Contacts of the strand formed by residues 323 - 328 (chain B) in PDB entry 2AYN
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 LEU 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B PHE 5.5 0.2 - - - +
248B VAL* 3.6 17.9 - - + -
274B LEU* 4.1 18.2 - - + +
319B LEU* 4.5 4.5 - - + -
320B PRO* 3.5 26.0 - - + -
322B TYR* 1.3 72.2 - - - +
324B THR* 1.3 64.4 + - - +
325B ILE* 3.7 18.9 + - + +
352B LEU* 4.3 2.2 - - + -
354B MET* 3.8 31.9 - - + -
417B TYR* 3.8 33.7 - - + +
477B LEU 3.6 2.4 - - - +
478B LEU* 3.7 2.1 - - - -
479B TYR* 2.6 38.7 + - + +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B TRP* 3.6 40.6 + - + +
207B MET* 4.9 1.2 - - - +
246B PHE* 4.1 18.5 - - - +
272B LEU 3.3 21.5 + - - -
273B GLN* 3.5 14.4 - - + +
274B LEU* 2.7 30.1 + - - +
322B TYR 3.7 0.6 + - - -
323B LEU* 1.3 73.9 - - - +
325B ILE* 1.3 63.0 + - - +
476B VAL* 4.0 15.3 - - + -
477B LEU 3.6 3.1 - - - +
478B LEU* 4.8 4.6 - - + +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLN* 4.9 0.4 - - - -
274B LEU* 2.9 13.9 - - + +
276B CYS* 4.4 2.2 - - + -
285B LEU* 4.3 4.3 - - + -
289B LEU* 3.9 33.0 - - + -
323B LEU* 4.2 28.0 - - + +
324B THR* 1.3 78.6 - - - +
326B GLN* 1.3 61.3 + - - +
327B MET* 3.2 26.4 + - + +
352B LEU* 4.2 8.3 - - + -
476B VAL* 3.5 5.5 - - - +
477B LEU* 2.7 50.5 + - + +
479B TYR* 3.9 25.8 - - + -
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Residues in contact with GLN 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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200B ASN* 3.7 25.4 + - - +
273B GLN* 3.3 27.6 + - - +
274B LEU 2.7 12.2 + - - +
275B SER* 3.5 19.2 - - - -
276B CYS 2.9 26.2 + - - -
324B THR 4.2 0.6 + - - -
325B ILE* 1.3 73.2 - - - +
327B MET* 1.3 66.2 + - - +
328B VAL* 3.1 17.7 + - - +
475B TYR* 3.8 29.8 + - + +
476B VAL* 4.8 0.9 - - - +
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Residues in contact with MET 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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276B CYS* 3.8 23.3 - - + -
278B ILE* 3.8 17.0 - - + -
285B LEU* 3.9 11.7 - - + -
325B ILE* 3.2 38.1 - - + +
326B GLN* 1.3 70.4 - - - +
328B VAL* 1.3 58.9 + - - +
329B ARG* 3.0 16.1 + - + +
346B VAL* 5.4 7.4 - - - -
348B PHE* 5.7 4.7 - - + -
474B ALA* 3.5 28.5 - - + +
475B TYR* 2.9 36.0 + - - +
477B LEU* 4.0 22.7 - - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 4.0 13.9 - - - -
276B CYS 3.2 21.2 + - - +
277B PHE* 4.5 10.5 - - + -
278B ILE* 3.9 18.5 + - - +
292B ARG* 3.8 27.6 - - - +
326B GLN* 3.1 24.5 + - - +
327B MET* 1.3 67.1 - - - +
329B ARG* 1.3 60.1 + - - +
330B PHE 4.4 13.9 - - - +
342B VAL* 4.7 2.6 - - - +
475B TYR* 5.3 0.7 - - - -
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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