Contacts of the helix formed by residues 346 - 357 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D ASP* 4.9 3.1 + - - +
345I PHE* 1.3 75.0 - - - +
347I PHE* 1.3 58.9 + - - +
348I ASP* 3.1 11.4 + - - +
349I ARG* 2.8 57.2 + - + +
350I ASN* 2.9 33.0 + - - +
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Residues in contact with PHE 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D ARG* 3.2 74.5 - - + +
328I PRO* 4.8 5.6 - - + -
329I GLU* 3.2 48.2 - - + -
336I LEU* 3.9 8.1 - - + -
345I PHE 3.0 8.1 + - - +
346I ASP* 1.3 71.1 + - - +
348I ASP* 1.3 80.6 + - - +
350I ASN* 3.2 7.5 + - - +
351I VAL* 2.8 61.8 + - + +
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Residues in contact with ASP 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ARG* 4.5 10.5 + - - -
346I ASP* 3.1 7.2 + - - +
347I PHE* 1.3 96.4 - - - +
349I ARG* 1.3 59.5 + - + +
351I VAL* 4.1 3.9 - - - +
352I ALA* 3.0 30.3 + - - +
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Residues in contact with ARG 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346I ASP* 2.8 36.9 + - - +
348I ASP* 1.3 76.2 - - + +
350I ASN* 1.3 65.7 + - - +
352I ALA* 4.1 5.6 - - - +
353I ALA* 3.3 22.5 + - - +
356I ARG* 5.5 1.0 + - - -
367I SER 5.7 0.2 + - - -
368I LEU* 3.3 41.5 + - - +
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Residues in contact with ASN 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D ARG 5.1 0.9 - - - +
336I LEU* 3.7 14.1 - - + +
339I LEU* 3.5 36.7 + - + +
340I ASN* 4.0 13.3 + - - -
345I PHE 3.8 15.1 + - - +
346I ASP 2.9 29.8 + - - +
347I PHE* 3.5 6.0 + - - +
349I ARG* 1.3 78.2 - - - +
351I VAL* 1.3 53.9 + - - +
353I ALA* 3.3 4.9 + - - +
354I LEU* 2.7 41.8 + - - +
368I LEU* 3.6 19.2 - - - +
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Residues in contact with VAL 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I PRO* 3.9 31.2 - - + -
332I TYR* 4.3 6.2 - - + -
336I LEU* 4.2 9.4 - - + -
347I PHE* 2.8 57.0 + - + +
348I ASP* 4.1 5.8 - - - +
350I ASN* 1.3 68.9 - - - +
352I ALA* 1.3 61.4 + - - +
354I LEU* 3.8 6.8 - - - +
355I ARG* 2.9 41.5 + - - +
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Residues in contact with ALA 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348I ASP 3.0 20.6 + - - +
349I ARG* 4.1 6.7 - - - +
351I VAL* 1.3 74.9 - - - +
353I ALA* 1.3 59.1 + - - +
355I ARG* 3.5 7.7 + - - +
356I ARG* 3.0 46.8 + - - +
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Residues in contact with ALA 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ARG 3.3 16.6 + - - +
350I ASN 3.3 5.2 + - - +
352I ALA* 1.3 78.6 - - - +
354I LEU* 1.3 57.9 + - - +
356I ARG* 3.7 17.6 + - - +
357I SER* 2.9 32.0 + - - -
364I ALA* 3.7 17.5 - - + +
367I SER* 3.6 21.7 + - - +
368I LEU* 4.2 10.5 - - + -
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Residues in contact with LEU 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332I TYR* 3.6 43.0 + - + -
335I GLN* 3.5 26.2 - - + -
336I LEU* 3.9 13.9 - - + -
339I LEU* 3.7 19.3 - - + -
350I ASN 2.7 24.6 + - - +
351I VAL 4.0 0.7 - - - +
353I ALA* 1.3 70.0 - - - +
355I ARG* 1.3 63.1 + - - +
357I SER* 3.4 2.0 - - - -
358I GLY 3.2 1.6 + - - -
359I GLY* 2.6 48.4 + - - +
360I SER 3.8 5.6 - - - +
361I VAL* 4.4 2.0 - - - -
364I ALA* 3.6 20.0 - - + -
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Residues in contact with ARG 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I PRO* 6.4 0.2 - - - -
332I TYR* 3.7 19.5 - - + +
351I VAL* 2.9 30.5 + - + +
352I ALA* 3.7 8.3 - - - +
354I LEU* 1.3 75.7 - - - +
356I ARG* 1.3 64.1 + - + +
358I GLY* 3.3 12.0 + - - -
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Residues in contact with ARG 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349I ARG 5.5 0.8 + - - -
352I ALA* 3.0 33.0 + - + +
353I ALA* 3.7 17.4 + - - +
354I LEU 3.3 0.2 - - - -
355I ARG* 1.3 78.8 - - + +
357I SER* 1.3 58.0 + - - +
358I GLY 3.4 0.6 + - - -
367I SER* 3.9 27.1 + - - -
368I LEU* 6.3 0.8 - - - +
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Residues in contact with SER 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I ALA 2.9 20.7 + - - -
354I LEU* 3.4 10.4 + - - -
355I ARG 3.3 0.2 - - - -
356I ARG* 1.3 76.1 - - - +
358I GLY* 1.3 59.9 + - - +
360I SER* 2.8 43.5 + - - -
363I GLY* 3.8 10.8 - - - -
364I ALA 3.5 14.1 + - - -
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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