Contacts of the helix formed by residues 1816 - 1820 (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 ASN1816 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1814J GLY 3.6 0.2 + - - -
1815J PRO* 1.3 89.5 + - - +
1817J LEU* 1.3 55.6 + - - +
1818J ASN* 3.0 14.1 - - - -
1819J LEU* 3.0 19.9 + - - +
1857J ASN* 2.9 12.3 + - - -
1960J CA2 3.4 31.2 - - + -
2063K VAL* 3.8 3.0 - - - +
2067K HIS* 2.7 28.4 + - - +
2089K ALA* 3.2 24.2 + - - +
2092K ASP* 3.5 15.0 + - + +
2093K ALA* 3.3 21.6 - - - +
2096K THR* 4.6 4.7 - - + +
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Residues in contact with LEU1817 (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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1813J ASN* 3.8 14.8 - - + +
1814J GLY 3.5 19.7 + - - +
1815J PRO 3.1 4.8 + - - +
1816J ASN* 1.3 73.0 - - - +
1818J ASN* 1.3 66.0 + - - +
1819J LEU 2.9 3.2 + - - -
1820J LEU* 3.1 25.1 + - + +
1833J LEU* 3.6 20.5 - - + +
1855J GLN* 4.5 0.7 - - + -
1879J ASN* 3.6 51.8 - - + +
1881J ALA* 4.0 3.6 - - + -
1907J ILE* 4.4 16.8 - - + -
1938J TYR* 4.1 1.6 - - - +
1960J CA2 3.8 36.6 - - + +
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Residues in contact with ASN1818 (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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1816J ASN* 3.1 21.3 - - - -
1817J LEU* 1.3 80.5 - - - +
1819J LEU* 1.3 68.3 + - - +
1820J LEU 3.3 2.9 + - - +
1822J GLN* 4.4 4.3 - - - +
1833J LEU* 4.3 15.3 + - + +
1855J GLN* 3.5 29.5 + - - +
1857J ASN* 3.6 5.4 - - - +
2067K HIS* 3.3 29.3 + - - +
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Residues in contact with LEU1819 (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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1816J ASN 3.0 10.4 + - - +
1817J LEU 2.9 1.4 - - - -
1818J ASN* 1.3 94.9 - - - +
1820J LEU* 1.3 68.3 + - - +
1822J GLN* 3.1 49.1 + - + +
1960J CA2 3.3 16.3 - - + -
2067K HIS* 3.8 26.7 - - + +
2070K ARG* 3.9 23.1 - - - +
2071K LEU* 6.4 0.9 - - + -
2096K THR* 3.7 28.3 - - + +
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Residues in contact with LEU1820 (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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1817J LEU* 3.1 23.2 + - + +
1818J ASN 3.3 2.5 - - - +
1819J LEU* 1.3 79.3 - - - +
1821J GLY* 1.3 61.9 + - - +
1822J GLN* 3.6 5.5 + - - +
1828J TYR* 3.6 30.7 - - + +
1831J ASP 3.5 14.6 - - - +
1832J THR* 3.4 21.1 - - - +
1833J LEU* 4.0 17.2 + - + +
1836J VAL* 3.9 24.7 - - + -
1907J ILE* 3.6 35.0 - - + -
1935J VAL* 4.4 4.0 - - + -
1960J CA2 3.8 17.6 - - + -
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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