Contacts of the helix formed by residues 1606 - 1615 (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 ASP1606 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1604r LEU* 4.3 8.3 - - + +
1605r SER* 1.3 79.5 - - - +
1607r SER* 1.3 65.3 + - - +
1608r THR* 4.9 0.7 - - - +
1609r LEU* 3.7 23.6 - - + +
1610r LYS* 3.6 16.1 + - - +
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Residues in contact with SER1607 (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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1605r SER 3.2 6.9 + - - -
1606r ASP* 1.3 70.7 - - - +
1608r THR* 1.3 65.8 + - - +
1609r LEU 3.3 0.2 - - - -
1610r LYS* 3.3 20.1 - - - +
1611r GLU* 3.5 5.4 + - - +
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Residues in contact with THR1608 (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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1570r ARG* 6.1 4.5 - - - -
1606r ASP* 3.5 1.2 - - - +
1607r SER* 1.3 76.0 - - - +
1609r LEU* 1.3 61.1 + - - +
1611r GLU* 3.0 10.8 + - - +
1612r THR* 2.9 28.2 + - - -
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Residues in contact with LEU1609 (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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1604r LEU* 5.9 3.1 - - + -
1606r ASP* 3.7 26.9 + - + +
1607r SER 3.3 0.4 - - - -
1608r THR* 1.3 78.8 - - - +
1610r LYS* 1.3 62.8 + - - +
1612r THR* 3.9 6.1 - - - +
1613r LEU* 2.9 28.2 + - - +
1618r GLY* 5.1 3.2 - - - -
1619r TYR 6.0 4.3 - - - +
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Residues in contact with LYS1610 (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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1601r LEU* 5.5 12.3 - - + +
1604r LEU* 5.4 8.9 - - + +
1606r ASP 3.6 8.0 + - - +
1607r SER* 3.3 15.9 + - - +
1609r LEU* 1.3 79.5 - - - +
1611r GLU* 1.3 57.1 + - - +
1613r LEU* 3.4 5.1 + - - +
1614r LEU* 2.9 28.7 + - - +
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Residues in contact with GLU1611 (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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1607r SER 3.5 5.4 + - - +
1608r THR* 3.0 14.6 + - - +
1610r LYS* 1.3 76.4 - - - +
1612r THR* 1.3 61.0 + - - +
1614r LEU* 2.9 27.2 + - - +
1615r ASN* 3.3 8.8 + - - +
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Residues in contact with THR1612 (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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1573r ALA* 4.3 22.4 - - - -
1574r ILE* 5.5 1.1 - - - -
1577r LEU* 6.1 4.7 - - - -
1608r THR 2.9 17.9 + - - -
1609r LEU* 4.1 6.1 - - - -
1611r GLU* 1.3 74.4 - - - +
1613r LEU* 1.3 54.8 + - - +
1615r ASN* 3.5 5.1 + - - +
1616r GLY 3.4 2.9 + - - -
1617r VAL* 2.7 34.1 + - - +
1618r GLY* 3.6 18.2 - - - -
1619r TYR* 5.6 0.4 - - - -
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Residues in contact with LEU1613 (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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1609r LEU 2.9 19.7 + - - +
1610r LYS* 3.7 5.4 - - - +
1612r THR* 1.3 74.5 - - - +
1614r LEU* 1.3 65.1 + - - +
1616r GLY* 3.0 13.9 + - - -
1617r VAL 4.2 2.0 - - - +
1618r GLY* 3.9 14.7 - - - +
1641r ILE* 5.4 2.3 - - - +
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Residues in contact with LEU1614 (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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1587r GLN* 5.2 2.4 - - - +
1590r LEU* 4.5 8.5 - - - +
1594r GLU* 6.0 2.1 - - - +
1597r LEU* 6.1 4.3 - - - -
1610r LYS 2.9 14.5 + - - +
1611r GLU* 2.9 15.6 + - - +
1613r LEU* 1.3 78.6 - - - +
1615r ASN* 1.3 56.2 + - + +
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Residues in contact with ASN1615 (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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1577r LEU* 5.1 15.7 - - + -
1587r GLN* 3.9 26.3 - - + +
1589r PHE* 4.1 6.1 + - - +
1590r LEU* 3.8 14.5 + - - -
1611r GLU 3.3 8.6 + - - +
1612r THR* 3.5 5.6 + - - +
1613r LEU 3.1 0.6 - - - -
1614r LEU* 1.3 78.1 - - + +
1616r GLY* 1.3 59.0 + - - +
1617r VAL* 3.6 3.1 - - + -
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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