Contacts of the helix formed by residues 360 - 369 (chain H) 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 SER 360 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354H LEU* 4.2 0.7 - - - -
357H SER* 2.8 34.3 + - - -
358H GLY 3.4 1.4 + - - -
359H GLY* 1.3 74.3 - - - +
361H VAL* 1.3 65.7 + - - +
362H GLN* 3.4 10.2 + - - +
363H GLY* 3.0 16.2 + - - -
364H ALA* 2.9 12.3 + - - +
337I ARG* 3.7 11.8 - - - +
340I ASN* 3.7 20.8 + - - +
341I ASP* 4.0 16.8 + - - -
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Residues in contact with VAL 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H HIS* 5.6 0.7 - - - +
335H GLN* 3.6 30.3 - - + +
338H GLN* 3.5 45.3 - - + +
339H LEU* 4.3 19.3 - - + -
342H MET* 5.4 5.2 - - - -
354H LEU* 4.4 6.5 - - - -
359H GLY 3.3 2.0 + - - -
360H SER* 1.3 70.5 - - - +
362H GLN* 1.3 67.8 + - - +
364H ALA* 3.0 3.0 + - - +
365H LEU* 2.8 31.8 + - + +
337I ARG* 5.2 0.2 - - - +
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Residues in contact with GLN 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360H SER* 3.6 7.9 - - - +
361H VAL* 1.3 81.7 - - - +
363H GLY* 1.3 60.9 + - - +
365H LEU* 3.4 19.9 - - - +
366H ASP* 3.5 9.0 + - - +
340I ASN 4.4 8.0 + - - +
341I ASP* 4.6 10.1 + - - +
343I GLY* 5.1 3.8 - - - +
345I PHE* 3.5 27.0 - - + -
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Residues in contact with GLY 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H SER* 3.9 5.8 - - - -
360H SER* 3.0 13.6 + - - -
362H GLN* 1.3 74.1 - - - +
364H ALA* 1.3 63.6 + - - +
365H LEU 3.2 1.3 - - - -
366H ASP* 3.2 4.9 + - - +
367H SER* 3.1 22.7 + - - -
340I ASN* 3.5 22.6 - - - +
345I PHE* 3.5 16.9 - - - +
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Residues in contact with ALA 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H LEU* 4.6 9.0 - - + -
353H ALA* 3.8 31.2 - - + +
354H LEU* 3.7 24.0 - - + -
357H SER* 3.7 1.4 - - - -
360H SER 2.9 19.9 + - - +
361H VAL* 3.7 2.9 - - - +
363H GLY* 1.3 72.5 - - - +
365H LEU* 1.3 51.8 + - - +
367H SER* 3.2 4.5 + - - -
368H LEU* 2.8 41.0 + - - +
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Residues in contact with LEU 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H LEU* 4.4 10.0 - - + +
342H MET* 3.9 33.7 - - + -
344H PHE* 3.5 37.5 - - + -
361H VAL* 2.8 15.3 + - + +
362H GLN* 3.4 16.8 - - - +
364H ALA* 1.3 75.5 - - - +
366H ASP* 1.3 63.4 + - - +
368H LEU* 3.0 8.7 + - + +
369H LEU* 2.9 39.2 + - + +
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Residues in contact with ASP 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H GLN 3.5 6.0 + - - +
363H GLY 3.2 9.1 + - - +
365H LEU* 1.3 78.2 - - - +
367H SER* 1.3 58.4 + - - +
369H LEU* 3.2 16.0 + - - +
370H ASN* 2.8 37.4 + - - +
345I PHE* 3.3 45.2 - - + +
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Residues in contact with SER 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H ALA* 4.2 17.5 + - - -
356H ARG* 4.4 18.8 + - - +
357H SER* 5.9 0.9 - - - -
363H GLY 3.1 12.5 + - - -
364H ALA* 3.3 13.0 - - - -
366H ASP* 1.3 78.6 + - - +
368H LEU* 1.3 61.9 + - - +
370H ASN* 3.2 6.8 + - - +
371H GLY 3.1 35.8 + - - +
345I PHE 4.6 10.2 + - - -
347I PHE* 5.9 0.3 - - - +
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Residues in contact with LEU 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H LEU* 3.9 27.6 - - + -
344H PHE* 3.9 27.5 - - + -
349H ARG* 3.2 64.5 + - + +
350H ASN* 3.5 26.2 - - - +
353H ALA* 3.9 9.4 - - + -
364H ALA 2.8 23.8 + - - +
365H LEU* 3.0 7.8 + - - +
367H SER* 1.3 73.9 - - - +
369H LEU* 1.3 62.9 + - - +
370H ASN 3.4 0.7 + - - -
371H GLY 3.7 5.4 + - - -
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Residues in contact with LEU 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344H PHE* 3.5 28.9 - - + -
365H LEU* 2.9 35.8 + - + +
366H ASP* 3.2 8.9 + - - +
367H SER 3.2 0.6 - - - -
368H LEU* 1.3 78.9 - - - +
370H ASN* 1.3 65.5 + - - +
371H GLY 3.9 0.2 - - - -
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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
------------------------------------------------------------
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