Contacts of the helix formed by residues 246 - 256 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B CYS* 5.0 0.9 - - - +
231B ALA* 4.2 12.3 - - + +
232B TYR* 3.9 31.0 - - + +
235B LYS* 4.1 17.9 - - + -
244B ALA 4.0 0.2 + - - -
245B THR* 1.3 72.4 - - - +
247B LYS* 1.3 57.4 + - - +
249B VAL* 3.2 6.8 + - - +
250B ILE* 2.9 42.9 + - + +
320B THR* 3.4 29.8 - - - +
322B GLU* 3.9 29.4 + - + +
325B LEU* 4.0 18.2 - - + -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 3.0 23.6 + - - +
88B LEU* 4.1 24.5 - - + +
245B THR* 3.2 7.4 + - - +
246B ILE* 1.3 74.2 - - - +
248B GLU* 1.3 61.3 + - + +
250B ILE* 3.7 6.5 - - - +
251B PHE* 2.8 29.9 + - - +
317B GLU* 2.7 40.6 + - - -
320B THR* 3.6 23.6 - - + +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B TYR* 5.2 2.0 - - + -
243B ASN 4.4 1.4 - - - +
244B ALA* 3.2 16.5 - - + +
245B THR* 2.6 48.3 + - - +
247B LYS* 1.3 74.2 - - + +
249B VAL* 1.3 68.1 + - - +
251B PHE* 3.3 7.6 + - - +
252B ASP* 3.1 26.8 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B MET* 3.5 10.1 - - + +
231B ALA* 3.5 33.2 - - + +
234B ILE* 3.9 19.7 - - + -
235B LYS* 4.2 18.6 - - + -
241B TYR* 3.8 35.2 - - + -
244B ALA* 4.2 3.4 - - + -
245B THR 3.1 12.4 + - - +
246B ILE* 3.4 8.1 - - - +
248B GLU* 1.3 79.9 - - - +
250B ILE* 1.3 61.9 + - - +
252B ASP 3.2 2.1 + - - -
253B MET* 3.0 21.6 + - - +
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Residues in contact with ILE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.7 21.3 - - + +
89B PHE* 4.1 3.6 - - + -
227B PHE* 3.9 37.0 - - + +
228B CYS* 4.3 4.5 - - - -
231B ALA* 3.8 15.5 - - + -
246B ILE* 2.9 31.0 + - + +
247B LYS* 3.7 9.4 - - + +
249B VAL* 1.3 74.5 - - - +
251B PHE* 1.3 65.6 + - - +
253B MET* 3.1 16.9 + - - -
254B TYR* 3.3 24.4 + - + -
320B THR* 3.7 30.5 - - + -
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LYS 4.9 1.1 - - - -
87B GLU 4.0 15.0 - - - -
88B LEU 3.8 18.8 - - - +
89B PHE* 4.7 2.4 - - - +
90B ASN* 3.6 44.4 - - + -
247B LYS 2.8 18.4 + - - +
248B GLU* 3.6 8.5 - - - +
250B ILE* 1.3 78.4 - - - +
252B ASP* 1.3 63.4 + - - +
254B TYR* 3.6 9.1 + - - +
255B LYS* 3.7 32.6 + - + +
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B MET* 3.5 20.9 - - + -
240B LYS* 4.3 4.0 + - - -
241B TYR* 2.5 29.7 + - + +
248B GLU 3.1 14.1 + - - +
249B VAL 3.7 2.0 - - - +
251B PHE* 1.3 77.1 - - - +
253B MET* 1.3 68.4 + - - +
255B LYS* 2.9 50.2 + - + +
256B TYR* 3.4 13.2 - - + -
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B VAL* 3.8 33.2 - - + -
203B MET* 3.7 22.9 - - + +
206B LEU* 4.0 7.6 - - + +
222B MET* 3.1 20.5 - - + +
227B PHE 4.0 11.7 - - - +
230B ASN* 3.9 12.8 - - - +
231B ALA* 4.0 32.1 - - - -
234B ILE* 4.0 10.8 - - + -
249B VAL* 3.0 17.8 + - - +
250B ILE* 3.1 10.7 + - - +
252B ASP* 1.3 77.6 - - - +
254B TYR* 1.3 72.1 + - + +
256B TYR* 3.1 22.3 + - - +
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Residues in contact with TYR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.6 52.9 - + + +
91B TYR* 2.8 48.6 + + + +
222B MET* 3.5 28.1 - - + +
224B SER* 2.5 39.0 + - - -
227B PHE* 3.1 26.3 - + + +
250B ILE* 3.3 20.9 + - + +
251B PHE 3.6 3.1 + - - +
252B ASP 3.2 0.8 - - - -
253B MET* 1.3 86.2 - - + +
255B LYS* 1.3 62.5 + - - +
256B TYR 3.1 1.7 + - - -
257B ALA 3.6 3.1 - - - +
260B LEU* 3.8 14.1 - - + -
279B ARG* 3.9 2.4 + - - -
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Residues in contact with LYS 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B TYR* 3.7 7.6 - - - -
251B PHE* 3.7 31.0 + - + +
252B ASP* 2.9 44.9 + - - +
254B TYR* 1.3 78.9 - - - +
256B TYR* 1.3 76.0 + - + +
257B ALA 3.5 1.3 - - - -
279B ARG* 2.8 33.0 + - - +
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Residues in contact with TYR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B SER* 5.0 2.8 + - - -
203B MET* 3.9 24.0 - - + +
206B LEU* 3.7 23.9 - - + +
207B LYS* 3.3 61.2 - - + +
210B TYR* 3.4 34.0 - + + +
211B GLU* 6.1 1.1 - - + -
220B VAL* 3.7 8.5 - - - +
222B MET* 4.5 4.3 - - + +
240B LYS* 5.8 1.4 + - - -
252B ASP* 3.4 29.3 - - + +
253B MET 3.1 13.6 + - - +
255B LYS* 1.3 94.4 - - + +
257B ALA* 1.4 60.9 - - - +
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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