Contacts of the strand formed by residues 1565 - 1570 (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 GLN1565 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1550F TRP* 5.2 0.7 - - - -
1564F ILE* 1.3 82.6 + - - +
1566F LEU* 1.3 55.8 + - - +
1567F PHE* 4.1 19.0 - - + -
1582F GLU* 3.4 23.9 + - - +
1586F TYR* 2.8 25.8 - - + +
1611F LEU* 2.7 27.8 - - - +
1612F THR* 2.7 40.1 + - - +
1613F SER 4.8 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1566 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535F PHE* 3.3 36.6 - - + -
1548F CYS* 4.5 7.0 - - + -
1550F TRP* 4.1 23.1 - - + -
1565F GLN* 1.3 76.1 - - - +
1567F PHE* 1.3 78.3 + - - +
1568F TYR* 4.4 4.0 - - + +
1582F GLU* 3.7 3.1 - - - +
1583F CYS* 3.0 33.4 + - + +
1586F TYR* 3.1 7.7 + - - -
1594F CYS* 3.5 28.5 - - + -
1596F PHE* 3.8 13.0 - - + -
1609F ILE* 3.6 20.9 - - + -
1610F LYS 3.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1567 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 3.6 48.0 - - + -
1565F GLN* 4.1 20.4 - - + -
1566F LEU* 1.3 77.9 - - - +
1568F TYR* 1.3 59.4 + - - +
1580F TRP* 3.3 7.8 - - + -
1581F LYS* 3.0 27.8 - - - +
1582F GLU* 2.9 37.7 - - + -
1609F ILE* 3.2 3.3 - - - +
1610F LYS* 2.6 40.2 + - + +
1612F THR* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1568 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1566F LEU* 4.4 4.0 - - + -
1567F PHE* 1.3 72.4 - - - +
1569F THR* 1.3 72.0 + - - +
1570F ARG* 4.6 24.0 - - + -
1579F GLU 4.0 0.3 - - - +
1580F TRP* 3.7 2.9 - - - -
1581F LYS* 2.7 70.3 + - + +
1582F GLU 3.5 24.9 - - - -
1584F PRO* 3.7 16.5 - - + +
1596F PHE* 3.4 28.3 - + + -
1600F PHE* 3.6 26.2 - + + -
1607F TYR* 4.7 8.1 - + + -
1608F CYS 3.3 6.3 - - - -
1609F ILE* 3.6 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1569 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1568F TYR* 1.3 79.8 - - - +
1570F ARG* 1.3 76.8 + - - +
1578F GLN* 3.6 26.3 + - - +
1579F GLU 2.6 28.4 + - - -
1580F TRP* 4.0 17.5 - - + -
1607F TYR* 3.4 8.5 - - - +
1608F CYS* 3.0 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1570 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661C ARG* 6.1 1.4 - - - +
1119D GLU* 4.2 4.4 + - - -
1568F TYR* 4.6 13.6 - - + -
1569F THR* 1.3 85.1 + - - +
1571F ARG* 1.3 63.9 + - - +
1578F GLN* 5.3 4.7 + - - +
1599F SER 4.9 4.8 + - - -
1600F PHE* 4.0 27.2 + - - +
1602F SER* 3.9 19.4 - - - -
1605F ILE* 3.7 32.8 - - + +
1606F PRO 3.4 15.0 - - - +
1607F TYR* 3.4 39.9 + - - -
1608F CYS 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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