Contacts of the helix formed by residues 346 - 357 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A ASP* 5.8 0.2 - - - -
344B PHE 3.7 0.8 - - - -
345B PHE* 1.3 73.4 - - - +
347B PHE* 1.3 58.2 + - - +
348B ASP* 3.2 12.6 + - - +
349B ARG* 2.9 47.1 + - + +
350B ASN* 2.9 33.7 + - - +
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Residues in contact with PHE 347 (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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356A ARG* 3.4 75.2 - - + +
367A SER* 6.0 1.1 - - - +
328B PRO* 4.1 11.7 - - + -
329B GLU* 3.7 41.1 - - + -
336B LEU* 4.2 8.3 - - + -
345B PHE 3.1 8.3 + - - +
346B ASP* 1.3 70.8 + - - +
348B ASP* 1.3 73.3 + - - +
350B ASN* 3.3 5.9 + - - +
351B VAL* 2.9 62.4 + - + +
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Residues in contact with ASP 348 (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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356A ARG* 4.7 8.4 + - - -
346B ASP* 3.2 8.1 + - - +
347B PHE* 1.3 95.3 - - - +
349B ARG* 1.3 57.1 + - + +
351B VAL* 3.9 4.0 - - - +
352B ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 349 (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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344B PHE* 6.0 0.6 - - - -
346B ASP* 2.9 38.5 + - + +
348B ASP* 1.3 74.4 - - + +
350B ASN* 1.3 61.2 + - - +
352B ALA* 3.5 5.5 + - - +
353B ALA* 3.0 31.0 + - - +
367B SER 5.3 1.8 + - - -
368B LEU* 3.4 48.7 + - + +
370B ASN 5.8 1.4 + - - -
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Residues in contact with ASN 350 (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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336B LEU* 3.7 16.9 - - + +
339B LEU* 3.9 19.1 - - + +
340B ASN* 3.6 16.2 - - - +
344B PHE* 2.9 32.3 + - - +
345B PHE 4.3 0.4 - - - -
346B ASP 2.9 26.0 + - - +
347B PHE* 3.3 6.5 + - - +
349B ARG* 1.3 76.6 - - - +
351B VAL* 1.3 57.6 + - - +
353B ALA* 3.5 5.8 + - - +
354B LEU* 3.0 34.3 + - - +
368B LEU* 3.6 23.4 - - - +
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Residues in contact with VAL 351 (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 PRO* 4.0 21.3 - - + -
332B TYR* 4.4 7.4 - - + -
336B LEU* 4.3 10.1 - - + -
347B PHE* 2.9 53.4 + - + +
348B ASP* 3.9 4.9 - - - +
350B ASN* 1.3 74.0 - - - +
352B ALA* 1.3 64.9 + - - +
354B LEU* 3.4 6.3 + - - +
355B ARG* 3.0 57.3 + - - +
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Residues in contact with ALA 352 (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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348B ASP 3.0 18.6 + - - +
349B ARG* 3.7 7.9 - - - +
351B VAL* 1.3 78.1 - - - +
353B ALA* 1.3 61.9 + - - +
355B ARG* 3.4 10.1 + - - +
356B ARG* 3.3 29.4 + - - +
329C GLU* 4.4 1.7 - - - +
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Residues in contact with ALA 353 (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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349B ARG 3.0 17.7 + - - +
350B ASN 3.6 4.0 - - - +
352B ALA* 1.3 77.0 - - - +
354B LEU* 1.3 57.3 + - - +
356B ARG* 3.4 9.7 + - - +
357B SER* 3.1 27.5 + - - -
364B ALA* 3.8 32.1 - - + +
367B SER* 4.1 15.9 + - - -
368B LEU* 4.2 11.2 - - + -
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Residues in contact with LEU 354 (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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332B TYR* 3.7 42.5 + - + -
335B GLN* 3.7 26.5 - - + -
336B LEU* 4.3 10.8 - - + -
339B LEU* 4.1 11.9 - - + -
350B ASN 3.0 21.7 + - - +
351B VAL 3.9 3.8 - - - +
352B ALA 3.4 0.2 - - - -
353B ALA* 1.3 74.0 - - - +
355B ARG* 1.3 60.1 + - - +
357B SER* 3.5 2.2 - - - -
358B GLY 3.0 6.9 + - - -
359B GLY* 2.7 41.4 + - - -
360B SER 3.8 13.9 - - - +
361B VAL* 4.3 2.2 - - - +
364B ALA* 3.7 19.7 - - + -
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Residues in contact with ARG 355 (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 PRO* 4.3 18.8 - - - +
331B ARG* 5.7 2.9 - - - +
332B TYR* 3.3 24.1 + - + +
351B VAL* 3.0 42.1 + - - +
352B ALA* 3.7 9.0 - - - +
353B ALA 3.3 0.2 - - - -
354B LEU* 1.3 76.3 - - - +
356B ARG* 1.3 60.8 + - - +
358B GLY* 3.5 9.6 + - - -
329C GLU* 3.5 50.2 + - + +
336C LEU* 4.3 2.6 - - - +
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Residues in contact with ARG 356 (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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352B ALA* 3.3 17.1 + - - +
353B ALA* 3.5 9.0 - - - +
354B LEU 3.3 0.2 - - - -
355B ARG* 1.3 77.5 - - - +
357B SER* 1.3 59.2 + - - +
358B GLY 3.3 0.6 + - - -
367B SER* 4.2 23.3 + - - +
329C GLU* 3.9 12.3 - - - +
336C LEU* 4.0 11.5 - - - +
340C ASN* 4.2 2.9 + - - -
345C PHE 5.2 5.7 + - - +
346C ASP* 5.7 0.4 - - - +
347C PHE* 3.2 76.1 - - + +
348C ASP* 4.3 15.0 + - - -
350C ASN* 5.4 0.2 + - - -
359H GLY 5.4 3.6 + - - -
360H SER* 5.9 3.0 - - - +
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Residues in contact with SER 357 (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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353B ALA 3.1 11.2 + - - -
354B LEU* 3.2 13.5 + - - -
355B ARG 3.3 0.4 - - - -
356B ARG* 1.3 74.8 - - - +
358B GLY* 1.3 59.6 + - - +
360B SER* 2.6 48.3 + - - -
363B GLY 3.9 1.6 - - - -
364B ALA 3.6 10.3 + - - -
336C LEU* 3.5 14.8 - - - +
337C ARG* 3.5 1.6 - - - -
340C ASN* 3.5 26.8 + - - +
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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