Contacts of the helix formed by residues 327 - 332 (chain D) 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 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D PRO* 1.3 71.8 - - - +
329D GLU* 3.5 20.0 + - - +
330D GLU* 3.0 55.0 + - - +
331D ARG* 3.0 28.1 + - - +
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Residues in contact with PRO 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ASP* 1.3 86.9 - - + +
329D GLU* 1.3 60.0 + - + +
331D ARG* 3.7 5.8 - - + -
332D TYR* 2.7 57.4 + - + +
336D LEU* 4.0 3.4 - - - +
347D PHE* 4.0 19.5 - - + -
351D VAL* 3.9 24.5 - - + -
355D ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 329 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352C ALA 4.4 1.0 - - - +
355C ARG* 3.4 52.0 - - + +
356C ARG* 3.2 27.9 + - - +
327D ASP* 3.3 17.1 - - - +
328D PRO* 1.3 78.4 - - + +
330D GLU* 1.3 60.5 + - - +
332D TYR 4.1 0.3 - - - -
333D GLU* 3.3 26.5 + - - +
336D LEU* 4.0 9.0 - - - +
347D PHE* 3.6 23.9 - - + -
342H MET* 6.1 1.4 - - - +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C LEU* 5.5 16.7 + - + +
355C ARG* 5.1 12.3 - - - +
327D ASP* 3.0 36.0 + - - +
329D GLU* 1.3 75.7 - - + +
331D ARG* 1.3 66.8 + - - +
332D TYR 3.3 0.5 + - - -
333D GLU* 3.3 18.9 + - - +
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Residues in contact with ARG 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ASP 3.0 16.1 + - - +
328D PRO* 4.0 6.3 - - + -
330D GLU* 1.3 83.0 - - - +
332D TYR* 1.3 99.6 + - + +
333D GLU 3.5 0.9 + - - -
334D HIS* 5.0 6.2 - - - -
335D GLN* 3.9 7.3 + - - +
355D ARG* 4.4 17.2 - - - +
330I GLU* 5.8 3.6 - - - +
333I GLU* 2.8 31.2 + - - +
337I ARG* 4.3 9.6 + - - +
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Residues in contact with TYR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PRO* 2.7 44.3 + - + +
329D GLU 4.1 0.4 - - - -
331D ARG* 1.3 110.3 + - + +
333D GLU* 1.3 54.0 + - - +
335D GLN* 3.1 28.7 + - - +
336D LEU* 2.8 37.9 + - + +
351D VAL* 4.4 8.1 - - + -
354D LEU* 4.0 31.3 + - + -
355D ARG* 3.7 37.6 - - + +
358D GLY 5.3 0.5 - - - -
359D GLY* 3.9 20.1 + - - -
333I GLU* 5.1 3.3 - - - +
337I ARG* 4.0 12.4 + - - -
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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