Contacts of the helix formed by residues 1882 - 1887 (chain J) in PDB entry 2BT4
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 ALA1882 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1815J PRO* 4.1 4.5 - - + +
1816J ASN* 5.3 0.2 - - - +
1881J ALA* 1.3 78.6 - - - +
1883J TYR* 1.3 57.4 + - + +
1884J SER 3.0 0.9 - - - -
1885J HIS* 3.0 31.0 + - - +
1886J THR* 3.6 9.1 + - - +
1960J CA2 3.4 11.9 + - - -
2088K VAL* 3.6 6.8 - - + +
2089K ALA* 3.3 44.0 - - + +
2092K ASP* 3.4 13.9 + - + +
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Residues in contact with TYR1883 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1815J PRO* 3.5 28.0 - - + -
1857J ASN 2.6 25.6 + - - -
1858J HIS* 3.9 2.2 - - - -
1859J GLU* 3.5 34.5 + - + -
1862J LEU* 3.7 15.9 - - + -
1880J PRO* 3.1 10.5 + - + +
1881J ALA 2.9 1.0 + - - -
1882J ALA* 1.3 75.4 - - + +
1884J SER* 1.3 65.2 + - - +
1885J HIS 3.0 0.7 - - - -
1886J THR* 3.7 16.4 - - - -
1887J SER* 2.9 37.5 + - - +
1890J ILE* 4.0 11.0 - - + -
1922J VAL* 5.0 2.6 - - - +
2059K GLU* 3.4 42.7 + - - +
2060K GLY* 4.3 1.7 + - - -
2063K VAL* 5.0 0.2 - - - +
2089K ALA* 3.8 12.8 - - + +
2408L TRS 4.1 5.6 - - - -
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Residues in contact with SER1884 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1880J PRO* 3.2 22.0 - - - +
1881J ALA 2.8 19.2 + - - -
1883J TYR* 1.3 79.8 - - - +
1885J HIS* 1.3 70.0 + - - +
1886J THR 3.8 0.2 + - - -
1904J GLU* 4.2 0.2 - - - -
1906J HIS* 2.9 34.0 - - - -
1920J SER* 3.3 12.8 + - - -
1921J TYR* 2.9 30.5 + - - +
1922J VAL* 4.0 3.8 + - - -
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Residues in contact with HIS1885 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1882J ALA* 3.0 25.9 + - - +
1884J SER* 1.3 91.0 - - - +
1886J THR* 1.3 65.0 + - + +
1906J HIS* 5.0 0.2 - + - -
1910J ILE* 4.5 12.8 - - + -
1916J PHE* 3.8 16.4 + + + +
1917J ARG* 3.1 34.4 + - + -
1919J HIS* 2.7 31.4 + - - +
1920J SER* 5.2 0.2 - - - -
1921J TYR* 3.5 17.1 - - - -
1960J CA2 2.9 31.4 + - - -
2088K VAL* 4.4 16.2 - - + -
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Residues in contact with THR1886 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1882J ALA* 4.0 4.7 - - - +
1883J TYR* 3.3 17.4 + - - -
1885J HIS* 1.3 84.3 - - + +
1887J SER* 1.3 59.5 + - - +
1888J VAL 3.3 6.6 + - - -
1921J TYR* 3.9 8.8 - - - -
2086K THR 3.4 21.8 - - - +
2088K VAL* 3.8 27.4 - - + +
2089K ALA 5.6 0.6 + - - +
2121K TYR* 5.4 2.9 - - + +
2286L THR* 3.5 12.5 - - - +
2408L TRS 2.7 42.6 + - - -
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Residues in contact with SER1887 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1859J GLU* 2.7 27.8 + - - -
1883J TYR* 2.9 31.9 + - - +
1885J HIS 3.9 0.2 - - - -
1886J THR* 1.3 75.7 + - - +
1888J VAL* 1.3 60.2 + - - +
1889J ALA 3.5 0.3 + - - -
1890J ILE* 2.8 38.4 + - - +
1891J LEU 3.4 13.5 + - - -
1921J TYR* 3.9 15.5 - - - +
1922J VAL* 5.2 1.2 - - - +
2408L TRS 3.8 2.9 - - - -
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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