Contacts of the helix formed by residues 246 - 256 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D CYS* 5.0 0.9 - - - +
231D ALA* 4.1 13.2 - - + +
232D TYR* 4.0 27.8 - - + -
235D LYS* 4.2 18.8 - - + -
245D THR* 1.3 73.4 - - - +
247D LYS* 1.3 57.5 + - - +
249D VAL* 3.2 8.0 + - - +
250D ILE* 3.0 43.6 + - + +
320D THR* 3.3 29.2 - - - +
322D GLU* 4.0 28.4 + - + +
325D LEU* 4.0 18.2 - - + -
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Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D LYS* 4.3 0.2 - - - +
87D GLU* 3.0 23.4 + - - +
88D LEU* 4.2 23.7 - - + +
245D THR* 3.3 7.5 + - - +
246D ILE* 1.3 76.5 - - - +
248D GLU* 1.3 56.2 + - + +
250D ILE* 3.3 7.2 + - - +
251D PHE* 2.9 29.3 + - - +
317D GLU* 2.7 41.6 + - - -
320D THR* 3.7 24.5 - - + +
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Residues in contact with GLU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D TYR* 5.3 2.9 - - + -
243D ASN 4.5 1.0 - - - +
244D ALA* 3.2 18.1 - - + -
245D THR* 2.6 49.2 + - - +
247D LYS* 1.3 70.4 - - + +
249D VAL* 1.3 65.4 + - - +
251D PHE* 3.3 8.2 + - - +
252D ASP* 3.1 27.3 + - - +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D MET* 3.6 13.0 - - + +
231D ALA* 3.6 31.6 - - + +
234D ILE* 3.9 20.0 - - + -
235D LYS* 4.2 17.5 - - + -
241D TYR* 3.9 32.1 - - + -
244D ALA* 4.3 3.4 - - + -
245D THR 3.2 13.2 + - - +
246D ILE* 3.2 9.5 + - - +
248D GLU* 1.3 78.4 - - - +
250D ILE* 1.3 62.5 + - - +
252D ASP 3.2 1.7 + - - -
253D MET* 3.0 23.0 + - - +
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Residues in contact with ILE 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LEU* 3.6 21.3 - - + +
89D PHE* 4.2 3.1 - - + -
227D PHE* 3.9 32.5 - - + +
228D CYS* 4.2 4.9 - - - -
231D ALA* 3.7 15.7 - - + -
246D ILE* 3.0 29.1 + - + +
247D LYS* 3.6 10.3 - - + +
249D VAL* 1.3 74.7 - - - +
251D PHE* 1.3 63.3 + - - +
253D MET* 3.1 14.0 + - - -
254D TYR* 3.1 37.1 - - + -
320D THR* 3.6 31.4 - - + -
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Residues in contact with PHE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D LYS 4.9 0.9 - - - -
87D GLU 4.0 14.6 - - - -
88D LEU 3.8 18.8 + - - +
89D PHE* 4.7 1.9 - - - +
90D ASN* 3.6 44.1 - - + +
247D LYS 2.9 17.6 + - - +
248D GLU* 3.5 9.0 - - - +
249D VAL 3.3 0.2 - - - -
250D ILE* 1.3 77.8 - - - +
252D ASP* 1.3 63.9 + - - +
254D TYR* 3.5 10.7 + - - +
255D LYS* 3.6 31.4 + - + +
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Residues in contact with ASP 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D MET* 3.6 13.5 - - + -
240D LYS* 4.4 3.8 + - - -
241D TYR* 2.5 37.1 + - + +
248D GLU* 3.1 15.4 + - - +
249D VAL 3.2 2.4 + - - +
251D PHE* 1.3 76.1 - - - +
253D MET* 1.3 66.3 + - - +
255D LYS* 2.9 44.3 + - + +
256D TYR* 3.3 19.7 - - + -
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Residues in contact with MET 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D VAL* 3.9 32.3 - - + -
203D MET* 3.8 20.8 - - + -
206D LEU* 4.0 16.4 - - + +
222D MET* 3.1 17.9 - - + +
227D PHE* 3.9 14.1 - - + +
230D ASN* 4.0 13.0 - - + +
231D ALA* 4.1 26.0 - - - -
234D ILE* 4.0 11.9 - - + -
249D VAL 3.0 15.1 + - - +
250D ILE* 3.5 10.8 - - - +
252D ASP* 1.3 77.4 - - - +
254D TYR* 1.3 72.5 + - + +
256D TYR* 3.1 21.5 + - - +
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Residues in contact with TYR 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D PHE* 3.5 53.2 - + + +
91D TYR* 2.9 47.2 + + + +
191D VAL* 4.4 0.2 - - - +
222D MET* 3.7 26.6 - - + +
224D SER* 2.6 37.8 + - - -
227D PHE* 3.3 17.1 - + - +
250D ILE* 3.1 32.4 + - + +
251D PHE 3.5 3.1 + - - +
252D ASP 3.2 0.8 - - - -
253D MET* 1.3 87.0 - - + +
255D LYS* 1.3 63.4 + - - +
256D TYR 3.0 1.9 + - - -
257D ALA 3.6 3.6 + - - +
260D LEU* 3.7 14.1 - - + -
279D ARG* 3.9 1.4 + - - -
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Residues in contact with LYS 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D TYR* 3.6 9.2 - - - -
251D PHE* 3.6 29.0 + - + +
252D ASP* 2.9 43.1 + - - +
254D TYR* 1.3 76.5 - - - +
256D TYR* 1.3 79.9 + - + +
257D ALA 3.4 1.7 + - - -
279D ARG* 3.0 34.4 + - - +
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Residues in contact with TYR 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D SER* 5.0 2.8 + - - -
203D MET* 3.9 23.1 - - + +
206D LEU* 3.6 25.8 - - + +
207D LYS* 3.5 59.2 - - + +
210D TYR* 3.3 32.6 - + + +
211D GLU* 6.1 1.1 - - + -
220D VAL* 3.7 7.8 - - - +
222D MET* 4.4 4.0 - - + +
240D LYS* 6.0 0.5 + - - -
252D ASP* 3.3 30.1 - - + +
253D MET 3.1 11.8 + - - +
254D TYR 3.0 1.4 - - - -
255D LYS* 1.3 96.3 - - + +
257D ALA* 1.3 61.3 + - - +
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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