Contacts of the helix formed by residues 222 - 238 (chain C) in PDB entry 5I94
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 222 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ARG* 3.5 32.0 + - - +
220C ILE* 3.6 4.8 - - - +
221C PRO* 1.3 77.9 - - + +
223C PHE* 1.3 59.6 + - - +
224C MET* 3.7 6.4 + - - +
225C SER* 3.2 32.1 + - - -
226C PHE* 3.3 16.8 + - - +
541C PRO 5.1 0.6 + - - -
543C ARG 5.5 3.3 + - - +
544C GLU* 5.4 8.5 - - - +
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Residues in contact with PHE 223 (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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164C SER 4.4 3.7 + - - +
165C THR 3.9 10.1 - - - +
166C GLY* 3.4 25.1 - - - -
220C ILE* 4.0 16.8 - - + +
221C PRO 3.0 10.1 + - - +
222C ASP* 1.3 74.2 + - - +
224C MET* 1.3 69.5 + - + +
226C PHE* 3.2 20.4 + + - +
227C THR* 3.0 47.5 + - + +
264C VAL* 4.6 5.2 - - + -
266C THR* 3.9 13.5 - - + -
270C GLN* 3.7 46.4 - - + +
271C ARG 3.3 29.2 - - - -
272C HIS* 4.3 3.4 - - + -
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Residues in contact with MET 224 (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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163C LYS 3.7 9.4 - - - +
164C SER* 3.6 47.9 + - - +
166C GLY* 4.8 0.2 - - - -
222C ASP* 3.3 6.1 + - - +
223C PHE* 1.3 95.0 - - + +
225C SER* 1.3 59.3 + - - +
227C THR* 3.1 23.9 + - + +
228C SER* 3.6 12.3 + - - -
272C HIS* 6.1 1.1 - - - +
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Residues in contact with SER 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ASP* 3.2 34.8 + - - -
223C PHE 3.2 0.4 - - - -
224C MET* 1.3 76.1 - - - +
226C PHE* 1.3 64.4 + - - +
228C SER* 3.0 21.8 + - - -
229C HIS* 3.4 23.1 + - - -
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Residues in contact with PHE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ILE* 3.7 33.2 - - + -
222C ASP 3.3 9.8 + - - +
223C PHE* 3.2 27.2 + + - +
225C SER* 1.3 79.4 - - - +
227C THR* 1.3 63.2 + - + +
229C HIS* 3.1 15.5 + - + +
230C ILE* 3.1 43.4 + - + +
264C VAL* 4.3 7.0 - - + -
272C HIS* 6.6 0.2 - - + -
495C MET* 3.6 35.4 - - + -
520C LEU* 5.3 1.3 - - + -
524C CYS* 4.7 6.5 - - - -
526C PHE* 4.3 8.1 - + - -
539C LEU* 5.9 1.3 - - + -
541C PRO* 3.8 33.0 - - + -
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Residues in contact with THR 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 3.0 46.7 + - + +
224C MET* 3.1 27.7 + - + -
226C PHE* 1.3 77.5 - - + +
228C SER* 1.3 57.5 + - - +
230C ILE* 3.8 10.6 - - - +
231C ASP* 3.1 33.9 + - - -
272C HIS* 3.5 34.6 + - + +
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Residues in contact with SER 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C MET 3.6 9.0 + - - -
225C SER* 3.0 16.5 + - - -
227C THR* 1.3 78.2 + - - +
229C HIS* 1.3 62.7 + - - +
231C ASP* 3.3 9.1 + - - +
232C GLU* 3.0 38.2 + - - +
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Residues in contact with HIS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C SER* 3.4 29.6 + - - -
226C PHE* 3.1 14.8 + - + +
228C SER* 1.3 78.0 - - - +
230C ILE* 1.3 54.4 + - - +
232C GLU* 3.1 25.8 + - - +
233C LEU* 2.7 40.8 + - - +
523C LEU* 3.7 37.2 - - + +
539C LEU* 4.2 25.2 - - + +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C PHE* 3.1 46.1 + - + +
227C THR* 3.8 11.0 - - + +
229C HIS* 1.3 76.4 - - - +
231C ASP* 1.3 59.1 + - - +
233C LEU* 3.3 6.9 + - + +
