Contacts of the helix formed by residues 322 - 337 (chain B) in PDB entry 2BXE
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 ALA 322 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ASN 3.2 4.1 + - - +
319B TYR 3.2 2.5 - - - -
320B ALA 4.3 0.2 - - - -
321B GLU* 1.3 81.6 - - + +
323B LYS* 1.3 61.0 + - - +
324B ASP 3.3 2.0 - - - -
325B VAL* 3.4 26.6 + - + -
326B PHE* 2.9 29.5 + - - +
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Residues in contact with LYS 323 (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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209B ARG* 5.9 2.0 - - - +
319B TYR* 2.8 70.4 + - + +
320B ALA* 3.9 22.8 - - - +
322B ALA* 1.3 69.6 - - - +
324B ASP* 1.3 62.3 + - - +
326B PHE* 3.7 0.7 - - - +
327B LEU* 2.9 38.8 + - + +
358B GLU* 4.3 11.5 + - - -
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Residues in contact with ASP 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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209B ARG* 2.7 45.7 + - - +
322B ALA 3.3 0.4 - - - -
323B LYS* 1.3 79.8 - - - +
325B VAL* 1.3 64.8 + - + +
327B LEU* 4.6 5.2 - - - +
328B GLY* 2.6 28.5 + - - +
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Residues in contact with VAL 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE* 4.3 11.9 - - + -
322B ALA* 3.4 23.6 + - + +
324B ASP* 1.3 77.7 - - + +
326B PHE* 1.3 54.2 + - - +
328B GLY* 3.2 2.0 + - - -
329B MET* 2.7 59.4 + - + +
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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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308B ASP 4.6 5.8 - - - -
309B PHE* 3.5 31.9 - + - -
315B VAL* 4.2 17.3 - - + -
318B ASN* 3.8 34.3 - - + +
319B TYR* 4.0 29.8 - + + -
322B ALA 2.9 18.6 + - - +
323B LYS 3.7 3.6 - - - +
325B VAL* 1.3 78.3 - - - +
327B LEU* 1.3 59.6 + - + +
329B MET* 3.0 15.3 + - - +
330B PHE* 2.8 26.0 + - - +
353B TYR* 3.7 25.8 - + - -
357B LEU* 3.8 15.7 - - + -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ARG* 4.6 11.2 - - - +
319B TYR* 4.2 16.6 - - + +
323B LYS* 2.9 22.8 + - + +
324B ASP* 4.2 4.7 - - - +
326B PHE* 1.3 73.1 - - + +
328B GLY* 1.3 68.1 + - - +
330B PHE* 3.0 8.6 + - + +
331B LEU* 2.9 26.4 + - - +
350B ALA 4.4 6.1 - - - +
353B TYR* 3.9 29.6 - - + -
354B GLU* 3.7 50.5 - - + +
357B LEU* 5.0 1.3 - - + -
2002B 1FL 4.5 16.4 - - + -
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Residues in contact with GLY 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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216B VAL* 3.7 13.5 - - - +
228B PHE* 3.9 14.4 - - - -
324B ASP 2.6 25.4 + - - -
325B VAL 3.5 1.3 - - - -
327B LEU* 1.3 75.1 - - - +
329B MET* 1.3 59.7 + - - +
331B LEU* 3.4 8.8 + - - +
332B TYR* 3.1 21.1 + - - +
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Residues in contact with MET 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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228B PHE* 3.5 38.4 - - + -
309B PHE* 4.0 13.7 - - + -
325B VAL* 2.7 42.9 + - + +
326B PHE* 3.0 16.4 + - - +
328B GLY* 1.3 71.2 - - - +
330B PHE* 1.3 66.2 + - - +
332B TYR* 3.2 7.9 + - + +
333B GLU* 2.9 31.5 + - + +
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Residues in contact with PHE 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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305B LEU* 5.0 2.5 - - + -
309B PHE* 3.5 40.1 - + + -
326B PHE 2.8 16.4 + - - +
327B LEU* 3.5 13.2 - - + +
329B MET* 1.3 73.1 - - - +
