Contacts of the helix formed by residues 346 - 358 (chain D) in PDB entry 2BWB
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 ASP 346 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344D PHE 3.7 0.8 - - - -
345D PHE* 1.3 74.0 - - - +
347D PHE* 1.3 59.1 + - - +
348D ASP* 3.2 11.6 + - - +
349D ARG* 2.8 54.3 + - + +
350D ASN* 2.9 33.9 + - - -
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Residues in contact with PHE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ARG* 3.2 64.6 - - + +
328D PRO* 4.0 15.7 - - + -
329D GLU* 3.6 36.3 - - + -
336D LEU* 4.0 13.9 - - + -
345D PHE 3.1 8.3 + - - +
346D ASP* 1.3 70.1 + - - +
348D ASP* 1.3 76.1 + - - +
350D ASN* 3.2 6.9 + - - +
351D VAL* 2.9 56.0 + - + +
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Residues in contact with ASP 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ARG* 5.4 3.5 + - - -
346D ASP* 3.2 7.7 + - - +
347D PHE* 1.3 96.6 - - - +
349D ARG* 1.3 58.2 + - + +
351D VAL* 3.5 3.6 + - - +
352D ALA* 3.0 30.4 + - - +
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Residues in contact with ARG 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D PHE* 6.0 1.0 - - - -
346D ASP* 2.8 41.2 + - + +
348D ASP* 1.3 70.3 - - + +
350D ASN* 1.3 60.9 + - - +
352D ALA* 3.7 5.7 - - - +
353D ALA* 3.0 30.7 + - - +
367D SER 5.4 2.0 + - - -
368D LEU* 3.2 55.9 + - + +
370D ASN 5.5 2.6 + - - -
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Residues in contact with ASN 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ARG 5.6 0.2 + - - -
336D LEU* 3.9 11.6 - - + +
339D LEU* 3.6 20.7 - - + +
340D ASN* 3.8 14.1 - - - +
344D PHE* 2.8 33.1 + - - +
345D PHE 3.8 2.0 + - - -
346D ASP 2.9 31.3 + - - +
347D PHE* 3.2 6.2 + - - +
349D ARG* 1.3 77.8 - - - +
351D VAL* 1.3 56.9 + - - +
353D ALA* 3.4 6.1 + - - +
354D LEU* 3.0 34.2 + - - +
368D LEU* 3.3 25.6 - - - +
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Residues in contact with VAL 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PRO* 3.9 28.7 - - + -
332D TYR* 4.4 7.2 - - + -
336D LEU* 4.3 9.4 - - + -
347D PHE* 2.9 52.4 + - + +
348D ASP* 4.1 3.6 - - - +
350D ASN* 1.3 73.0 - - - +
352D ALA* 1.3 61.5 + - - +
354D LEU* 3.2 6.9 + - - +
355D ARG* 2.9 54.5 + - + +
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D ASP 3.0 18.6 + - - +
349D ARG* 3.7 7.6 - - - +
351D VAL* 1.3 78.2 - - - +
353D ALA* 1.3 60.9 + - - +
355D ARG* 3.4 8.3 + - - +
356D ARG* 3.3 33.7 + - - +
329I GLU* 5.2 0.7 - - - +
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Residues in contact with ALA 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D ARG 3.0 19.0 + - - +
350D ASN* 3.6 4.7 - - - +
352D ALA* 1.3 75.6 - - - +
354D LEU* 1.3 58.5 + - - +
356D ARG* 3.4 8.6 + - - +
357D SER* 3.1 28.1 + - - -
364D ALA* 3.8 31.5 - - + +
367D SER* 4.1 18.1 - - - +
368D LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D TYR* 4.0 32.2 + - + -
335D GLN* 3.6 32.8 - - + -
336D LEU* 4.4 8.5 - - + -
339D LEU* 3.7 18.4 - - + -
350D ASN 3.0 24.8 + - - +
351D VAL* 3.2 4.2 + - - +
353D ALA* 1.3 73.6 - - - +
355D ARG* 1.3 60.5 + - - +
357D SER* 3.3 2.2 + - - -
358D GLY 3.0 7.4 + - - -
359D GLY* 2.7 40.8 + - - -
360D SER 3.8 12.1 - - - +
361D VAL* 4.3 2.0 - - - +
364D ALA* 3.8 20.6 - - + -
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Residues in contact with ARG 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PRO* 6.3 0.4 - - - +
331D ARG* 4.4 16.9 - - - +
332D TYR* 3.7 25.5 + - + +
351D VAL* 2.9 34.6 + - - +
352D ALA* 3.6 8.5 - - - +
353D ALA 3.3 0.2 - - - -
354D LEU* 1.3 75.7 - - - +
356D ARG* 1.3 60.7 + - - +
358D GLY* 3.4 10.0 + - - -
327I ASP* 5.3 3.4 + - - -
329I GLU* 3.3 68.6 + - + +
330I GLU* 4.2 23.8 + - - +
333I GLU* 5.7 0.4 - - - +
336I LEU* 3.9 3.3 - - - +
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Residues in contact with ARG 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D ALA* 3.3 21.4 + - - +
353D ALA* 3.7 10.8 - - - +
354D LEU 3.3 0.2 - - - -
355D ARG* 1.3 76.8 - - - +
357D SER* 1.3 57.8 + - - +
358D GLY 3.4 0.4 + - - -
367D SER* 4.9 12.0 + - - +
371D GLY 5.2 6.7 + - - -
329I GLU* 4.1 16.5 + - - +
336I LEU* 3.8 12.6 - - - +
340I ASN* 5.0 0.2 - - - +
345I PHE 5.0 3.1 - - - +
347I PHE* 3.2 84.4 - - + +
348I ASP* 4.5 11.3 + - - -
350I ASN* 5.1 1.7 - - - +
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Residues in contact with SER 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D ALA 3.1 16.3 + - - -
354D LEU* 3.8 5.6 - - - -
355D ARG 3.2 0.4 - - - -
356D ARG* 1.3 76.9 - - - +
358D GLY* 1.3 60.7 + - - +
360D SER* 2.4 38.2 + - - -
363D GLY 4.0 1.8 - - - -
364D ALA 3.4 10.0 + - - -
336I LEU 3.0 20.9 - - - +
337I ARG* 3.4 2.1 - - - -
340I ASN* 2.8 28.7 + - - -
345I PHE 5.5 1.6 - - - -
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Residues in contact with GLY 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D TYR* 5.0 1.1 - - - -
354D LEU 3.0 4.6 + - - -
355D ARG* 3.4 7.3 + - - -
356D ARG 3.4 3.8 + - - -
357D SER* 1.3 79.2 - - - +
359D GLY* 1.3 55.3 + - - +
360D SER 3.4 0.2 - - - -
333I GLU* 3.4 24.7 - - - -
336I LEU* 3.8 3.1 - - - +
337I ARG* 2.5 49.9 + - - +
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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