Contacts of the helix formed by residues 235 - 243 (chain A) in PDB entry 4BNR
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 HIS 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 4.0 16.2 + - - -
101A ASN* 3.2 39.8 - - + -
103A ILE* 4.0 26.5 - - + -
179A SER* 4.3 11.1 + - - -
230A THR* 3.6 27.5 - - + +
231A GLU 3.4 24.1 + - - -
232A VAL* 2.7 8.7 + - - +
234A TYR* 1.3 90.7 + - + +
236A VAL* 1.3 58.8 + - - +
237A ASP 3.4 2.2 - - - -
238A TRP* 3.2 12.6 + - + +
239A ILE* 2.9 31.9 + - + +
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Residues in contact with VAL 236 (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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123A LEU* 4.4 7.8 - - + +
124A PRO* 3.3 36.8 - - + +
126A GLN* 3.1 26.4 + - + +
232A VAL* 3.2 17.0 + - + +
233A SER* 3.8 14.4 - - - -
235A HIS* 1.3 76.7 - - - +
237A ASP* 1.3 65.1 + - - +
239A ILE* 3.3 7.9 + - - +
240A LYS* 3.0 53.3 + - + +
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Residues in contact with ASP 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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126A GLN* 2.9 41.5 + - - +
236A VAL* 1.3 76.9 - - - +
238A TRP* 1.3 58.5 + - - +
240A LYS* 3.8 11.2 + - - +
241A ALA* 2.9 31.4 + - - +
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Residues in contact with TRP 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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89A ILE* 3.5 31.2 - - + -
90A LEU 4.2 0.2 - - - -
91A HIS* 3.3 52.9 - + - +
92A GLU* 2.8 31.3 + - - -
103A ILE* 4.1 28.0 - - + -
104A SER* 4.1 2.9 - - - -
105A LEU* 3.7 30.7 - - + -
235A HIS* 3.2 17.2 + - + +
237A ASP* 1.3 78.5 - - - +
239A ILE* 1.3 84.1 + - + +
241A ALA* 3.2 3.4 + - - -
242A ASN* 2.8 51.3 + - - +
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Residues in contact with ILE 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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47A TYR* 3.9 24.0 - - + -
53A ILE* 3.9 19.5 - - + -
103A ILE* 3.9 20.6 - - + -
105A LEU* 4.2 14.8 - - + +
123A LEU* 3.8 31.9 - - + -
232A VAL* 4.2 13.9 - - + -
235A HIS 2.9 22.5 + - - +
236A VAL 3.3 3.8 + - - +
238A TRP* 1.3 92.9 - - + +
240A LYS* 1.3 59.7 + - - +
242A ASN 3.1 0.7 + - - -
243A ALA* 2.8 35.2 + - - +
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Residues in contact with LYS 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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47A TYR* 3.9 21.3 - - - +
123A LEU* 4.6 11.9 - - + -
124A PRO 5.3 1.4 + - - -
125A GLU* 5.9 2.0 - - - +
126A GLN 5.8 0.6 - - - +
236A VAL* 3.0 41.1 + - + +
237A ASP* 3.9 11.2 + - - +
239A ILE* 1.3 76.4 - - - +
241A ALA* 1.3 61.1 + - - +
243A ALA* 4.1 2.6 + - - +
244A VAL* 3.4 19.1 - - - +
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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 ASP 2.9 19.3 + - - +
238A TRP* 3.7 5.6 - - - +
239A ILE 3.2 0.2 - - - -
240A LYS* 1.3 78.9 - - - +
242A ASN* 1.3 65.0 + - - +
244A VAL* 3.8 16.2 - - - +
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Residues in contact with ASN 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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51A TYR* 3.7 2.6 + - - -
89A ILE* 3.6 38.4 - - + +
92A GLU* 4.7 5.2 + - - +
105A LEU* 3.5 20.2 - - + -
238A TRP* 2.8 56.8 + - + +
241A ALA* 1.3 87.1 - - - +
243A ALA* 1.3 59.5 + - - +
244A VAL* 3.0 14.5 + - - +
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Residues in contact with ALA 243 (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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47A TYR* 3.5 36.6 + - + -
48A ASN* 4.4 4.5 + - - -
51A TYR* 3.4 31.2 - - + -
105A LEU* 3.7 9.4 - - + +
239A ILE* 2.8 20.0 + - + +
240A LYS 4.4 2.0 - - - +
241A ALA 3.7 0.2 - - - -
242A ASN* 1.3 74.3 - - - +
244A VAL* 1.3 61.3 + - - +
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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