Contacts of the strand formed by residues 1593 - 1596 (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 SER1593 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1548F CYS 2.9 7.6 - - - -
1549F HIS* 3.0 36.8 - - - -
1550F TRP* 3.7 9.8 - - - -
1585F ASP 3.8 0.2 - - - +
1586F TYR* 3.2 26.4 + - - +
1589F ALA* 2.6 35.9 + - - +
1590F GLY 3.5 3.5 + - - -
1591F GLU 3.2 3.3 - - - -
1592F ASN* 1.3 75.5 - - - +
1594F CYS* 1.3 60.0 + - - +
1595F TYR 4.0 0.2 + - - -
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Residues in contact with CYS1594 (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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1547F SER* 3.2 6.8 - - - -
1548F CYS* 2.7 34.4 + - + +
1550F TRP* 3.9 12.0 - - + -
1566F LEU* 3.5 16.2 - - + -
1583F CYS* 2.0 55.4 - - + -
1584F PRO* 3.8 4.5 - - - -
1589F ALA* 4.6 0.4 - - - -
1593F SER* 1.3 72.4 - - - +
1595F TYR* 1.3 60.5 + - - +
1596F PHE* 3.5 27.9 - - + -
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Residues in contact with TYR1595 (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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1545F THR* 4.7 17.1 - - - +
1546F PHE 4.1 6.5 - - - -
1547F SER* 4.4 4.3 - - - -
1584F PRO* 4.3 6.2 - - - +
1585F ASP* 2.9 46.4 + - + +
1588F SER* 3.6 25.1 - - - -
1589F ALA* 3.4 33.2 - - + +
1593F SER 4.0 0.6 + - - -
1594F CYS* 1.3 73.4 - - - +
1596F PHE* 1.3 68.1 + - - +
1597F ASN* 3.8 32.1 + - + +
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Residues in contact with PHE1596 (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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1545F THR* 3.4 13.9 - - - -
1546F PHE* 3.0 67.0 + + + +
1548F CYS* 4.5 7.6 - - - -
1566F LEU* 3.8 12.8 - - + -
1568F TYR* 3.4 38.6 - + + -
1584F PRO* 4.0 12.6 - - + -
1594F CYS* 3.5 34.3 - - + -
1595F TYR* 1.3 76.7 - - - +
1597F ASN* 1.3 66.9 + - - +
1600F PHE* 4.1 24.0 - - + -
1601F THR* 3.2 9.4 + - - +
1607F TYR* 5.3 1.3 - + - -
1609F ILE* 5.1 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