Contacts of the strand formed by residues 1707 - 1716 (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 GLU1707 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1680F GLU* 3.5 4.7 - - - -
1681F VAL* 2.8 49.5 + - + +
1706F LYS* 1.3 78.4 - - - +
1708F TYR* 1.3 67.3 + - - +
1730F TYR* 3.8 19.0 - - + +
1731F VAL 3.2 13.7 - - - +
1732F THR* 3.8 23.8 - - + +
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Residues in contact with TYR1708 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1678F TYR* 4.2 8.1 - + + -
1679F LYS 3.4 8.7 - - - +
1680F GLU* 3.7 28.2 - - + +
1681F VAL* 4.1 0.7 - - - +
1683F GLU* 4.7 4.0 - - - -
1687F LYS* 4.7 9.6 - - - -
1701F SER 4.9 0.2 + - - -
1702F LEU* 3.7 37.4 - - + -
1703F LYS* 2.9 55.4 + - - +
1706F LYS* 3.9 20.9 + - + +
1707F GLU* 1.3 79.9 - - - +
1709F GLU* 1.3 61.3 + - - +
1710F VAL* 5.2 4.3 - - + -
1730F TYR* 3.5 2.1 - - - +
1731F VAL* 2.6 47.5 + - + +
1733F LEU* 4.1 10.3 - - + -
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Residues in contact with GLU1709 (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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1678F TYR* 3.2 1.6 - - - -
1679F LYS* 2.6 57.1 + - + +
1681F VAL* 3.6 17.9 - - + +
1686F TRP* 3.1 41.5 - - + -
1708F TYR* 1.3 76.3 - - - +
1710F VAL* 1.3 63.6 + - - +
1728F VAL* 4.2 16.5 - - + +
1729F LEU 3.3 7.9 - - - +
1730F TYR* 4.0 20.3 + - + -
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Residues in contact with VAL1710 (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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1637F LEU* 4.5 3.0 - - + +
1653F ILE* 5.5 2.0 - - + -
1655F VAL* 4.4 19.7 - - + -
1676F LEU* 3.2 37.7 - - + -
1677F GLN 3.4 3.1 - - - +
1678F TYR* 3.7 15.9 - - + -
1699F VAL* 5.4 4.7 - - + -
1708F TYR* 5.2 3.6 - - + -
1709F GLU* 1.3 78.5 - - - +
1711F ARG* 1.3 65.3 + - - +
1712F VAL* 4.2 6.3 - - + -
1727F GLU 4.1 0.7 - - - +
1728F VAL* 3.4 2.7 - - - -
1729F LEU* 2.7 54.2 + - + +
1731F VAL* 4.2 19.1 - - + -
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Residues in contact with ARG1711 (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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1637F LEU* 4.6 0.7 - - - -
1677F GLN* 2.8 51.0 + - + +
1686F TRP* 2.7 71.5 - - + +
1710F VAL* 1.3 73.7 - - - +
1712F VAL* 1.3 65.5 + - - +
1725F PHE* 3.1 51.2 - - + +
1726F SER* 3.9 19.5 - - - +
1727F GLU 4.5 0.2 - - - -
1728F VAL* 4.3 16.4 - - + -
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Residues in contact with VAL1712 (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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1634F PRO* 3.1 34.3 - - + +
1637F LEU* 4.0 18.2 - - + -
1655F VAL* 5.0 0.2 - - + -
1657F TRP* 4.0 20.2 - - + -
1674F TYR* 3.8 24.9 - - + -
1675F GLU 3.1 16.4 - - - +
1676F LEU* 3.6 31.0 - - + -
1710F VAL* 4.2 0.9 - - + -
1711F ARG* 1.3 81.6 - - - +
1713F ARG* 1.3 59.6 - - - +
1725F PHE* 4.1 3.3 - - - -
1726F SER* 3.4 17.0 + - - -
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Residues in contact with ARG1713 (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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1634F PRO* 4.2 3.4 - - - -
1674F TYR* 3.5 4.5 - - - +
1675F GLU* 2.8 68.5 + - + -
1677F GLN* 2.9 16.4 - - - +
1688F MET* 5.6 0.8 - - - -
1712F VAL* 1.3 77.3 - - - +
1714F SER* 1.3 61.5 + - - +
1722F TYR* 3.2 50.9 - - + +
1723F GLY 4.0 17.1 + - - +
1724F GLU 4.1 7.6 - - - +
1725F PHE* 3.1 38.4 - - + -
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Residues in contact with SER1714 (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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1631F PRO* 3.3 13.8 - - - +
1632F ASP 3.3 22.9 + - - -
1633F PRO* 5.4 0.2 - - - +
1634F PRO* 4.1 5.3 - - - +
1660F PRO* 4.0 6.6 - - - +
1672F LEU* 4.1 7.2 - - - +
1673F GLU 3.7 7.9 - - - -
1674F TYR* 3.6 28.9 - - - -
1713F ARG* 1.3 75.9 - - - +
1715F LYS* 1.3 60.0 + - - +
1722F TYR* 3.3 4.4 - - - -
1723F GLY* 2.6 33.4 + - - +
1724F GLU 5.0 1.6 + - - -
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Residues in contact with LYS1715 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1631F PRO* 3.5 5.6 - - - -
1672F LEU* 3.2 14.9 - - - +
1673F GLU* 3.4 38.7 + - + +
1714F SER* 1.3 73.7 + - - +
1716F GLN* 1.3 82.7 + - - +
1718F ASN* 3.4 10.7 - - - +
1719F SER 2.7 34.8 + - - +
1720F GLY 3.4 15.8 + - - -
1721F ASN* 2.9 31.4 - - - +
1722F TYR* 3.7 22.9 - - + -
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Residues in contact with GLN1716 (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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1543F ARG* 2.4 57.5 + - - +
1626F ASP* 4.1 2.0 + - - -
1629F VAL* 4.2 8.9 - - + +
1631F PRO* 3.9 4.8 - - - +
1669F TRP 3.4 7.7 - - - +
1670F MET* 4.1 13.5 - - + +
1671F VAL* 2.9 41.2 + - - +
1672F LEU* 3.6 4.7 - - - +
1715F LYS* 1.3 109.5 + - - +
1717F ARG* 1.3 77.9 + - + +
1719F SER* 3.2 16.5 + - - +
1721F ASN 4.6 0.4 + - - -
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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