Contacts of the helix formed by residues 226 - 237 (chain C) in PDB entry 4IRQ
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 ARG 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B SER 4.0 5.9 + - - -
90B TRP* 5.1 0.2 - - - +
91B GLY* 3.9 17.8 - - - +
221C PHE* 3.5 19.4 - - + -
224C TRP* 6.4 0.2 - - + -
225C GLY* 1.3 69.8 - - - +
227C GLU* 1.3 61.2 + - - +
228C ASP* 3.2 10.3 + - - -
229C ASP* 3.0 35.7 + - - +
230C GLU* 3.1 23.9 + - - +
233C ARG* 2.9 43.4 - - - +
278C GLN* 3.1 41.3 + - + +
279C PHE* 3.3 38.7 - - - +
403C TRS 4.1 1.4 + - - -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ARG* 3.0 25.5 + - + +
142C ALA* 3.8 33.4 - - + +
217C MET* 3.8 10.4 - - + +
218C SER* 5.7 1.0 + - - -
221C PHE* 3.7 33.3 - - + -
225C GLY 2.8 13.0 + - - +
226C ARG* 1.3 73.3 - - - +
228C ASP* 1.3 65.1 + - - +
230C GLU* 3.8 3.3 + - - +
231C PHE* 3.3 24.3 + - - +
403C TRS 2.5 51.4 + - - -
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Residues in contact with ASP 228 (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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141C ARG* 4.5 3.8 - - - +
196C TYR* 4.5 2.3 + - - -
199C TYR* 3.7 7.9 - - - -
200C VAL* 3.2 27.9 - - + +
201C GLY* 3.6 21.6 - - - +
217C MET* 4.7 3.4 - - + -
226C ARG 3.8 7.1 + - - -
227C GLU* 1.3 82.4 + - - +
229C ASP* 1.3 79.6 + - - +
230C GLU 3.2 0.9 - - - -
231C PHE* 3.2 4.4 + - - +
232C TYR* 2.9 25.3 + - - +
403C TRS 2.6 35.9 + - - -
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Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER 5.5 0.4 - - - +
196C TYR* 2.7 41.0 + - - -
198C THR* 4.1 12.4 - - + +
199C TYR* 4.9 0.9 - - - -
226C ARG* 3.0 56.8 + - - +
227C GLU 3.5 0.4 - - - -
228C ASP* 1.3 89.7 + - - +
230C GLU* 1.3 61.1 + - - +
232C TYR* 3.4 10.2 + - - +
233C ARG* 3.4 30.1 + - - +
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C SER* 3.5 20.8 + - - -
221C PHE* 3.6 20.9 - - + -
226C ARG 3.1 17.5 + - - +
227C GLU 3.8 3.6 - - - +
229C ASP* 1.3 74.1 - - - +
231C PHE* 1.3 66.0 + - - +
233C ARG* 3.2 25.0 + - - +
234C ARG* 3.2 38.3 + - - +
280C LYS 3.6 20.9 - - - +
281C VAL* 3.3 9.1 - - - +
282C ASP* 2.6 28.0 + - - +
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Residues in contact with PHE 231 (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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161C MET* 3.8 8.5 - - + -
200C VAL* 4.6 2.0 - - + -
204C LEU* 3.6 33.2 - - + -
206C LEU* 3.8 24.2 - - + -
211C TYR* 4.1 13.5 - + - -
214C CYS* 4.2 14.4 - - + -
216C GLY 3.3 32.3 - - - -
217C MET* 3.7 29.4 - - + -
227C GLU 3.3 14.6 + - - +
228C ASP* 3.2 5.7 + - - +
230C GLU* 1.3 80.8 + - - +
232C TYR* 1.3 66.2 + - - +
234C ARG* 3.2 8.6 + - - +
235C ILE* 3.0 37.1 + - + +
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Residues in contact with TYR 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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88B ALA* 4.2 23.0 + - + -
197C LYS 5.1 3.0 + - - -
198C THR* 3.8 52.0 + - + +
200C VAL* 4.1 14.7 - - + +
228C ASP 2.9 12.8 + - - +
229C ASP* 3.4 10.5 - - - +
231C PHE* 1.3 77.0 - - - +
233C ARG* 1.3 69.2 + - + +
235C ILE* 3.0 23.7 + - + +
236C LYS* 3.1 52.9 + - + +
242C LEU* 4.8 17.9 - - + -
244C ARG* 5.4 0.4 - - - -
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Residues in contact with ARG 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA* 4.5 19.7 - - + -
89B SER 3.3 19.0 + - - +
90B TRP* 4.8 8.2 - - - +
198C THR* 6.1 0.8 - - - +
226C ARG* 2.9 35.3 - - - +
229C ASP* 3.4 15.3 + - - +
230C GLU* 3.2 24.6 + - - +
232C TYR* 1.3 86.0 - - + +
234C ARG* 1.3 58.9 + - - +
236C LYS* 4.1 3.4 - - - +
237C GLY* 2.8 28.8 + - - -
278C GLN 4.1 3.8 + - - -
279C PHE* 3.6 25.5 + - - +
280C LYS 4.0 5.7 - - - +
281C VAL* 3.4 33.6 - - + +
283C ARG* 4.8 2.1 + - - -
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Residues in contact with ARG 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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214C CYS* 3.3 25.0 + - + +
215C ASN* 3.1 19.4 + - - +
216C GLY 3.0 29.2 + - - -
217C MET* 3.7 2.0 - - - +
218C SER* 3.5 28.5 - - - +
230C GLU* 3.2 32.7 + - - +
231C PHE* 3.3 13.2 - - + +
233C ARG* 1.3 75.1 - - - +
235C ILE* 1.3 64.1 + - - +
237C GLY 3.4 1.6 + - - +
238C ALA* 3.1 26.5 + - - +
281C VAL* 4.2 7.8 - - + +
282C ASP* 2.8 23.4 + - - +
283C ARG* 4.7 10.1 - - - +
285C GLY 2.6 28.0 + - - -
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Residues in contact with ILE 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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182C PRO* 4.1 28.0 - - + -
200C VAL* 4.6 3.4 - - + -
204C LEU* 4.5 8.1 - - + -
214C CYS* 4.1 16.4 - - - -
231C PHE* 3.0 47.4 + - + +
232C TYR* 3.0 14.8 + - + +
234C ARG* 1.3 75.4 - - - +
236C LYS* 1.3 67.1 + - + +
238C ALA* 3.1 10.9 + - - +
240C LEU* 3.2 44.5 + - + +
242C LEU* 4.6 23.6 - - + -
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Residues in contact with LYS 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 TYR* 3.1 48.8 + - + +
233C ARG* 4.3 3.1 - - - +
235C ILE* 1.3 80.0 - - + +
237C GLY* 1.3 56.9 + - - +
238C ALA 3.0 0.2 - - - -
239C GLY* 3.0 19.1 + - - -
240C LEU 3.5 11.9 + - - +
241C GLN* 3.7 11.5 - - - +
242C LEU* 3.1 44.4 + - - +
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Residues in contact with GLY 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 ARG 2.8 19.7 + - - -
234C ARG 3.5 3.4 - - - -
236C LYS* 1.3 75.0 - - - +
238C ALA* 1.3 58.0 + - - +
239C GLY 3.4 0.7 - - - -
283C ARG* 3.9 24.5 + - - -
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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