Contacts of the helix formed by residues 1710 - 1718 (chain r) 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 LYS1710 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1666r THR* 5.8 4.9 - - - -
1678r ASP* 6.2 4.0 - - + -
1706r CYS* 4.5 16.7 - - + +
1707r GLN* 3.2 15.2 + - + +
1708r GLY 3.1 1.0 - - - -
1709r SER* 1.3 80.5 - - - +
1711r LYS* 1.3 63.9 + - - +
1712r ASP 3.6 0.4 - - - -
1713r PHE* 3.8 10.9 + - + +
1714r PHE* 3.6 18.5 + - - +
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Residues in contact with LYS1711 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1527r ILE* 5.2 10.2 - - + +
1528r GLN 6.0 0.4 - - - -
1529r GLY* 4.8 13.5 - - - +
1706r CYS* 5.5 3.6 - - - -
1707r GLN 3.3 8.1 + - - +
1708r GLY* 3.1 17.1 + - - +
1710r LYS* 1.3 76.9 - - - +
1712r ASP* 1.3 68.7 + - - +
1713r PHE 3.2 0.3 + - - -
1714r PHE* 3.2 6.5 + - - +
1715r LYS* 3.0 20.7 + - - +
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Residues in contact with ASP1712 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1708r GLY 4.6 0.2 + - - -
1709r SER 4.2 6.2 + - - +
1710r LYS 3.6 0.2 - - - -
1711r LYS* 1.3 80.1 - - - +
1713r PHE* 1.3 64.3 + - - +
1715r LYS* 3.1 9.3 + - - +
1716r LYS* 2.9 24.4 + - - +
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Residues in contact with PHE1713 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255r PHE* 5.5 12.3 - - + +
1709r SER 4.8 2.3 + - - +
1710r LYS* 3.8 15.4 + - + +
1711r LYS 3.1 0.6 - - - -
1712r ASP* 1.3 80.4 - - - +
1714r PHE* 1.3 58.3 + - - +
1716r LYS* 3.3 6.0 + - - +
1717r PHE* 3.0 31.1 + - - +
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Residues in contact with PHE1714 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1527r ILE* 5.2 10.1 - - + -
1704r ILE* 6.0 5.8 - - + -
1710r LYS 3.6 9.4 + - - +
1711r LYS* 3.2 7.7 + - - +
1713r PHE* 1.3 77.1 - - - +
1715r LYS* 1.3 64.7 + - - +
1717r PHE* 4.5 1.1 - - - +
1718r LEU* 3.1 35.6 + - + +
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Residues in contact with LYS1715 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1711r LYS 3.0 13.6 + - - +
1712r ASP* 3.1 13.9 + - - +
1714r PHE* 1.3 77.4 - - - +
1716r LYS* 1.3 61.0 + - - +
1719r TYR* 4.6 11.8 + - - +
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Residues in contact with LYS1716 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1712r ASP 2.9 11.9 + - - +
1713r PHE* 3.6 9.2 - - - +
1715r LYS* 1.3 81.0 - - - +
1717r PHE* 1.3 63.1 + - + +
1718r LEU 3.6 0.4 + - - -
1719r TYR* 4.1 1.7 + - - +
1720r GLU* 3.7 22.9 + - - +
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Residues in contact with PHE1717 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713r PHE 3.0 16.7 + - - +
1714r PHE* 5.3 0.9 - - - -
1716r LYS* 1.3 75.7 - - + +
1718r LEU* 1.3 62.6 + - - +
1719r TYR 3.4 1.3 - - - -
1720r GLU* 3.8 15.5 - - - +
1722r LEU* 5.6 5.4 - - - +
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Residues in contact with LEU1718 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1516r PRO* 4.7 7.8 - - - +
1714r PHE* 3.1 21.3 + - + +
1717r PHE* 1.3 78.2 - - - +
1719r TYR* 1.3 61.7 + - - +
1720r GLU 4.3 1.9 - - - +
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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