Contacts of the helix formed by residues 294 - 303 (chain B) in PDB entry 1AOX
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 LYS 294 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B ASP* 3.0 35.5 + - - +
293B THR* 1.3 79.1 + - - +
295B ASN* 1.3 60.8 + - - +
297B ILE* 3.7 8.0 + - + +
298B LYS* 3.0 27.4 + - - +
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Residues in contact with ASN 295 (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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256B GLU* 3.6 32.3 + - + +
292B ASP* 3.7 22.3 + - - +
293B THR 3.3 0.8 - - - -
294B LYS* 1.3 77.8 - - - +
296B LEU* 1.3 61.0 + - - +
298B LYS* 3.5 10.4 + - - +
299B GLU* 3.0 28.8 + - - +
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Residues in contact with LEU 296 (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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253B THR* 4.5 3.4 - - - +
254B ASP* 4.2 8.7 - - - -
255B GLY 3.7 33.0 - - - +
256B GLU* 4.1 11.5 + - + +
281B ALA* 4.0 10.1 - - + -
282B VAL 4.0 13.9 - - - +
283B LEU* 3.5 28.0 - - + -
286B LEU* 4.0 20.4 - - + -
292B ASP 5.4 0.4 + - - -
293B THR 3.3 9.3 + - - +
295B ASN* 1.3 73.4 - - - +
297B ILE* 1.3 66.4 + - - +
299B GLU* 3.0 7.1 + - - +
300B ILE* 2.9 44.4 + - + +
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Residues in contact with ILE 297 (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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281B ALA* 4.7 5.8 - - + -
283B LEU* 4.1 26.5 - - + -
293B THR* 3.2 31.7 + - - +
294B LYS* 3.9 7.0 - - - +
296B LEU* 1.3 80.1 - - - +
298B LYS* 1.3 62.4 + - - +
300B ILE* 3.4 0.9 + - - +
301B LYS* 3.0 54.4 + - - +
312B PHE* 3.9 19.7 - - + -
314B ASN* 4.4 9.6 - - - +
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Residues in contact with LYS 298 (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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294B LYS 3.0 18.9 + - - +
295B ASN* 3.7 11.7 - - - +
296B LEU 3.1 0.2 - - - -
297B ILE* 1.3 79.8 - - - +
299B GLU* 1.3 61.7 + - - +
301B LYS* 3.6 8.5 + - - +
302B ALA* 3.2 21.8 + - + +
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Residues in contact with GLU 299 (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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223B THR* 5.0 1.9 + - - -
224B PHE* 3.7 20.7 - - + -
255B GLY 4.2 2.6 - - - +
256B GLU* 3.5 11.1 - - - +
257B SER* 2.6 52.7 + - - +
260B GLY* 4.2 5.2 - - - -
263B LEU* 4.4 7.9 - - + +
295B ASN 3.0 16.3 + - - +
296B LEU* 3.0 6.3 + - - +
298B LYS* 1.3 76.1 - - - +
300B ILE* 1.3 74.3 + - + +
302B ALA* 3.2 16.5 + - - +
303B ILE* 3.2 14.4 + - - +
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Residues in contact with ILE 300 (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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223B THR* 5.3 2.2 - - + +
251B VAL* 5.2 3.4 - - + +
253B THR* 3.9 22.4 - - + +
279B GLY* 3.5 35.7 - - - -
280B ILE 3.7 4.0 - - - +
281B ALA* 4.0 12.8 - - + +
296B LEU* 2.9 34.3 + - + +
299B GLU* 1.3 80.9 - - + +
301B LYS* 1.3 64.9 + - - +
303B ILE* 3.0 26.4 + - + +
304B ALA* 3.0 21.5 + - - +
312B PHE* 3.7 17.5 - - + -
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Residues in contact with LYS 301 (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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297B ILE* 3.0 44.4 + - + +
298B LYS* 3.9 7.6 - - - +
300B ILE* 1.3 75.9 - - - +
302B ALA* 1.3 61.6 + - - +
303B ILE 3.3 0.5 + - - -
304B ALA* 3.4 18.5 + - - +
308B THR* 3.8 26.7 + - + +
312B PHE* 3.6 35.2 - - + -
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Residues in contact with ALA 302 (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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263B LEU* 3.9 25.9 - - + +
267B ILE* 3.9 16.6 - - - +
277B ARG* 5.4 0.7 + - - -
298B LYS* 3.2 12.0 + - + +
299B GLU* 3.2 11.4 + - - +
300B ILE 3.1 0.6 - - - -
301B LYS* 1.3 79.3 - - - +
303B ILE* 1.3 60.3 - - - +
304B ALA 4.2 3.1 - - - +
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Residues in contact with ILE 303 (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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223B THR* 4.0 16.8 - - + -
224B PHE* 3.6 37.2 - - + -
227B ILE* 4.0 7.9 - - + -
251B VAL* 4.2 27.4 - - + -
263B LEU* 4.9 0.7 - - + -
267B ILE* 4.2 10.8 - - + -
277B ARG* 2.8 40.7 + - + -
279B GLY* 4.9 5.6 - - - -
299B GLU* 3.5 10.8 - - + +
300B ILE* 3.0 34.8 + - + +
302B ALA* 1.3 78.6 - - - +
304B ALA* 1.3 62.7 + - - +
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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