Contacts of the strand formed by residues 1546 - 1550 (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 PHE1546 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539F ARG 3.3 13.9 - - - +
1540F SER* 3.7 4.3 - - - -
1541F PRO* 4.7 2.5 - - - -
1545F THR* 1.3 80.1 + - - +
1547F SER* 1.3 67.6 + - - +
1548F CYS* 4.1 6.3 - - - -
1595F TYR* 4.1 3.5 - - - -
1596F PHE* 3.0 79.4 + + + +
1600F PHE 4.5 2.7 - - - -
1601F THR* 3.8 16.6 - - + -
1607F TYR* 4.0 34.3 - + - -
1623F PHE* 3.5 26.2 - + - -
1625F VAL* 4.6 5.6 - - + -
1628F ILE* 3.4 28.9 - - + -
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Residues in contact with SER1547 (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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1537F LYS 3.7 1.4 - - - +
1538F CYS* 2.9 23.6 - - - +
1539F ARG* 3.0 18.3 + - - +
1546F PHE* 1.3 77.2 - - - +
1548F CYS* 1.3 63.8 + - - +
1549F HIS* 3.0 23.3 + - - -
1589F ALA* 4.1 19.9 - - - +
1594F CYS 3.2 11.4 - - - -
1595F TYR* 4.4 5.8 - - - -
1596F PHE* 4.5 0.2 - - - -
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Residues in contact with CYS1548 (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* 4.7 2.0 - - + -
1537F LYS 3.7 0.2 - - - -
1538F CYS* 2.0 48.0 - - - -
1546F PHE* 4.1 17.5 - - - -
1547F SER* 1.3 76.2 - - - +
1549F HIS* 1.3 62.2 + - - +
1550F TRP* 3.8 4.1 - - + -
1566F LEU* 4.5 12.1 - - + -
1593F SER* 2.9 6.1 - - - -
1594F CYS* 2.7 41.0 + - + +
1596F PHE* 4.5 5.1 - - - -
1609F ILE* 3.7 19.7 - - + -
1623F PHE* 4.4 2.0 - - - -
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Residues in contact with HIS1549 (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* 3.6 7.8 - - - -
1536F THR* 2.8 43.7 + - + +
1537F LYS* 3.1 30.7 + - + +
1547F SER* 3.0 26.5 + - - -
1548F CYS* 1.3 73.6 - - - +
1550F TRP* 1.3 61.6 + - - +
1589F ALA* 3.5 14.6 - - + -
1591F GLU 4.5 3.6 + - - -
1592F ASN 3.2 9.4 + - - +
1593F SER* 3.0 27.4 - - - -
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Residues in contact with TRP1550 (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 5.6 0.4 - - - -
1534F LYS 3.1 18.2 - - - +
1535F PHE* 3.3 41.1 - + + -
1536F THR* 3.4 8.1 - - - +
1548F CYS 3.8 14.6 - - - -
1549F HIS* 1.3 88.2 - - - +
1551F THR* 1.3 70.5 + - - +
1564F ILE* 4.3 25.6 + - + +
1566F LEU* 4.1 26.7 - - + -
1586F TYR* 4.5 11.9 - + - -
1592F ASN* 3.2 48.6 + - - +
1593F SER 3.7 19.3 - - - -
1594F CYS* 3.9 11.7 - - + -
1611F LEU* 4.2 26.2 - - + +
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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