Contacts of the strand formed by residues 324 - 331 (chain B) in PDB entry 3OPY
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 ASN 324 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B LYS* 3.4 41.4 - - - +
278B ASP 3.4 15.9 + - - +
279B ALA* 3.3 18.2 - - + +
280B LEU 2.7 32.8 + - - -
322B ASN* 3.5 16.3 + - - +
323B LEU* 1.3 73.4 - - - +
325B ILE* 1.3 55.4 + - - +
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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
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280B LEU* 3.3 35.7 - - + +
282B VAL* 4.3 2.9 - - + -
292B ALA* 3.7 39.0 - - + +
293B ASP* 6.2 0.2 - - - -
295B PHE* 4.4 2.7 - - + -
296B ARG* 4.2 28.9 - - + -
323B LEU* 3.3 24.4 + - + +
324B ASN* 1.3 74.3 - - - +
326B CYS* 1.3 68.7 + - - +
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Residues in contact with CYS 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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280B LEU 2.9 8.2 + - - +
281B ILE* 3.4 22.0 - - + +
282B VAL* 2.9 27.3 + - - +
325B ILE* 1.3 79.2 - - - +
327B GLY* 1.3 71.0 + - - +
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Residues in contact with GLY 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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281B ILE* 5.8 0.7 - - - -
282B VAL* 3.4 7.0 - - - -
289B LEU* 3.7 20.4 - - - -
326B CYS* 1.3 86.5 - - - +
328B ALA* 1.3 60.4 + - - +
329B VAL* 5.9 0.2 - - - -
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Residues in contact with ALA 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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199B PHE* 3.5 39.3 - - + -
282B VAL 3.0 7.1 + - - +
283B CYS* 3.4 7.6 - - - -
284B GLY 3.1 25.7 + - - +
289B LEU* 4.1 4.0 - - - +
327B GLY* 1.3 74.7 - - - +
329B VAL* 1.3 63.2 + - - +
330B GLY 3.3 0.3 + - - -
343B ILE* 4.5 7.0 - - + -
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Residues in contact with VAL 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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284B GLY 3.3 12.6 - - - +
285B GLY* 4.3 4.5 - - - -
289B LEU* 3.8 13.0 - - + -
328B ALA* 1.3 72.2 - - - +
330B GLY* 1.3 53.2 + - - +
331B SER* 3.5 13.0 - - - +
336B MET* 3.5 43.3 - - + -
339B THR* 4.2 13.0 - - + -
342B THR* 3.6 23.5 - - + -
343B ILE* 2.7 42.2 + - - +
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Residues in contact with GLY 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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189B SER 4.4 4.7 - - - +
190B GLY* 5.9 0.3 - - - -
191B GLY 4.5 4.5 - - - +
193B SER* 3.7 14.3 - - - -
196B MET* 4.6 5.3 - - - +
283B CYS* 4.2 14.1 - - - -
284B GLY* 2.7 32.0 + - - +
285B GLY* 3.7 2.3 + - - -
328B ALA 3.3 4.0 + - - -
329B VAL* 1.3 69.9 - - - +
331B SER* 1.4 59.2 + - - -
343B ILE* 3.6 11.0 - - - -
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Residues in contact with SER 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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191B GLY 5.8 0.4 - - - -
193B SER* 3.4 8.3 - - - -
285B GLY* 4.4 10.5 - - - -
286B ASP* 4.8 5.3 + - - -
329B VAL* 3.5 12.5 + - - +
330B GLY* 1.4 75.8 - - - +
332B ILE* 1.3 56.8 + - - +
333B ASP* 3.7 11.0 + - - +
334B ASN 3.5 11.8 + - - -
335B ASP 4.4 2.1 + - - -
342B THR* 2.6 38.5 + - - +
343B ILE 3.0 13.0 + - - +
345B ALA 3.4 4.7 + - - -
469B ARG* 6.0 2.0 - - - +
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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