Contacts of the helix formed by residues 346 - 357 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B ARG* 5.7 0.4 - - - +
344C PHE 3.7 1.0 - - - -
345C PHE* 1.3 72.8 - - - +
347C PHE* 1.3 58.1 + - - +
348C ASP* 2.9 12.0 + - - +
349C ARG* 2.6 59.0 + - + +
350C ASN* 2.9 32.9 + - - +
334H HIS* 3.7 29.6 + - + +
338H GLN* 4.5 2.3 - - - +
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Residues in contact with PHE 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ARG* 3.2 75.2 - - + +
328C PRO* 4.2 12.6 - - + -
329C GLU* 3.6 35.0 - - + -
336C LEU* 4.1 12.6 - - + -
345C PHE 3.1 7.2 + - - +
346C ASP* 1.3 70.0 + - - +
348C ASP* 1.3 71.6 + - - +
350C ASN* 3.2 6.4 + - - +
351C VAL* 2.9 61.0 + - + +
360H SER* 6.2 0.4 - - - -
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Residues in contact with ASP 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B ARG* 4.3 10.4 + - - -
346C ASP* 2.9 7.5 + - - +
347C PHE* 1.3 90.7 - - - +
349C ARG* 1.3 57.6 + - - +
351C VAL* 3.6 3.8 + - - +
352C ALA* 3.0 23.4 + - - +
335H GLN* 4.0 7.8 + - - +
338H GLN* 3.0 29.1 + - - +
359H GLY 3.9 11.1 - - - +
360H SER* 4.4 5.7 + - - -
361H VAL* 3.6 35.9 + - + +
362H GLN* 4.8 1.9 + - - +
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Residues in contact with ARG 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C ASP* 2.6 41.0 + - + +
348C ASP* 1.3 71.3 - - - +
350C ASN* 1.3 65.6 + - - +
352C ALA* 3.5 2.9 + - - +
353C ALA* 3.0 25.5 + - - +
368C LEU* 3.9 32.9 + - + +
371C GLY 5.0 14.5 + - - -
334H HIS* 5.5 8.0 + - - +
337H ARG* 4.5 32.7 - - - +
338H GLN* 3.7 24.4 - - + +
341H ASP* 5.9 0.2 + - - -
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Residues in contact with ASN 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B ARG 5.4 0.2 + - - -
336C LEU* 3.8 17.7 - - + +
339C LEU* 4.0 17.6 - - + +
340C ASN* 3.7 14.8 - - - +
344C PHE* 2.9 33.3 + - - +
345C PHE 4.1 1.0 - - - -
346C ASP* 2.9 28.0 + - - +
347C PHE* 3.2 6.3 + - - +
349C ARG* 1.3 75.6 - - - +
351C VAL* 1.3 56.2 + - - +
353C ALA* 3.4 2.9 + - - +
354C LEU* 2.9 36.3 + - - +
368C LEU* 3.5 26.4 - - - +
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C PRO* 4.0 28.0 - - + -
332C TYR* 4.8 3.5 - - + -
336C LEU* 4.5 9.0 - - + -
347C PHE* 2.9 53.9 + - + +
348C ASP* 4.0 4.9 - - - +
350C ASN* 1.3 73.7 - - - +
352C ALA* 1.3 65.0 + - - +
354C LEU* 3.3 8.1 + - - +
355C ARG* 2.9 51.5 + - + +
362H GLN* 4.3 12.1 - - + +
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Residues in contact with ALA 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ASP 3.0 19.5 + - - +
349C ARG* 3.7 4.5 - - - +
351C VAL* 1.3 80.3 - - - +
353C ALA* 1.3 61.8 + - - +
355C ARG* 3.4 9.7 + - - +
356C ARG* 3.3 30.0 + - - +
329D GLU* 4.4 1.2 - - - +
338H GLN* 3.7 14.6 - - - +
342H MET* 6.0 6.1 - - - -
362H GLN* 5.7 1.8 - - - -
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Residues in contact with ALA 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ARG 3.0 18.6 + - - +
350C ASN* 3.7 4.0 - - - +
352C ALA* 1.3 76.4 - - - +
354C LEU* 1.3 57.3 + - - +
356C ARG* 3.4 9.7 + - - +
357C SER* 3.1 27.7 + - - -
364C ALA* 3.8 31.2 - - + +
367C SER* 4.0 17.4 + - - -
368C LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C TYR* 3.8 38.4 + - + -
335C GLN* 3.6 26.9 - - + -
336C LEU* 4.2 11.2 - - + -
339C LEU* 3.8 21.1 - - + -
350C ASN 2.9 23.9 + - - +
351C VAL* 3.7 4.5 - - - +
353C ALA* 1.3 74.1 - - - +
355C ARG* 1.3 59.4 + - - +
357C SER* 3.4 3.4 - - - -
358C GLY 3.0 7.4 + - - -
359C GLY* 2.7 43.0 + - - -
360C SER 3.9 20.6 - - - +
361C VAL* 4.5 0.9 - - - +
364C ALA* 3.9 7.0 - - + -
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Residues in contact with ARG 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LEU* 3.7 47.7 + - - +
328C PRO* 4.6 13.9 - - - +
332C TYR* 4.3 23.2 + - + -
351C VAL* 2.9 29.2 + - + +
352C ALA* 3.6 8.3 - - - +
353C ALA 3.3 0.2 - - - -
354C LEU* 1.3 75.7 - - - +
356C ARG* 1.3 61.1 + - - +
358C GLY* 3.5 8.5 + - - -
329D GLU* 3.4 48.1 - - + +
330D GLU* 5.1 11.5 - - - +
336D LEU* 4.0 6.6 - - - +
362H GLN* 3.5 40.6 + - - +
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Residues in contact with ARG 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ALA* 3.3 16.5 + - - +
353C ALA* 3.6 9.0 - - - +
355C ARG* 1.3 76.7 - - - +
357C SER* 1.3 57.8 + - - +
358C GLY 3.3 1.1 + - - -
367C SER* 4.4 17.3 + - - +
329D GLU* 3.2 19.3 + - - +
336D LEU* 3.9 11.3 - - - +
340D ASN* 4.1 3.5 + - - +
345D PHE 5.5 1.6 - - - +
347D PHE* 3.2 70.2 - - + +
348D ASP* 5.4 3.6 + - - -
350D ASN* 5.6 0.2 + - - -
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Residues in contact with SER 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ALA 3.1 14.4 + - - -
354C LEU* 3.1 14.6 + - - -
356C ARG* 1.3 76.3 - - - +
358C GLY* 1.3 59.2 + - - +
360C SER* 2.7 39.0 + - - -
363C GLY* 3.9 1.8 - - - -
364C ALA 3.6 9.8 + - - -
336D LEU 3.2 16.3 - - - +
337D ARG* 3.3 6.2 - - - -
340D ASN* 3.4 26.4 + - - +
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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