Contacts of the strand formed by residues 1607 - 1612 (chain F) in PDB entry 1KF9
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 TYR1607 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546F PHE* 4.0 24.5 - + - -
1568F TYR* 4.7 17.9 - + + -
1569F THR 3.4 7.4 - - - -
1570F ARG* 3.4 32.7 + - - -
1596F PHE* 5.3 2.0 - + - -
1600F PHE 2.3 33.8 + - - -
1601F THR* 3.7 0.3 - - - -
1602F SER* 3.5 23.6 + - - -
1605F ILE* 3.2 17.9 - - + -
1606F PRO* 1.3 81.3 - - + +
1608F CYS* 1.3 62.7 + - - +
1609F ILE* 4.8 0.4 - - + -
1622F CYS* 3.0 4.0 - - - +
1623F PHE* 2.7 70.2 + + + +
1625F VAL* 4.3 11.9 - - + -
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Residues in contact with CYS1608 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568F TYR* 3.3 1.0 - - - -
1569F THR* 3.0 47.5 + - + +
1580F TRP* 3.8 7.5 - - + -
1607F TYR* 1.3 74.7 - - - +
1609F ILE* 1.3 64.6 + - - +
1620F GLU* 4.2 8.5 - - - +
1621F LYS 3.0 4.3 - - - -
1622F CYS* 2.0 44.9 - - - -
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Residues in contact with ILE1609 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535F PHE* 3.3 33.0 - - + -
1538F CYS* 3.8 7.9 - - - -
1548F CYS* 3.7 22.4 - - - -
1566F LEU* 3.6 18.6 - - + -
1567F PHE 3.2 4.3 - - - +
1568F TYR* 3.6 20.0 - - + -
1580F TRP* 4.3 1.3 - - - -
1596F PHE* 5.1 3.6 - - + -
1607F TYR* 4.8 1.8 - - + -
1608F CYS* 1.3 82.7 - - - +
1610F LYS* 1.3 60.2 + - - +
1620F GLU* 3.0 8.3 - - - +
1621F LYS* 2.5 59.3 + - + +
1623F PHE* 3.9 20.9 - - + -
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Residues in contact with LYS1610 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN 6.0 2.0 - - - -
101A LEU* 4.7 17.3 - - + -
1535F PHE* 3.9 4.3 - - - -
1565F GLN 3.7 0.2 - - - +
1566F LEU* 3.1 5.4 - - - +
1567F PHE* 2.6 42.6 + - + +
1580F TRP* 3.3 36.9 - - + -
1609F ILE* 1.3 71.8 - - - +
1611F LEU* 1.3 61.2 + - - +
1612F THR* 4.0 2.8 + - - +
1617F THR* 3.4 32.3 - - + +
1619F ASP 3.1 14.8 - - - +
1620F GLU* 3.2 36.6 + - + +
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Residues in contact with LEU1611 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1533F PRO* 4.0 20.9 - - + -
1535F PHE* 3.6 18.3 - - + -
1550F TRP* 4.2 33.7 - - + +
1564F ILE* 4.2 9.4 - - + -
1565F GLN 2.7 38.4 - - - +
1566F LEU* 4.4 1.8 - - - +
1610F LYS* 1.3 74.3 - - - +
1612F THR* 1.3 64.7 + - - +
1613F SER* 5.4 2.0 - - - +
1617F THR* 3.5 5.5 - - - +
1618F VAL* 2.9 47.4 + - + -
1619F ASP* 2.7 28.2 + - + +
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Residues in contact with THR1612 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.3 5.4 - - - +
1564F ILE* 2.8 27.4 - - - -
1565F GLN* 2.7 39.4 + - - +
1567F PHE* 3.6 25.2 - - + -
1610F LYS* 4.7 1.9 + - - +
1611F LEU* 1.3 75.2 - - - +
1613F SER* 1.3 67.9 + - - +
1615F GLY* 4.4 4.7 - - - -
1616F GLY 3.6 23.5 - - - +
1617F THR* 5.2 4.0 + - - -
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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