Contacts of the strand formed by residues 327 - 331 (chain B) in PDB entry 1RHR
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 PHE 327 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A THR* 3.6 25.8 - - - -
263A ASN* 5.6 0.7 - - - -
265A PHE* 3.3 23.6 - - + -
266A ARG* 3.5 20.6 - - + -
267A GLY 4.4 0.9 - - - -
278A LYS* 3.7 27.4 - - + -
280A PHE* 4.4 10.8 - + - -
323B VAL 3.6 17.9 - - - -
324B GLU* 3.7 24.5 - - - +
325B ALA 2.9 23.2 + - - -
326B ASP* 1.3 77.9 - - - +
328B LEU* 1.3 58.0 + - - +
329B TYR* 3.4 36.2 - + + +
392B SER* 4.0 0.3 - - - -
393B MET* 3.0 33.7 + - + +
394B LEU 3.8 0.4 + - - -
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Residues in contact with LEU 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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278A LYS 3.0 10.5 + - - +
279A LEU* 4.4 12.8 - - + -
280A PHE* 2.7 30.0 + - - +
326B ASP 3.7 0.4 + - - -
327B PHE* 1.3 74.6 - - - +
329B TYR* 1.3 67.6 + - - +
330B ALA* 5.0 2.0 - - + +
366B PHE* 3.1 41.1 - - + -
367B MET* 4.0 10.8 - - + -
370B LEU* 4.4 4.9 - - + -
389B ILE* 4.5 6.7 - - + -
390B VAL 2.9 28.5 - - - +
392B SER* 3.8 15.9 - - - +
394B LEU* 3.7 27.4 - - + -
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Residues in contact with TYR 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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258A LEU* 5.3 4.0 - - + -
262A THR* 4.1 26.0 + - + -
280A PHE* 3.3 17.9 - + + +
282A ILE* 4.7 6.1 - - + -
324B GLU* 5.5 2.4 + - - -
327B PHE* 3.4 47.8 - + + +
328B LEU* 1.3 81.8 - - - +
330B ALA* 1.3 59.7 + - - +
331B TYR* 3.3 38.5 + + + -
388B CYS 3.6 2.4 - - - +
389B ILE* 3.9 0.3 - - - -
390B VAL* 3.0 46.1 + - + +
393B MET* 4.2 18.6 - - + +
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Residues in contact with ALA 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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280A PHE 2.9 12.3 + - - +
281A ILE* 3.9 12.9 - - + -
282A ILE* 3.3 22.3 + - - +
328B LEU* 4.1 3.9 + - + -
329B TYR* 1.3 71.4 - - - +
331B TYR* 1.3 64.4 + - - +
349B PHE* 3.7 20.6 - - + -
353B LEU* 5.8 0.2 - - + -
366B PHE* 6.3 0.9 - - + -
370B LEU* 4.4 27.6 - - + -
388B CYS 3.6 6.1 - - - +
389B ILE* 4.8 4.5 - - + +
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Residues in contact with TYR 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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240A GLU* 5.4 1.8 - - - -
241A GLY* 6.0 3.1 - - - -
258A LEU* 3.8 24.5 - - + +
282A ILE* 3.8 25.8 - - + -
286A ARG* 3.3 55.9 - - + +
329B TYR* 3.3 49.0 - + + -
330B ALA* 1.3 74.2 - - - +
332B SER* 1.3 58.6 + - - +
333B THR 3.1 8.2 + - - +
349B PHE* 3.8 4.1 - - - -
387B PRO* 3.7 5.7 - - - +
388B CYS 2.9 36.4 + - - +
390B VAL* 4.2 14.6 - - + -
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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