Contacts of the helix formed by residues 324 - 331 (chain B) in PDB entry 1AE9
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 ASP 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319B GLU* 3.6 35.8 - - + +
323B SER* 1.3 73.2 - - - +
325B LYS* 1.3 66.9 + - + +
327B ALA* 3.4 3.5 + - - +
328B GLN* 3.0 33.1 + - + +
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Residues in contact with LYS 325 (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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323B SER* 3.0 11.6 - - - +
324B ASP* 1.3 83.1 - - + +
326B PHE* 1.3 56.9 + - - +
328B GLN* 3.3 8.2 + - + +
329B HIS* 2.9 30.5 + - - +
334B LYS 4.4 4.7 - - - +
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Residues in contact with PHE 326 (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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246B LEU* 3.6 26.9 - - + -
318B TYR* 3.6 35.9 - + + -
322B ILE* 3.8 33.4 - - + -
323B SER* 3.0 18.8 + - - +
325B LYS* 1.3 78.5 - - - +
327B ALA* 1.3 64.4 + - - +
329B HIS* 3.2 8.4 + - - +
330B LEU* 2.9 32.4 + - + +
353B ILE* 3.7 22.9 - - + -
354B GLU 3.3 29.8 - - - -
355B ILE* 4.2 9.2 - - + -
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Residues in contact with ALA 327 (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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315B ALA* 3.5 37.9 - - + +
318B TYR* 4.3 4.9 - - + -
319B GLU* 4.2 6.1 - - + +
323B SER 3.0 12.2 + - - +
324B ASP* 3.5 11.4 - - - +
325B LYS 3.3 0.2 - - - -
326B PHE* 1.3 83.5 - - - +
328B GLN* 1.3 63.4 + - - +
330B LEU* 3.3 4.1 + - - +
331B LEU* 3.0 33.3 + - - +
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Residues in contact with GLN 328 (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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315B ALA* 5.0 3.8 - - - +
324B ASP* 3.0 25.3 + - + +
325B LYS* 3.7 7.9 - - + +
327B ALA* 1.3 81.4 - - - +
329B HIS* 1.3 61.7 + - - +
331B LEU* 3.5 12.1 + - - +
332B GLY 3.3 3.5 + - - -
333B HIS* 2.8 63.1 + - + +
334B LYS 3.4 2.4 + - - -
335B SER 4.0 14.4 - - - +
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Residues in contact with HIS 329 (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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240B ILE* 4.4 4.2 - - - +
325B LYS 2.9 15.0 + - - +
326B PHE* 3.2 9.2 + - - +
328B GLN* 1.3 75.5 - - - +
330B LEU* 1.3 64.4 + - - +
332B GLY* 3.3 13.3 + - - -
334B LYS* 3.3 29.5 + - + +
351B ASP* 2.8 34.6 + - - -
352B LYS 3.2 26.0 - - - -
353B ILE* 3.5 28.8 - - + +
354B GLU 4.8 3.9 + - - -
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Residues in contact with LEU 330 (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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208B VAL 4.2 2.0 - - - +
209B THR 3.4 26.9 - - - +
210B GLY* 4.5 2.7 - - - +
211B GLN* 2.8 24.4 + - - -
240B ILE* 3.5 7.6 - - - +
242B ILE* 4.1 32.3 - - + -
246B LEU* 4.3 7.0 - - + -
314B SER* 4.6 1.8 - - - +
318B TYR* 3.4 40.8 - - + -
326B PHE* 2.9 28.9 + - + +
327B ALA* 3.7 4.3 - - - +
329B HIS* 1.3 72.3 - - - +
331B LEU* 1.3 61.8 + - + +
332B GLY 3.1 6.4 + - - -
353B ILE* 4.2 17.7 - - + +
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Residues in contact with LEU 331 (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 GLY* 3.2 29.6 - - - +
233B GLN* 3.0 14.6 + - - +
311B ARG* 2.9 59.7 + - + +
312B SER* 5.9 0.7 - - - -
314B SER* 5.1 0.7 - - - +
315B ALA* 3.7 27.6 - - + +
327B ALA 3.0 19.2 + - - +
328B GLN* 3.9 12.8 - - - +
329B HIS 3.4 0.2 - - - -
330B LEU* 1.3 78.2 - - + +
332B GLY* 1.3 59.0 + - - +
333B HIS* 3.9 25.5 - - + +
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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