Contacts of the helix formed by residues 227 - 237 (chain C) in PDB entry 1AX4
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 PHE 227 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C LEU* 4.7 6.7 - - + -
89C PHE* 3.6 23.8 - + - -
191C VAL* 3.5 14.3 + - + -
224C SER* 3.3 20.8 + - - +
226C ARG* 1.3 77.3 - - - +
228C CYS* 1.3 84.7 + - - +
230C ASN* 3.5 3.4 + - - +
231C ALA* 3.0 26.2 + - - +
250C ILE* 3.8 26.5 - - + -
253C MET* 3.9 4.1 - - + +
254C TYR* 3.1 31.0 - + + +
262C MET* 3.5 17.3 - - + -
267C ASP* 4.4 5.2 - - + -
268C PRO* 4.3 10.5 - - + -
316C LEU* 4.0 22.9 - - + -
320C THR* 5.0 1.8 - - + -
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Residues in contact with CYS 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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227C PHE* 1.3 107.2 - - - +
229C GLU* 1.3 63.2 + - - +
230C ASN 3.1 0.2 - - - -
231C ALA* 3.2 7.1 + - - +
232C TYR* 2.9 23.6 + - - +
250C ILE* 4.2 3.8 - - - -
267C ASP* 2.7 25.9 + - - +
316C LEU 5.2 0.7 - - - -
319C GLY* 3.3 37.0 - - - +
320C THR* 4.0 11.7 - - - -
325C LEU* 3.8 13.0 - - + +
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Residues in contact with GLU 229 (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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192C THR* 3.9 12.2 + - + -
226C ARG* 3.5 16.1 - - - +
228C CYS* 1.3 71.0 - - - +
230C ASN* 1.3 63.2 + - - +
232C TYR* 3.1 3.5 + - - +
233C PHE* 3.1 27.1 + - - -
267C ASP* 2.8 33.7 + - - +
324C TYR* 5.0 0.7 + - - -
325C LEU* 4.2 11.9 - - + -
328C ARG* 2.7 32.7 + - - +
329C ILE* 4.1 17.9 - - + -
352C GLY* 3.3 30.1 - - - -
353C HIS* 3.5 9.7 + - - +
419C ARG* 3.4 4.6 + - - -
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Residues in contact with ASN 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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191C VAL* 3.7 23.8 - - + +
192C THR* 3.3 19.1 - - + +
200C PRO* 3.2 8.9 - - - +
201C VAL 2.9 45.1 + - - -
206C LEU* 4.7 1.0 - - - +
226C ARG 3.1 12.8 + - - +
227C PHE 3.6 9.0 - - - +
228C CYS 3.1 0.2 - - - -
229C GLU* 1.3 76.1 - - - +
231C ALA* 1.3 61.6 + - - +
233C PHE* 3.2 6.7 + - - +
234C ILE* 3.0 33.1 + - - +
253C MET* 3.9 10.0 - - + +
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Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE 3.0 17.1 + - - +
228C CYS 3.2 4.5 + - - +
230C ASN* 1.3 73.6 - - - +
232C TYR* 1.3 66.7 + - - +
234C ILE* 3.3 1.0 + - - +
235C LYS* 3.1 22.7 + - - +
246C ILE* 4.2 11.6 - - + +
249C VAL* 3.5 31.9 - - + +
250C ILE* 3.8 23.3 - - + -
253C MET* 4.0 6.7 - - - -
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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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228C CYS 2.9 13.7 + - - +
229C GLU 3.1 8.2 + - - +
231C ALA* 1.3 76.8 - - - +
233C PHE* 1.3 66.9 + + - +
235C LYS* 3.1 7.4 + - + +
236C ALA* 2.8 40.5 + - + +
246C ILE* 3.9 17.2 - - + +
322C GLU* 4.5 13.7 - - + -
325C LEU* 3.8 20.9 - - + -
326C HIS* 2.8 50.8 + - + -
329C ILE* 3.3 42.6 - - + +
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Residues in contact with PHE 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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163C TRP* 4.3 2.9 - - + -
192C THR* 4.3 4.0 - - + -
198C GLY 4.2 6.3 - - - -
200C PRO* 3.6 37.7 - - + -
229C GLU 3.1 22.0 + - - -
230C ASN 3.6 2.2 - - - +
232C TYR* 1.3 84.7 - + - +
234C ILE* 1.3 66.4 + - - +
236C ALA* 3.7 4.6 - - + +
237C ARG* 2.8 63.3 + - - +
329C ILE* 3.9 26.9 - - + -
350C THR 3.9 8.1 - - - -
351C GLY* 3.8 18.4 - - - -
352C GLY* 3.6 23.8 - - - -
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Residues in contact with ILE 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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163C TRP* 3.8 15.3 - - + -
201C VAL 3.7 16.4 - - - +
202C SER 4.3 0.2 - - - -
203C MET* 3.9 22.0 - - + +
206C LEU* 4.7 0.7 - - + -
230C ASN* 3.0 34.3 + - - +
231C ALA 3.7 7.0 - - - +
232C TYR 3.3 0.2 - - - -
233C PHE* 1.3 76.2 - - - +
235C LYS* 1.3 58.4 + - - +
238C ASP* 2.9 42.6 + - + +
241C TYR* 3.6 30.9 - - + +
249C VAL* 3.9 10.8 - - + -
253C MET* 4.0 24.2 - - + -
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Residues in contact with LYS 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 ALA 3.1 13.6 + - - +
232C TYR* 3.6 9.9 - - + +
234C ILE* 1.3 77.8 - - - +
236C ALA* 1.3 63.0 + - - +
238C ASP 4.2 2.1 - - - +
241C TYR* 3.7 19.1 - - - +
242C LYS* 3.7 35.5 + - - +
243C ASN* 4.4 2.6 - - - +
244C ALA 2.5 31.4 + - - +
245C THR* 4.4 2.8 - - - +
246C ILE* 4.2 13.9 - - + -
249C VAL* 4.3 8.3 - - + +
322C GLU* 3.2 40.9 + - - +
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Residues in contact with ALA 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* 2.8 38.1 + - + +
233C PHE* 3.7 8.3 - - + +
235C LYS* 1.3 80.2 - - - +
237C ARG* 1.3 66.4 + - + +
238C ASP 3.8 0.4 - - - -
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Residues in contact with ARG 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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160C TYR* 3.6 13.9 + - - +
161C ASP 4.2 0.2 + - - -
162C ASP* 2.8 66.5 + - - +
163C TRP* 3.7 19.1 - - + -
199C GLN* 4.8 0.6 + - - -
200C PRO* 3.4 20.2 - - - +
233C PHE* 2.8 51.4 + - - +
236C ALA* 1.3 81.5 - - + +
238C ASP* 1.3 60.3 + - - +
239C PRO* 3.4 11.4 - - - +
349C PRO* 3.7 30.0 - - - +
350C THR 4.4 2.8 + - - -
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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