Contacts of the helix formed by residues 346 - 358 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A PHE 3.7 0.4 - - - -
345A PHE* 1.3 74.3 - - - +
347A PHE* 1.3 59.7 + - - +
348A ASP* 3.2 18.0 + - - +
349A ARG* 3.4 41.6 + - + +
350A ASN* 2.9 33.4 + - - +
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Residues in contact with PHE 347 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A PRO* 4.0 13.5 - - + -
329A GLU* 3.6 41.7 - - + -
336A LEU* 4.0 20.2 - - + -
345A PHE 3.1 8.8 + - - +
346A ASP* 1.3 70.9 + - - +
348A ASP* 1.3 75.9 + - - +
350A ASN* 3.3 7.0 + - - +
351A VAL* 2.9 57.3 + - + +
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Residues in contact with ASP 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 3.2 8.8 + - - +
347A PHE* 1.3 96.7 - - - +
349A ARG* 1.3 59.0 + - + +
351A VAL* 3.9 3.8 - - - +
352A ALA* 3.0 31.1 + - - +
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PHE* 4.9 7.7 - - - -
346A ASP* 3.4 36.7 + - - +
347A PHE 3.3 0.2 - - - -
348A ASP* 1.3 75.5 - - + +
350A ASN* 1.3 67.2 + - - +
352A ALA* 3.5 6.2 + - - +
353A ALA* 3.0 26.2 + - - +
367A SER 5.1 1.6 + - - -
368A LEU* 3.2 54.5 + - + +
371A GLY 4.6 8.9 + - - -
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 3.8 17.6 - - + +
339A LEU* 3.8 18.2 - - + +
340A ASN* 3.7 15.6 - - - +
344A PHE* 2.8 42.1 + - - +
345A PHE 4.1 2.4 + - - -
346A ASP 2.9 26.9 + - - +
347A PHE* 3.6 5.7 - - - +
349A ARG* 1.3 77.5 + - - +
351A VAL* 1.3 56.3 + - - +
353A ALA* 3.5 2.5 + - - +
354A LEU* 3.0 35.6 + - - +
368A LEU* 3.7 15.8 - - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PRO* 3.9 26.0 - - + -
332A TYR* 4.6 4.9 - - + -
336A LEU* 4.5 8.5 - - + -
347A PHE* 2.9 55.1 + - + +
348A ASP* 3.9 4.3 - - - +
350A ASN* 1.3 72.4 - - - +
352A ALA* 1.3 64.9 + - - +
354A LEU* 3.3 7.2 + - - +
355A ARG* 2.8 49.9 + - + +
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ASP 3.0 19.7 + - - +
349A ARG* 3.7 6.7 - - - +
351A VAL* 1.3 78.2 - - - +
353A ALA* 1.3 61.6 + - - +
355A ARG* 3.4 8.1 + - - +
356A ARG* 3.3 31.5 + - - +
329B GLU* 4.9 1.3 - - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ARG 3.0 18.6 + - - +
350A ASN 3.8 3.8 - - - +
352A ALA* 1.3 76.0 - - - +
354A LEU* 1.3 59.5 + - - +
356A ARG* 3.4 9.6 + - - +
357A SER* 3.1 27.4 + - - -
364A ALA* 3.9 30.1 - - + +
367A SER* 4.1 15.1 + - - -
368A LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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332A TYR* 3.7 31.1 + - + -
335A GLN* 3.6 39.7 - - + -
336A LEU* 4.3 10.8 - - + +
339A LEU* 3.9 14.8 - - + -
350A ASN 3.0 21.5 + - - +
351A VAL* 3.7 4.7 - - - +
353A ALA* 1.3 74.5 - - - +
355A ARG* 1.3 59.8 + - - +
357A SER* 3.1 2.2 + - - -
358A GLY 3.0 7.6 + - - -
359A GLY 2.7 37.5 + - - -
360A SER 3.7 12.6 - - - +
361A VAL* 4.3 1.8 - - - +
364A ALA* 3.6 20.9 - - + -
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PRO* 5.9 0.9 - - - -
331A ARG* 4.3 7.4 - - - +
332A TYR* 3.6 28.7 + - + +
351A VAL* 2.8 37.4 + - + +
352A ALA* 3.8 6.0 - - - +
353A ALA 3.3 0.2 - - - -
354A LEU* 1.3 76.3 - - - +
356A ARG* 1.3 61.4 + - - +
358A GLY* 3.4 11.4 + - - -
329B GLU* 3.2 59.1 + - + +
330B GLU* 2.7 41.9 + - - -
336B LEU* 4.2 1.7 - - - +
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Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ALA* 3.3 19.7 + - - +
353A ALA* 3.7 10.1 - - - +
354A LEU 3.3 0.2 - - - -
355A ARG* 1.3 76.7 - - - +
357A SER* 1.3 59.2 + - - +
358A GLY 3.4 0.4 + - - -
367A SER* 5.2 10.9 + - - +
329B GLU* 3.9 15.7 + - - +
336B LEU* 3.9 14.0 - - - +
340B ASN* 4.1 3.3 + - - -
345B PHE 5.5 1.5 - - - +
347B PHE* 3.4 77.0 - - + +
348B ASP* 4.7 9.5 + - - -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ALA 3.1 10.6 + - - -
354A LEU* 3.1 15.8 + - - -
356A ARG* 1.3 76.5 - - - +
358A GLY* 1.3 60.1 + - - +
360A SER* 2.7 48.2 + - - -
363A GLY 3.9 1.1 - - - -
364A ALA 3.6 11.2 - - - -
367A SER* 5.9 0.7 - - - -
336B LEU* 3.5 15.0 - - - +
337B ARG* 3.5 1.7 - - - -
340B ASN* 3.5 24.3 + - - +
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Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A TYR* 5.0 4.0 - - - -
354A LEU 3.0 4.1 + - - -
355A ARG* 3.4 8.3 + - - -
356A ARG 3.4 4.0 + - - -
357A SER* 1.3 78.0 - - - +
359A GLY* 1.3 56.5 + - - +
360A SER 3.4 0.2 - - - -
329B GLU 5.6 0.2 - - - -
333B GLU* 3.7 40.0 - - - +
336B LEU* 4.1 3.7 - - - +
337B ARG* 3.3 25.5 + - - +
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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