Contacts of the helix formed by residues 2314 - 2319 (chain L) 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 GLU2314 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1924J GLN* 5.1 2.7 - - - +
2313L ARG* 1.3 83.1 + - - +
2315L PRO* 1.3 76.5 - - + +
2316L PHE* 3.7 29.2 - - + -
2317L ARG* 2.9 43.7 + - + +
2318L HIS* 3.1 9.7 - - - -
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Residues in contact with PRO2315 (chain L).
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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2313L ARG 3.5 2.4 - - - +
2314L GLU* 1.3 86.8 - - + +
2316L PHE* 1.3 63.4 + - + +
2318L HIS* 3.0 35.2 + - + +
2319L HIS* 3.9 10.7 + - - -
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Residues in contact with PHE2316 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1888J VAL* 3.9 23.6 - - + -
1891J LEU* 3.8 7.9 - - + -
1921J TYR* 4.0 28.9 - + + +
1924J GLN* 3.1 33.4 - - - -
2285L HIS* 3.9 17.5 + + + +
2314L GLU* 3.7 21.5 - - + -
2315L PRO* 1.3 81.0 - - + +
2317L ARG* 1.3 106.9 + - + +
2318L HIS 3.3 0.9 + - - -
2319L HIS* 3.9 13.1 + - - +
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Residues in contact with ARG2317 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1888J VAL* 3.9 10.1 - - - +
1891J LEU* 3.8 11.3 - - - +
1892J ASP* 2.9 23.1 + - - -
1895J ASN* 4.3 9.1 - - - +
2285L HIS* 3.1 26.8 + - + +
2310L ILE* 3.3 24.8 - - + +
2313L ARG* 3.9 29.7 - - + +
2314L GLU* 2.9 40.1 + - - +
2316L PHE* 1.3 107.9 - - + +
2318L HIS* 1.3 62.0 + - - +
2319L HIS 3.2 0.9 - - - -
2360L CA2 3.1 40.5 + - - +
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Residues in contact with HIS2318 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911E HIS* 5.5 0.3 - - - -
924E GLN* 6.3 1.1 - - + -
2419E GOL 3.4 38.2 + - - +
2422E GOL 4.1 6.2 + - - -
2310L ILE* 3.2 22.6 - - - +
2311L HIS* 3.3 38.8 + - - -
2313L ARG 2.9 21.1 + - - -
2314L GLU 3.1 16.2 + - - -
2315L PRO* 3.0 23.9 + - + +
2317L ARG* 1.3 78.5 - - - +
2319L HIS* 1.3 66.7 + - + +
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Residues in contact with HIS2319 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2419E GOL 4.2 16.1 + - - -
2422E GOL 3.3 33.8 - - - -
2285L HIS* 2.8 38.7 + - - +
2310L ILE* 5.2 0.2 - - - -
2315L PRO 3.9 16.8 + - - -
2316L PHE* 3.9 8.9 + - - +
2317L ARG 3.2 0.6 - - - -
2318L HIS* 1.3 82.6 - - + +
2320L SER* 1.3 58.2 - - - +
2321L TYR* 6.4 0.2 - - - -
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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