Contacts of the helix formed by residues 1659 - 1664 (chain C) in PDB entry 5EK0
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 PHE1659 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1655C PHE 3.2 9.0 + - - +
1656C GLY 3.9 4.7 - - - -
1657C GLU 3.4 0.2 - - - -
1658C ARG* 1.4 88.3 - - + +
1660C PRO* 1.4 58.8 - - - +
1661C GLU* 3.3 16.6 - - - +
1662C TRP* 3.3 36.2 + + + -
1663C PHE* 2.8 40.1 + - + +
1689C PRO* 3.3 30.1 - - + -
1690C LEU* 3.5 27.6 - - + -
1693C VAL* 3.5 36.1 - - + -
1694C TYR* 3.8 11.9 - + - -
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Residues in contact with PRO1660 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526B GLU* 3.6 33.2 - - + +
1656C GLY 3.5 9.4 - - - +
1657C GLU 3.3 16.2 - - - +
1658C ARG 3.4 7.6 - - - +
1659C PHE* 1.4 88.3 - - - +
1661C GLU* 1.4 66.8 + - - +
1662C TRP 3.1 0.6 + - - -
1664C GLY* 3.0 19.1 + - - +
1668C GLU* 3.0 22.3 - - - +
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Residues in contact with GLU1661 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1658C ARG 4.1 2.9 - - - +
1659C PHE* 3.6 26.1 - - - -
1660C PRO* 1.4 93.0 - - - +
1662C TRP* 1.3 89.0 + - + +
1668C GLU* 3.3 15.9 - - - +
1688D ARG* 4.0 5.5 + - - -
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Residues in contact with TRP1662 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1659C PHE* 3.3 39.3 + + - +
1660C PRO 3.1 0.2 - - - -
1661C GLU* 1.3 102.4 - - + +
1663C PHE* 1.4 82.3 + + + +
1668C GLU* 2.9 22.0 - - - +
1672C THR* 2.8 29.4 + - + +
1685C GLY 3.2 26.9 - - - -
1686C ILE* 3.6 28.7 - - + +
1689C PRO* 3.9 16.8 - - + -
1690C LEU* 4.5 0.7 - - + -
1684D MET* 4.5 13.1 - - + +
1688D ARG* 3.3 30.2 + - - +
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Residues in contact with PHE1663 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1651C ALA* 3.7 18.8 - - + +
1652C THR* 3.4 10.0 - - - +
1655C PHE* 3.8 16.8 - + + -
1656C GLY* 3.2 26.8 - - - +
1659C PHE* 2.8 20.5 + - + +
1662C TRP* 1.4 93.9 - + + +
1664C GLY* 1.3 63.8 + - - +
1665C THR 3.8 4.3 - - - -
1668C GLU* 4.1 1.3 - - - -
1669C SER* 3.6 26.7 - - - +
1672C THR* 3.6 33.0 - - + -
1673C LEU* 5.0 3.1 - - + -
1686C ILE* 3.9 4.7 - - + -
1690C LEU* 3.8 23.3 - - + -
1701C PHE* 3.6 30.5 - + - -
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Residues in contact with GLY1664 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1525B LYS* 4.1 3.5 - - - -
1526B GLU* 3.7 34.5 + - - +
1652C THR* 3.5 9.9 - - - +
1656C GLY* 4.4 1.7 - - - -
1660C PRO* 3.0 29.2 + - - +
1663C PHE* 1.3 79.8 - - - +
1665C THR* 1.3 58.0 + - - +
1668C GLU* 3.8 6.1 - - - +
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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