Contacts of the helix formed by residues 346 - 357 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344E PHE 3.7 0.4 - - - -
345E PHE* 1.3 73.5 - - - +
347E PHE* 1.3 60.5 + - - +
348E ASP* 3.5 15.4 + - - +
349E ARG* 3.6 35.2 + - + +
350E ASN* 2.9 33.3 + - - +
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Residues in contact with PHE 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E PRO* 4.1 13.9 - - + -
329E GLU* 3.4 42.6 - - + -
336E LEU* 3.9 20.4 - - + -
345E PHE 3.1 8.6 + - - +
346E ASP* 1.3 70.9 + - - +
348E ASP* 1.3 74.9 + - - +
350E ASN* 3.2 7.0 + - - +
351E VAL* 2.9 56.7 + - + +
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Residues in contact with ASP 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E ASP* 3.4 8.5 + - - +
347E PHE* 1.3 93.7 - - - +
349E ARG* 1.3 58.6 + - + +
351E VAL* 3.9 3.4 - - - +
352E ALA* 3.0 30.5 + - - +
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Residues in contact with ARG 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E PHE* 6.0 0.8 - - - -
346E ASP* 3.5 36.7 + - + +
348E ASP* 1.3 79.3 - - + +
350E ASN* 1.3 59.8 + - - +
352E ALA* 3.5 6.4 + - - +
353E ALA* 3.0 30.8 + - - +
367E SER 4.9 1.4 + - - -
368E LEU* 3.2 50.7 + - + +
370E ASN 5.6 1.0 + - - -
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Residues in contact with ASN 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E LEU* 3.6 17.9 - - + +
339E LEU* 4.1 15.1 - - + +
340E ASN* 3.2 19.2 - - - +
344E PHE* 2.9 41.4 + - - +
345E PHE 4.1 1.4 + - - -
346E ASP* 2.9 28.6 + - - +
347E PHE* 3.5 6.5 - - - +
349E ARG* 1.3 76.5 - - - +
351E VAL* 1.3 57.3 + - - +
353E ALA* 3.4 3.5 + - - +
354E LEU* 3.0 34.3 + - - +
368E LEU* 3.7 15.2 - - - +
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Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328E PRO* 3.9 27.6 - - + -
332E TYR* 4.5 7.9 - - + -
336E LEU* 4.3 8.3 - - + -
347E PHE* 2.9 54.3 + - + +
348E ASP* 3.9 4.5 - - - +
350E ASN* 1.3 73.0 - - - +
352E ALA* 1.3 69.7 + - - +
354E LEU* 3.3 7.4 + - - +
355E ARG* 2.9 38.8 + - - +
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Residues in contact with ALA 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348E ASP 3.0 19.3 + - - +
349E ARG* 3.6 7.6 - - - +
351E VAL* 1.3 78.7 - - - +
353E ALA* 1.3 61.6 + - - +
355E ARG* 3.4 9.2 + - - +
356E ARG* 3.1 30.2 + - + +
329F GLU* 4.3 0.7 - - - +
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Residues in contact with ALA 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ARG 3.0 18.4 + - - +
350E ASN 3.7 4.5 - - - +
352E ALA* 1.3 75.8 - - - +
354E LEU* 1.3 57.4 + - - +
356E ARG* 3.6 9.1 + - - +
357E SER* 3.1 27.6 + - - -
364E ALA* 3.8 30.4 - - + +
367E SER* 4.1 14.8 - - - +
368E LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332E TYR* 3.7 41.0 + - + -
335E GLN* 3.6 35.0 - - + -
336E LEU* 4.2 11.9 - - + -
339E LEU* 3.9 17.7 - - + -
350E ASN 3.0 21.9 + - - +
351E VAL 3.7 4.3 - - - +
353E ALA* 1.3 73.4 - - - +
355E ARG* 1.3 60.6 + - - +
356E ARG 3.3 0.2 - - - -
357E SER* 3.4 3.1 - - - -
358E GLY 3.0 6.2 + - - -
359E GLY* 2.7 46.9 + - - -
360E SER 4.1 2.7 - - - +
361E VAL* 4.5 1.1 - - - +
364E ALA* 4.0 15.0 - - + -
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Residues in contact with ARG 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E ARG* 5.8 4.8 - - - +
332E TYR* 3.8 24.3 - - + +
351E VAL* 2.9 31.4 + - + +
352E ALA* 3.4 8.7 + - - +
354E LEU* 1.3 75.2 - - - +
356E ARG* 1.3 62.3 + - - +
357E SER 3.5 0.2 + - - -
358E GLY* 3.5 9.7 + - - -
327F ASP 5.0 2.4 - - - +
329F GLU* 3.1 61.0 + - + +
330F GLU* 3.9 29.4 + - - +
333F GLU* 5.7 0.7 - - - +
336F LEU* 4.3 2.1 - - - +
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Residues in contact with ARG 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352E ALA* 3.1 19.7 - - - +
353E ALA* 3.8 5.8 - - - +
354E LEU 3.3 0.2 - - - -
355E ARG* 1.3 77.3 - - - +
357E SER* 1.3 57.7 + - - +
358E GLY 3.3 0.2 - - - -
367E SER* 4.7 18.3 + - - +
329F GLU* 3.4 16.7 + - - +
336F LEU* 4.0 11.9 - - - +
340F ASN* 4.1 2.8 + - - +
345F PHE 5.4 1.6 - - - +
347F PHE* 3.4 72.8 - - + +
348F ASP* 4.6 5.9 + - - -
350F ASN* 5.5 0.2 + - - -
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Residues in contact with SER 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E ALA 3.1 16.2 + - - -
354E LEU* 3.4 10.9 + - - -
355E ARG 3.2 0.4 - - - -
356E ARG* 1.3 78.1 - - - +
358E GLY* 1.3 58.3 + - - +
360E SER* 2.8 34.2 + - - -
363E GLY 3.8 1.3 - - - -
364E ALA 3.4 9.3 + - - -
336F LEU 3.2 18.3 - - - +
337F ARG* 3.3 7.3 - - - -
340F ASN* 3.3 28.2 + - - +
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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