Contacts of the helix formed by residues 246 - 256 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A CYS* 5.0 0.9 - - - +
231A ALA* 4.2 11.4 - - + +
232A TYR* 3.9 35.4 - - + +
235A LYS* 4.2 17.2 - - + +
244A ALA 4.1 0.2 + - - -
245A THR* 1.3 73.6 - - - +
247A LYS* 1.3 56.9 + - + +
249A VAL* 3.2 7.8 + - - +
250A ILE* 2.9 43.8 + - + +
320A THR* 3.3 29.6 - - - +
322A GLU* 3.8 26.6 + - + +
325A LEU* 4.0 16.6 - - + -
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.0 23.6 + - - +
88A LEU* 4.2 19.6 - - + +
245A THR* 3.2 8.3 + - - +
246A ILE* 1.3 76.9 - - + +
248A GLU* 1.3 58.1 + - - +
250A ILE* 3.7 7.7 - - + +
251A PHE* 2.9 29.1 + - - +
317A GLU* 2.7 38.0 + - - -
320A THR* 3.6 28.3 - - + +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A TYR* 5.1 2.9 - - + -
243A ASN 4.3 1.9 - - - +
244A ALA* 3.3 18.2 - - + +
245A THR* 2.6 52.2 + - - +
247A LYS* 1.3 73.7 - - + +
249A VAL* 1.3 65.7 + - - +
251A PHE* 3.3 8.1 + - - +
252A ASP* 3.1 26.9 + - - +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 3.4 13.7 - - + +
231A ALA* 3.6 38.1 - - + +
234A ILE* 3.8 19.7 - - + -
235A LYS* 4.3 10.8 - - + -
241A TYR* 3.8 32.3 - - + -
244A ALA* 4.3 3.6 - - + -
245A THR 3.2 13.7 + - - +
246A ILE* 3.2 8.5 + - - +
248A GLU* 1.3 74.5 - - - +
250A ILE* 1.3 67.2 + - - +
252A ASP 3.2 1.9 + - - -
253A MET* 3.0 21.0 + - - +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LEU* 3.7 21.5 - - + +
89A PHE* 4.2 4.0 - - + -
227A PHE* 3.9 32.5 - - + +
228A CYS* 4.3 4.5 - - - -
231A ALA* 3.8 15.7 - - + -
246A ILE* 2.9 33.7 + - + +
247A LYS* 3.7 8.3 - - + +
249A VAL* 1.3 75.5 - - - +
251A PHE* 1.3 64.4 + - - +
253A MET* 3.2 17.7 + - - -
254A TYR* 3.2 33.0 + - + -
320A THR* 3.8 29.6 - - + -
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS 5.0 1.3 - - - -
87A GLU 4.2 13.9 - - - -
88A LEU 3.9 18.8 + - - +
89A PHE* 4.7 3.0 - - - +
90A ASN* 3.6 44.4 - - + -
247A LYS 2.9 18.2 + - - +
248A GLU* 3.6 8.1 - - - +
249A VAL 3.3 0.2 - - - -
250A ILE* 1.3 78.8 - - - +
252A ASP* 1.3 63.3 + - - +
254A TYR* 3.5 8.8 + - - +
255A LYS* 3.6 31.9 + - + +
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Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A MET* 3.5 20.6 - - + -
240A LYS* 4.3 4.0 + - - -
241A TYR* 2.4 30.7 + - + +
248A GLU 3.1 15.4 + - - +
249A VAL 3.6 2.2 - - - +
251A PHE* 1.3 76.9 - - - +
253A MET* 1.3 66.8 + - - +
255A LYS* 2.8 53.8 + - + +
256A TYR* 3.3 12.5 - - + -
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.9 31.4 - - + -
203A MET* 3.7 20.4 - - + +
206A LEU* 4.0 15.8 - - + +
222A MET* 3.2 17.9 - - + +
227A PHE* 3.9 22.4 - - + +
230A ASN* 3.9 13.5 - - + +
231A ALA* 4.1 22.0 - - - -
234A ILE* 4.0 8.3 - - + -
249A VAL 3.0 17.2 + - - +
250A ILE* 3.5 12.8 - - - +
252A ASP* 1.3 76.4 - - - +
254A TYR* 1.3 72.5 + - + +
255A LYS 3.2 0.2 - - - -
256A TYR* 3.1 21.6 + - - +
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Residues in contact with TYR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.6 52.2 - + + +
91A TYR* 2.9 47.6 + + + +
191A VAL* 4.4 0.5 - - - +
222A MET* 3.7 25.9 - - + +
224A SER* 2.6 30.6 + - - -
227A PHE* 3.1 34.6 - + + +
250A ILE* 3.2 19.6 + - + +
251A PHE 3.5 3.8 + - - +
252A ASP 3.2 0.8 - - - -
253A MET* 1.3 85.5 - - + +
255A LYS* 1.3 62.5 + - - +
256A TYR 3.1 1.9 + - - -
257A ALA 3.7 2.9 + - - +
260A LEU* 3.7 15.0 - - + -
279A ARG* 3.9 2.3 + - - -
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 3.6 11.1 - - - -
251A PHE* 3.6 28.7 + - + +
252A ASP* 2.8 46.8 + - - +
254A TYR* 1.3 76.9 - - - +
256A TYR* 1.3 77.7 + - + +
257A ALA 3.4 1.7 + - - -
279A ARG* 2.9 33.4 + - - +
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Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A SER* 5.0 2.8 + - - -
203A MET* 3.8 25.6 - - + +
206A LEU* 3.6 25.4 - - + +
207A LYS* 3.4 58.1 - - + +
210A TYR* 3.4 30.4 - + + +
211A GLU* 5.8 1.3 - - + -
220A VAL* 3.8 7.8 - - - +
222A MET* 4.4 4.2 - - - +
240A LYS* 5.8 2.1 + - - -
241A TYR* 5.8 0.2 + - - -
252A ASP* 3.3 27.6 - - + +
253A MET 3.1 12.9 + - - +
254A TYR 3.1 1.2 - - - -
255A LYS* 1.3 99.2 - - + +
257A ALA* 1.3 60.6 + - - +
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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