Contacts of the helix formed by residues 323 - 334 (chain B) in PDB entry 3BUW
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 PRO 323 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B GLN* 4.4 40.6 - - + +
250B PRO* 5.5 3.4 - - + -
322B LYS* 1.3 90.5 - - + +
324B LEU* 1.3 66.6 + - - +
325B PHE* 4.4 8.7 - - + +
326B GLN* 3.2 26.7 + - + +
327B ALA* 3.2 9.5 + - - +
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Residues in contact with LEU 324 (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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247B LEU 4.7 3.1 + - - +
249B GLN* 5.7 0.6 + - - +
261B LEU* 3.9 23.6 - - + -
293B PHE* 3.8 22.7 - - + -
303B TRP* 3.4 59.5 - - + +
305B ILE* 3.6 29.4 - - + -
319B PRO* 5.0 2.5 - - + -
322B LYS 3.9 0.2 + - - -
323B PRO* 1.3 72.6 - - - +
325B PHE* 1.3 63.6 + - - +
327B ALA* 3.2 11.0 + - + -
328B LEU* 2.9 37.2 + - + +
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Residues in contact with PHE 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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249B GLN 4.5 9.2 - - - -
250B PRO* 4.9 6.7 - - + -
257B ASN* 3.3 50.9 - - + -
260B SER* 4.3 8.1 - - - -
261B LEU* 3.9 26.2 - - + -
323B PRO* 3.2 8.0 - - + -
324B LEU* 1.3 78.2 - - - +
326B GLN* 1.3 58.0 + - - +
328B LEU* 3.9 3.6 - - - +
329B ILE* 2.9 42.7 + - + +
349B LEU* 4.0 42.0 - - + -
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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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322B LYS* 3.7 15.7 - - + -
323B PRO* 3.2 24.9 + - + +
325B PHE* 1.3 75.9 - - - +
327B ALA* 1.3 61.2 + - - +
329B ILE* 4.5 14.7 - - - +
330B ASP* 2.7 72.9 + - - +
333B ARG* 4.8 4.2 - - - +
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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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305B ILE* 5.5 2.0 - - + -
319B PRO* 3.8 31.9 - - + -
322B LYS* 3.6 16.5 - - + +
323B PRO 3.2 8.9 + - - +
324B LEU* 3.2 14.9 + - + +
326B GLN* 1.3 80.1 - - - +
328B LEU* 1.3 56.4 + - - +
330B ASP* 4.0 1.3 - - - +
331B GLY 2.9 23.9 + - - -
337B TYR* 3.6 15.9 - - + -
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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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261B LEU* 3.9 7.9 - - + -
265B HIS* 4.3 4.9 - - - +
291B TYR* 3.7 30.3 - - + +
293B PHE* 4.0 17.0 - - + -
305B ILE* 4.3 18.6 - - + -
324B LEU* 2.9 37.4 + - + +
325B PHE 3.9 2.7 - - - +
327B ALA* 1.3 75.8 - - - +
329B ILE* 1.3 59.3 + - - +
331B GLY 3.8 0.2 - - - -
332B PHE* 2.9 30.0 + - - +
337B TYR* 4.1 17.8 - - + +
349B LEU* 3.6 30.3 - - + -
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Residues in contact with ILE 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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325B PHE* 2.9 32.6 + - + +
326B GLN* 4.0 13.7 - - - +
328B LEU* 1.3 74.6 - - - +
330B ASP* 1.3 64.4 + - - +
332B PHE* 3.3 10.3 + - + +
333B ARG* 3.1 58.7 + - - +
349B LEU* 4.3 19.1 - - + +
350B THR* 3.9 36.3 - - + +
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Residues in contact with ASP 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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322B LYS* 2.6 31.5 + - - +
326B GLN* 2.7 46.2 + - - +
327B ALA 4.0 1.6 - - - +
329B ILE* 1.3 76.8 - - - +
331B GLY* 1.3 58.4 + - - +
333B ARG* 3.3 17.6 + - - +
334B GLU* 2.9 43.6 + - - +
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Residues in contact with GLY 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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327B ALA 2.9 12.0 + - - -
330B ASP* 1.3 74.3 - - - +
332B PHE* 1.3 63.8 + - - +
334B GLU* 3.5 13.1 + - - +
335B GLY 3.0 3.5 + - - -
336B PHE* 2.9 30.9 + - - -
337B TYR* 3.1 32.4 + - - -
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Residues in contact with PHE 332 (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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328B LEU 2.9 19.2 + - - +
329B ILE* 3.4 11.2 - - + +
331B GLY* 1.3 76.6 - - - +
333B ARG* 1.3 74.7 + - + +
335B GLY* 3.2 9.9 + - - -
337B TYR 3.4 22.4 + - - +
338B LEU* 3.3 36.6 - - + +
346B ASN* 3.5 31.6 - - + +
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Residues in contact with ARG 333 (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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326B GLN* 4.8 3.6 - - - +
329B ILE* 3.1 38.4 + - - +
330B ASP* 3.7 20.2 + - - +
332B PHE* 1.3 90.7 - - + +
334B GLU* 1.3 62.8 + - + +
335B GLY* 3.3 1.0 + - - -
350B THR* 4.1 19.4 + - - +
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Residues in contact with GLU 334 (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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330B ASP* 2.9 31.9 + - + +
331B GLY* 3.6 14.4 + - - +
332B PHE 3.3 0.2 - - - -
333B ARG* 1.3 77.8 - - + +
335B GLY* 1.3 57.4 + - - +
336B PHE* 3.6 37.1 - - + -
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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