C LEU* 5.1 13.1 - - + +
235C GLN* 3.0 17.4 + - - +
236C CYS 3.6 5.6 - - - +
238C GLN* 1.3 78.3 - - - +
240C TYR* 1.3 61.4 + - - +
242C ASP* 3.5 7.6 + - + +
243C MET* 3.1 36.1 + - + +
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Residues in contact with TYR 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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212C LEU* 3.7 13.2 - - + +
236C CYS 3.0 9.3 + - - +
237C GLN 3.1 6.0 + - - +
239C ARG* 1.3 75.2 - - - +
241C GLU* 1.3 88.6 + - - +
243C MET* 3.2 15.4 + - - +
244C LYS* 3.2 46.6 + - + +
252C ILE* 3.8 16.4 - - + -
253C PHE* 2.4 57.5 + + - -
254C SER* 3.5 9.9 - - - -
255C ALA* 3.6 17.2 + - + -
257C PHE* 3.5 27.8 - + + -
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Residues in contact with GLU 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 GLN* 2.9 33.6 + - + +
238C GLN* 3.5 19.1 - - - +
240C TYR* 1.3 103.1 - - - +
242C ASP* 1.3 57.7 + - - +
244C LYS* 3.4 11.6 + - - +
245C ASN* 2.9 51.9 + - - +
257C PHE* 5.0 1.2 - - - -
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Residues in contact with ASP 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 GLN* 2.7 48.4 + - - +
239C ARG* 3.9 7.0 - - + +
241C GLU* 1.3 78.3 - - - +
243C MET* 1.3 61.8 + - + +
245C ASN* 3.4 7.2 + - - +
246C ARG* 3.3 27.2 + - - +
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Residues in contact with MET 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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212C LEU* 3.9 27.8 - - - -
213C LEU* 3.2 47.1 - - + +
216C LYS* 3.7 33.3 - - + -
239C ARG* 3.1 25.5 + - + +
240C TYR* 3.2 7.8 + - - +
242C ASP* 1.3 78.9 - - + +
244C LYS* 1.3 59.1 + - - +
246C ARG* 3.7 19.6 + - - +
249C SER* 4.0 10.2 - - - -
252C ILE* 4.2 12.4 - - + +
253C PHE* 6.0 0.2 - - - -
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C TYR* 3.2 40.3 + - + +
241C GLU* 3.8 13.5 + - - +
243C MET* 1.3 78.6 - - - +
245C ASN* 1.3 65.1 + - - +
246C ARG 3.4 3.4 + - - +
249C SER* 3.4 19.6 + - - +
252C ILE* 3.4 37.0 - - + -
254C SER* 5.7 1.8 - - - +
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Residues in contact with ASN 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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241C GLU* 2.9 38.7 + - - +
242C ASP* 3.6 9.3 + - - +
243C MET 3.3 0.2 - - - -
244C LYS* 1.3 87.7 - - - +
246C ARG* 1.3 62.3 + - - -
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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