234C TYR* 2.8 26.9 + - - +
262C VAL* 4.6 12.6 - - + +
264C VAL* 4.2 17.0 - - + -
272C HIS* 4.1 19.7 - - + -
274C THR* 4.6 5.4 - - - +
497C MET* 4.8 3.4 - - - -
516C PHE* 4.0 24.9 - - + -
520C LEU* 4.3 15.5 - - + -
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Residues in contact with ASP 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C THR* 3.1 26.1 + - - +
228C SER* 3.5 9.1 - - - +
229C HIS 3.1 0.2 - - - -
230C ILE* 1.3 74.7 - - - +
232C GLU* 1.3 64.6 + - + +
234C TYR* 3.1 7.0 + - - +
235C GLU* 3.0 31.6 + - + +
272C HIS* 3.1 11.2 + - - -
274C THR* 2.4 38.7 - - - +
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C SER* 3.0 25.3 + - - +
229C HIS* 3.1 27.4 + - - +
231C ASP* 1.3 75.3 - - + +
233C LEU* 1.3 64.8 + - + +
235C GLU* 3.4 7.5 + - - +
236C SER* 3.1 24.6 + - - -
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Residues in contact with LEU 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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229C HIS 2.7 22.6 + - - +
230C ILE* 3.5 4.0 - - + +
232C GLU* 1.3 79.6 - - + +
234C TYR* 1.3 62.5 + - - +
236C SER* 3.5 4.0 + - - -
237C ALA* 3.2 24.6 + - - +
515C HIS* 5.6 0.3 - - - -
516C PHE* 3.5 25.6 - - + +
519C ASP* 3.8 30.3 - - + +
520C LEU* 3.6 46.2 - - + +
523C LEU* 4.3 18.8 - - + -
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Residues in contact with TYR 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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230C ILE 2.8 17.4 + - - +
231C ASP* 3.1 5.8 + - - +
233C LEU* 1.3 76.7 - - - +
235C GLU* 1.3 78.6 + - - +
237C ALA 3.5 0.2 + - - -
238C LYS* 3.0 51.7 + - + +
260C TRP* 2.9 76.9 + + - +
261C GLY 4.2 0.4 - - - -
262C VAL* 3.8 17.0 - - + -
274C THR* 3.6 31.0 - - - +
275C GLY* 3.0 18.9 - - - -
276C ASP* 4.4 2.4 + - - -
516C PHE* 3.9 7.6 - - - -
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Residues in contact with GLU 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 ASP* 3.0 22.9 + - + +
232C GLU* 3.9 7.0 - - - +
234C TYR* 1.3 93.8 - - - +
236C SER* 1.3 64.4 + - - +
238C LYS* 3.4 35.7 + - - +
239C LYS* 3.5 27.9 - - - +
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Residues in contact with SER 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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232C GLU 3.1 18.3 + - - -
233C LEU* 3.8 5.8 - - - -
234C TYR 3.3 0.2 - - - -
235C GLU* 1.3 77.3 - - - +
237C ALA* 1.3 64.1 + - - +
238C LYS 3.4 0.2 + - - -
239C LYS* 3.4 18.3 + - - +
240C GLN* 3.4 13.9 - - - +
515C HIS* 3.8 9.1 + - - -
519C ASP* 3.6 20.7 + - - -
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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 LEU 3.2 15.1 + - - +
234C TYR 4.0 0.2 - - - +
236C SER* 1.3 75.1 - - - +
238C LYS* 1.3 65.5 + - - +
239C LYS 3.0 4.1 + - - -
240C GLN* 3.1 16.3 + - - +
260C TRP* 3.7 25.6 - - + -
512C LYS* 3.2 28.0 - - - +
515C HIS* 3.8 20.6 - - + -
516C PHE* 4.1 6.5 - - + -
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Residues in contact with LYS 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 TYR* 3.0 40.5 + - + +
235C GLU* 3.4 31.3 + - - +
236C SER 3.2 0.4 - - - -
237C ALA* 1.3 78.4 - - - +
239C LYS* 1.3 56.6 + - + +
240C GLN 3.2 4.7 + - - -
241C SER 4.9 0.3 + - - -
258C ASP 5.9 3.1 - - - -
260C TRP* 3.5 23.5 - - + +
512C LYS* 3.4 14.1 - - - -
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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