Contacts of the helix formed by residues 246 - 256 (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 ILE 246 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C CYS* 5.0 0.9 - - - +
231C ALA* 4.2 12.8 - - + +
232C TYR* 3.9 28.7 - - + -
235C LYS* 4.2 19.2 - - + +
244C ALA 4.1 0.2 + - - -
245C THR* 1.3 72.4 - - - +
247C LYS* 1.3 58.4 + - - +
249C VAL* 3.2 6.7 + - - +
250C ILE* 2.9 44.1 + - + +
320C THR* 3.3 28.5 - - - +
322C GLU* 3.9 31.3 + - + +
325C LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 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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87C GLU* 3.0 22.8 + - - +
88C LEU* 4.2 22.7 - - + +
245C THR* 3.2 8.3 + - - +
246C ILE* 1.3 75.6 - - - +
248C GLU* 1.3 60.2 + - - +
250C ILE* 3.7 7.0 - - - +
251C PHE* 2.8 29.8 + - - +
317C GLU* 2.7 41.0 + - - -
320C THR* 3.6 24.5 - - + +
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Residues in contact with GLU 248 (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 TYR* 5.2 2.5 - - + -
243C ASN 4.4 1.4 - - - +
244C ALA* 3.2 17.3 - - + -
245C THR* 2.6 50.1 + - - +
247C LYS* 1.3 71.4 - - + +
249C VAL* 1.3 67.9 + - - +
251C PHE* 3.2 7.4 + - - +
252C ASP* 3.0 26.8 + - - +
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Residues in contact with VAL 249 (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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203C MET* 3.5 14.1 - - + +
231C ALA* 3.5 39.5 - - + +
234C ILE* 3.9 20.6 - - + -
235C LYS* 4.3 10.5 - - + -
241C TYR* 3.8 33.4 - - + -
244C ALA* 4.2 4.3 - - + -
245C THR 3.2 13.3 + - - +
246C ILE* 3.5 7.4 - - - +
248C GLU* 1.3 77.6 - - - +
250C ILE* 1.3 61.5 + - - +
252C ASP 3.2 1.6 + - - -
253C MET* 3.0 21.0 + - - +
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Residues in contact with ILE 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.7 22.4 - - + +
89C PHE* 4.1 3.8 - - + -
227C PHE* 3.8 36.6 - - + +
228C CYS* 4.2 4.9 - - - -
231C ALA* 3.8 15.5 - - + -
246C ILE* 2.9 37.3 + - + +
247C LYS* 3.7 7.9 - - + +
249C VAL* 1.3 76.0 - - - +
251C PHE* 1.3 65.2 + - - +
253C MET* 3.1 17.2 + - - -
254C TYR* 3.1 34.6 - - + -
320C THR* 3.8 19.7 - - + -
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Residues in contact with PHE 251 (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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86C LYS 5.0 0.7 - - - -
87C GLU 4.1 13.9 - - - -
88C LEU 3.8 17.9 + - - +
89C PHE 4.7 2.6 - - - +
90C ASN* 3.6 43.5 - - + -
247C LYS 2.8 18.4 + - - +
248C GLU* 3.2 8.9 + - - +
250C ILE* 1.3 78.3 - - - +
252C ASP* 1.3 63.0 + - - +
254C TYR* 3.5 9.8 + - - +
255C LYS* 3.6 37.1 + - + +
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Residues in contact with ASP 252 (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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203C MET* 3.4 21.3 - - + -
240C LYS* 4.4 3.3 + - - -
241C TYR* 2.5 30.5 + - + +
248C GLU 3.0 14.7 + - - +
249C VAL 3.2 2.2 + - - +
251C PHE* 1.3 74.3 - - - +
253C MET* 1.3 69.6 + - - +
255C LYS* 2.9 51.3 + - + +
256C TYR* 3.3 14.1 - - + -
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Residues in contact with MET 253 (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* 3.8 32.3 - - + -
203C MET* 3.7 21.1 - - + +
206C LEU* 3.9 16.8 - - + +
222C MET* 3.1 20.5 - - + +
227C PHE* 3.9 12.8 - - + +
230C ASN* 3.9 13.7 - - + +
231C ALA* 4.0 26.9 - - - -
234C ILE* 4.0 11.2 - - + -
249C VAL* 3.0 16.0 + - - +
250C ILE* 3.1 12.1 + - - +
252C ASP* 1.3 77.9 - - - +
254C TYR* 1.3 73.5 + - + +
255C LYS 3.1 0.2 - - - -
256C TYR* 3.1 19.2 + - - +
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Residues in contact with TYR 254 (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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89C PHE* 3.6 50.9 - + + +
91C TYR* 2.9 46.7 + + + +
191C VAL* 4.3 0.5 - - - +
222C MET* 3.6 28.1 - - + +
224C SER* 2.6 38.2 + - - -
227C PHE* 3.1 18.4 - + - +
250C ILE* 3.1 32.6 + - + +
251C PHE 3.5 3.6 + - - +
252C ASP 3.1 1.2 - - - -
253C MET* 1.3 87.6 - - + +
255C LYS* 1.3 63.8 + - - +
256C TYR 3.1 1.8 + - - -
257C ALA 3.6 3.7 + - - +
260C LEU* 3.8 13.9 - - + -
279C ARG* 3.9 1.9 + - - -
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Residues in contact with LYS 255 (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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210C TYR* 3.7 7.3 - - - -
251C PHE* 3.6 31.8 + - + +
252C ASP* 2.9 41.8 + - - +
254C TYR* 1.3 78.9 - - - +
256C TYR* 1.3 77.3 + - + +
257C ALA 3.5 0.7 - - - -
279C ARG* 2.9 33.7 + - - +
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Residues in contact with TYR 256 (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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189C SER* 5.0 2.3 + - - -
203C MET* 3.9 23.7 - - + +
206C LEU* 3.6 25.6 - - + +
207C LYS* 3.4 59.2 - - + +
210C TYR* 3.4 32.2 - + + +
211C GLU* 6.2 1.1 - - + -
220C VAL* 3.8 7.6 - - - +
222C MET* 4.4 3.9 - - - +
240C LYS* 5.7 2.8 + - - -
241C TYR* 5.7 0.5 + - - -
252C ASP* 3.3 30.1 - - + +
253C MET 3.1 12.2 + - - +
254C TYR 3.1 1.4 - - - -
255C LYS* 1.3 96.2 - - + +
257C ALA* 1.3 60.7 + - - +
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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