Contacts of the helix formed by residues 236 - 242 (chain A) in PDB entry 1B3U
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 GLN 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU 3.9 1.0 + - - -
235A PRO* 1.3 71.4 - - - +
237A GLU* 1.3 73.9 + - + +
238A ASP 3.2 1.2 + - - -
239A LEU* 3.2 31.6 + - - +
240A GLU* 4.6 1.9 + - - +
272A ALA 4.5 2.1 - - - +
273A VAL 2.9 20.9 + - - +
274A GLY* 3.5 24.9 - - - -
275A PRO* 4.6 4.9 - - - +
276A GLU* 5.3 10.7 + - - +
277A ILE* 4.7 6.3 - - - +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A PRO* 3.0 17.7 + - + +
236A GLN* 1.3 93.6 + - + +
238A ASP* 1.3 66.0 + - - +
239A LEU 3.5 0.4 + - - -
240A GLU* 4.8 5.6 + - - +
241A ALA* 5.2 3.8 + - - +
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 3.0 30.0 + - - -
234A LEU* 4.6 4.7 - - + -
235A PRO* 2.8 37.4 + - + +
237A GLU* 1.3 83.7 - - - +
239A LEU* 1.3 61.5 + - - +
240A GLU 3.5 0.4 - - - -
241A ALA* 3.3 6.5 + - - +
242A LEU* 2.8 49.4 + - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ALA* 4.0 33.9 - - + +
234A LEU* 4.1 16.4 - - + +
235A PRO 3.7 4.9 - - - +
236A GLN* 3.2 40.3 + - - +
238A ASP* 1.3 76.0 - - - +
240A GLU* 1.3 61.5 + - - +
243A VAL* 2.7 42.1 + - + +
244A MET* 3.0 10.4 + - + -
272A ALA 3.8 14.6 - - - +
273A VAL* 3.8 22.4 - - + +
277A ILE* 4.0 10.3 - - + -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A GLN 4.6 2.0 + - - +
237A GLU 4.8 4.9 + - - +
238A ASP 3.5 0.6 - - - -
239A LEU* 1.3 78.5 - - - +
241A ALA* 1.3 58.3 + - + +
244A MET* 3.7 12.9 - - - +
245A PRO* 3.2 23.6 - - - +
248A ARG* 2.9 40.1 + - - -
277A ILE* 4.5 12.8 - - + +
280A THR* 6.1 0.2 - - - +
281A ASP* 4.0 5.2 - - - +
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLU 5.2 2.2 + - - +
238A ASP* 3.3 8.7 + - - +
239A LEU 3.1 0.4 - - - -
240A GLU* 1.3 80.8 - - + +
242A LEU* 1.3 70.4 + - + +
245A PRO* 4.2 11.4 - - - +
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 4.1 39.0 - - + +
205A ILE* 3.8 46.2 - - + +
208A PHE* 4.6 5.9 - - - -
234A LEU* 4.2 11.7 - - + -
238A ASP* 2.8 44.3 + - + +
241A ALA* 1.3 84.4 - - + +
243A VAL* 1.3 62.3 + - - +
245A PRO* 4.5 2.7 - - - -
246A THR* 5.0 3.5 + - - -
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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