331B LEU* 1.3 72.5 + - + +
333B GLU* 3.2 1.7 + - - +
334B TYR* 2.9 55.8 + + + +
346B LEU 5.5 0.4 - - - -
349B LEU* 5.2 0.7 - - + -
350B ALA* 3.7 35.2 - - + -
353B TYR* 4.0 31.6 - + + -
374B PHE* 4.8 11.0 - + - -
377B PHE* 3.9 20.2 - + - -
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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
----------------------------------------------------------
213B ALA* 3.5 29.4 - - + +
216B VAL* 4.2 5.6 - - + -
217B ALA* 3.8 26.5 - - + +
327B LEU 2.9 10.8 + - - +
328B GLY* 3.5 12.1 - - - +
330B PHE* 1.3 83.9 - - + +
332B TYR* 1.3 65.5 + - - +
334B TYR* 2.9 3.0 + - + +
335B ALA* 2.8 25.4 + - - +
346B LEU* 4.1 20.0 - - + +
347B LEU* 3.8 12.8 - - + -
350B ALA* 3.6 22.7 - - + -
2002B 1FL 4.0 15.9 - - - -
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Residues in contact with TYR 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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216B VAL* 3.9 5.7 - - + +
220B SER* 3.1 35.4 - - - +
223B PHE 5.1 2.7 - - - -
226B ALA 2.7 28.9 + - - -
227B GLU* 4.0 3.5 + - - -
228B PHE* 3.5 44.3 + + + -
231B VAL* 3.9 16.4 - - + -
328B GLY 3.1 10.7 + - - +
329B MET* 3.4 8.1 - - + +
331B LEU* 1.3 79.1 - - - +
333B GLU* 1.3 79.3 + - + +
336B ARG* 2.8 71.1 + - + +
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Residues in contact with GLU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.3 19.7 - - + -
309B PHE* 3.9 17.0 - - + -
329B MET* 2.9 28.5 + - + +
330B PHE 3.7 2.9 - - - +
332B TYR* 1.3 92.0 - - + +
334B TYR* 1.3 58.3 + - - +
336B ARG* 2.9 27.9 + - - +
337B ARG* 2.5 64.7 + - - +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.4 28.2 - - + +
330B PHE* 2.9 41.5 + + + +
331B LEU* 2.9 6.3 + - + +
333B GLU* 1.3 74.0 - - - +
335B ALA* 1.3 65.6 + - - +
337B ARG 3.5 1.4 + - - -
338B HIS* 3.0 58.1 + + - +
341B TYR* 3.9 23.6 + + - -
346B LEU* 3.6 18.6 - - + -
349B LEU* 3.9 13.4 - - + +
374B PHE* 4.6 12.8 - + - -
377B PHE* 3.8 28.9 - + - +
381B VAL* 5.8 0.5 - - - +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ALA* 3.5 31.0 - - + +
220B SER* 3.8 10.5 - - - -
221B GLN* 3.8 9.6 - - + +
331B LEU 2.8 15.3 + - - +
334B TYR* 1.3 73.8 - - - +
336B ARG* 1.3 58.5 + - - +
337B ARG 3.0 1.3 - - - -
338B HIS* 2.6 33.7 + - - +
339B PRO 4.1 0.2 - - - -
346B LEU* 3.9 25.0 - - + +
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Residues in contact with ARG 336 (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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220B SER* 3.3 23.6 + - - +
221B GLN* 4.6 2.1 - - - +
224B PRO* 3.0 41.3 + - + +
225B LYS* 4.0 5.5 + - - +
226B ALA 3.9 4.4 + - - -
227B GLU* 4.9 4.0 + - - -
298B MET* 3.9 18.1 - - - +
299B PRO* 4.6 2.6 - - - +
302B LEU* 4.5 24.4 - - + +
332B TYR* 2.8 51.5 + - + +
333B GLU* 2.9 48.0 + - - +
335B ALA* 1.3 79.2 - - - +
337B ARG* 1.3 66.3 + - + +
338B HIS 3.5 0.3 + - - -
339B PRO* 4.4 3.1 - - - +
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Residues in contact with ARG 337 (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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298B MET* 3.4 29.0 - - - +
302B LEU* 3.5 32.2 + - + +
303B PRO* 2.7 43.8 + - - +
304B SER* 4.9 1.2 + - - +
305B LEU* 3.8 29.5 - - - +
333B GLU* 2.5 59.1 + - - +
334B TYR 3.5 4.0 + - - +
335B ALA 3.0 1.2 - - - -
336B ARG* 1.3 85.6 - - + +
338B HIS* 1.3 74.5 + - + +
339B PRO* 3.9 0.3 - - - +
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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