Contacts of the helix formed by residues 1899 - 1908 (chain A) in PDB entry 6FF7
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 VAL1899 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5223 LEU* 5.0 13.9 - - + -
1895A ALA 3.9 4.2 + - - +
1896A CYS* 3.8 13.1 + - - +
1897A LEU 3.5 3.5 - - - +
1898A LYS* 1.3 82.2 - - - +
1900A GLU* 1.3 60.6 + - - +
1901A LYS 3.6 3.1 - - - +
1902A PHE* 3.9 4.6 + - + +
1903A GLY* 3.1 22.7 + - - -
1967A ILE* 6.5 0.7 - - + -
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Residues in contact with GLU1900 (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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5213 PRO* 4.8 18.2 - - + -
5223 LEU* 5.4 5.4 - - + +
1898A LYS 4.0 0.9 + - - +
1899A VAL* 1.3 72.9 - - - +
1901A LYS* 1.3 61.9 + - - +
1902A PHE 3.3 0.7 - - - -
1903A GLY* 4.2 1.8 - - - +
1904A ASP* 2.9 32.2 + - - +
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Residues in contact with LYS1901 (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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1899A VAL* 3.6 1.8 - - + +
1900A GLU* 1.3 79.5 - - - +
1902A PHE* 1.3 60.0 + - - +
1904A ASP* 5.2 1.2 - - - +
1905A LEU* 3.5 19.6 + - - +
1967A ILE* 5.5 11.2 - - + -
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Residues in contact with PHE1902 (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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1896A CYS* 3.3 27.4 - - + +
1897A LEU* 5.1 2.0 - - - -
1899A VAL* 3.9 6.6 + - + +
1901A LYS* 1.3 78.4 - - - +
1903A GLY* 1.3 59.4 + - - +
1905A LEU* 3.4 4.8 + - - +
1906A ILE* 2.9 32.1 + - - +
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Residues in contact with GLY1903 (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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1897A LEU* 4.4 11.7 - - - -
1899A VAL 3.1 16.8 + - - -
1900A GLU* 3.1 6.0 + - - -
1902A PHE* 1.3 77.0 - - - +
1904A ASP* 1.3 63.5 + - - +
1906A ILE* 3.6 4.1 + - - +
1907A LEU* 3.2 26.3 + - - +
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Residues in contact with ASP1904 (chain A).
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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1900A GLU 2.9 15.4 + - - +
1901A LYS* 5.2 1.6 - - - +
1903A GLY* 1.3 76.8 - - - +
1905A LEU* 1.3 61.2 + - - +
1907A LEU* 4.0 3.6 - - - +
1908A LYS* 3.3 27.8 + - + +
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Residues in contact with LEU1905 (chain A).
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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1901A LYS 3.5 19.9 + - - +
1902A PHE* 3.4 5.8 + - - +
1903A GLY 3.2 0.4 - - - -
1904A ASP* 1.3 79.0 - - - +
1906A ILE* 1.3 63.1 + - - +
1908A LYS 3.6 14.7 - - - +
1909A ALA* 4.0 9.9 - - - +
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Residues in contact with ILE1906 (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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1804A ASN* 4.2 23.6 - - - +
1805A GLY 5.7 5.0 - - - +
1806A ALA* 5.3 13.9 - - + -
1821A ILE* 6.5 1.1 - - - -
1897A LEU* 6.4 2.0 - - + -
1902A PHE 2.9 17.7 + - - +
1903A GLY* 4.3 3.8 - - - +
1905A LEU* 1.3 77.7 - - - +
1907A LEU* 1.3 61.0 + - - +
1908A LYS 5.0 0.2 - - - -
1909A ALA* 4.9 5.1 - - - +
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Residues in contact with LEU1907 (chain A).
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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1804A ASN* 5.8 2.5 - - - +
1903A GLY 3.2 17.9 + - - +
1904A ASP* 4.6 3.8 - - - +
1906A ILE* 1.3 80.1 - - - +
1908A LYS* 1.3 58.9 + - + +
1909A ALA 3.8 2.5 + - - +
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Residues in contact with LYS1908 (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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1904A ASP* 3.3 17.9 + - + +
1905A LEU* 3.6 8.5 - - - +
1907A LEU* 1.3 76.6 - - + +
1909A ALA* 1.3 61.2 + - - +
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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