Contacts of the helix formed by residues 346 - 357 (chain P) in PDB entry 2BWE
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344P PHE 3.5 2.6 - - - -
345P PHE* 1.3 75.3 - - - +
347P PHE* 1.3 60.5 + - - +
348P ASP* 3.2 17.0 + - - +
349P ARG* 3.2 39.6 + - + +
350P ASN* 2.9 33.3 + - - +
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Residues in contact with PHE 347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356O ARG* 3.2 77.1 - - + +
367O SER* 5.7 1.1 - - - +
328P PRO* 4.2 9.4 - - + -
329P GLU* 3.7 40.2 - - + -
336P LEU* 3.9 16.2 - - + -
345P PHE 3.1 8.6 + - - +
346P ASP* 1.3 72.4 + - - +
348P ASP* 1.3 63.6 + - - +
350P ASN* 2.9 9.9 + - - +
351P VAL* 2.8 60.9 + - + +
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Residues in contact with ASP 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356O ARG* 4.2 11.4 + - - -
346P ASP* 3.2 8.1 + - - +
347P PHE* 1.3 95.0 - - - +
349P ARG* 1.3 63.3 + - - +
351P VAL* 3.5 4.2 + - - +
352P ALA* 3.0 25.6 + - - +
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Residues in contact with ARG 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344P PHE* 5.3 3.6 - - - -
346P ASP* 3.2 39.2 + - + +
348P ASP* 1.3 78.1 - - - +
350P ASN* 1.3 57.1 + - - +
352P ALA* 3.3 7.1 + - - +
353P ALA* 2.9 31.0 + - - +
367P SER 5.1 2.6 + - - -
368P LEU* 3.2 59.9 + - + +
370P ASN 5.1 8.1 - - - -
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Residues in contact with ASN 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336P LEU* 3.8 12.6 - - + +
339P LEU* 3.8 21.2 - - + +
340P ASN* 3.7 15.4 - - - +
344P PHE* 2.7 34.9 + - - +
345P PHE 4.1 0.4 - - - -
346P ASP* 2.9 25.4 + - - +
347P PHE* 2.9 9.8 + - - +
349P ARG* 1.3 75.1 - - - +
351P VAL* 1.3 59.3 + - - +
353P ALA* 3.2 5.4 + - - +
354P LEU* 2.8 35.0 + - - +
368P LEU* 3.5 24.0 - - - +
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Residues in contact with VAL 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328P PRO* 4.1 22.9 - - + -
332P TYR* 4.3 9.9 - - + -
336P LEU* 4.6 6.5 - - + -
347P PHE* 2.8 59.7 + - + +
348P ASP* 4.0 4.5 - - - +
350P ASN* 1.3 70.6 - - - +
352P ALA* 1.3 57.2 + - - +
354P LEU* 3.1 7.7 + - - +
355P ARG* 2.8 55.6 + - + +
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Residues in contact with ALA 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348P ASP 3.0 18.7 + - - +
349P ARG* 3.4 7.6 - - - +
351P VAL* 1.3 79.2 - - - +
353P ALA* 1.3 62.1 + - - +
355P ARG* 3.5 10.8 + - - +
356P ARG* 3.3 31.9 + - - +
329Q GLU* 5.4 0.2 - - - +
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Residues in contact with ALA 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349P ARG 2.9 20.0 + - - +
350P ASN* 3.6 4.5 - - - +
352P ALA* 1.3 72.7 - - - +
354P LEU* 1.3 57.6 + - - +
356P ARG* 3.4 11.5 + - - +
357P SER* 3.1 27.0 + - - -
364P ALA* 3.8 30.1 - - + +
367P SER* 4.2 12.3 + - - -
368P LEU* 3.9 14.8 - - + +
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Residues in contact with LEU 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332P TYR* 4.0 29.6 - - + -
335P GLN* 3.8 27.4 - - + -
336P LEU* 4.4 8.5 - - + -
339P LEU* 3.9 16.4 - - + -
350P ASN 2.8 22.6 + - - +
351P VAL* 3.7 4.5 - - - +
353P ALA* 1.3 74.3 - - - +
355P ARG* 1.3 64.5 - - - +
356P ARG 3.1 1.3 - - - -
357P SER* 3.1 2.6 + - - -
358P GLY 2.9 4.0 + - - -
359P GLY* 2.8 54.8 + - - +
360P SER 4.0 4.0 - - - +
361P VAL* 4.4 2.9 - - - -
364P ALA* 3.7 20.4 - - + -
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Residues in contact with ARG 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332P TYR* 3.5 28.7 - - + +
351P VAL* 2.8 37.1 + - - +
352P ALA* 3.9 8.6 - - - +
354P LEU* 1.3 71.8 - - - +
356P ARG* 1.3 61.1 - - - +
358P GLY* 3.3 12.0 + - - -
327Q ASP* 3.4 24.5 + - - -
329Q GLU* 3.5 48.9 + - + +
330Q GLU* 2.5 42.4 + - - -
333Q GLU* 5.7 0.7 - - - +
336Q LEU* 4.3 1.4 - - - +
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Residues in contact with ARG 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352P ALA* 3.3 21.7 + - - +
353P ALA* 3.5 11.4 - - - +
354P LEU 3.1 0.2 - - - -
355P ARG* 1.3 79.4 - - - +
357P SER* 1.3 58.1 + - - +
358P GLY 3.2 1.0 + - - -
367P SER* 4.4 16.5 + - - +
329Q GLU* 4.0 15.4 + - - +
336Q LEU* 3.8 13.3 - - - +
340Q ASN* 4.0 2.1 + - - -
347Q PHE* 3.3 80.2 - - + +
348Q ASP* 4.4 12.3 + - - -
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Residues in contact with SER 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353P ALA 3.1 13.4 + - - -
354P LEU* 3.1 10.4 + - - -
356P ARG* 1.3 76.0 - - - +
358P GLY* 1.3 60.0 + - - +
360P SER* 2.8 44.6 + - - -
363P GLY 3.9 1.3 - - - -
364P ALA* 3.7 10.2 + - - -
367P SER* 5.8 0.9 - - - -
336Q LEU 4.3 2.0 - - - -
337Q ARG* 3.7 4.7 - - - -
340Q ASN* 3.4 37.5 + - - +
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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