Contacts of the helix formed by residues 1668 - 1689 (chain A) in PDB entry 4W8F
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 GLN1668 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662A LYS* 4.9 11.1 - - - +
1663A CYS* 3.2 25.6 + - - +
1666A THR* 3.4 25.4 + - - +
1667A ASN* 1.3 74.7 - - - +
1669A PHE* 1.3 51.8 + - - +
1670A SER* 2.7 3.2 + - - -
1671A LYS* 2.7 55.2 + - + +
1672A TYR* 3.5 6.0 + - + +
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Residues in contact with PHE1669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1660A VAL* 4.8 2.7 - - + -
1663A CYS* 3.4 27.1 - - - -
1664A LEU* 3.6 26.0 - - + -
1667A ASN* 3.0 43.3 + - + -
1668A GLN* 1.3 77.2 - - - +
1670A SER* 1.3 52.1 + - - +
1672A TYR 3.6 0.4 - - - -
1673A TRP* 2.7 39.4 + - - +
1712A ILE* 3.8 15.2 - - + +
1715A LEU* 3.5 46.7 - - + -
1716A LYS* 4.0 31.6 - - + -
1724A ALA* 5.1 3.8 - - + -
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Residues in contact with SER1670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1668A GLN 2.7 5.6 + - - -
1669A PHE* 1.3 75.5 - - - +
1671A LYS* 1.3 72.8 + - - -
1673A TRP* 3.7 4.3 - - - +
1674A LYS* 3.0 52.8 + - - +
1716A LYS* 4.9 12.3 - - - +
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Residues in contact with LYS1671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1668A GLN* 2.7 37.7 + - + +
1670A SER* 1.3 84.7 + - - +
1672A TYR* 1.3 56.2 + - - +
1674A LYS* 4.0 15.5 - - + +
1675A GLU* 3.0 32.4 + - - +
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Residues in contact with TYR1672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655A MET* 4.7 4.2 - - - +
1656A TRP* 3.6 24.2 - + - +
1659A LEU* 3.2 47.0 - - + +
1660A VAL* 4.0 11.0 - - + -
1663A CYS* 4.0 30.3 - - + -
1668A GLN* 3.5 5.8 + - + +
1669A PHE* 3.4 3.0 + - - +
1670A SER 3.3 0.2 - - - -
1671A LYS* 1.3 77.3 - - - +
1673A TRP* 1.3 60.9 + - - +
1675A GLU* 4.1 22.4 - - + -
1676A VAL* 3.0 44.3 + - + +
1679A LYS* 5.3 6.7 + - - -
1705A TYR* 6.0 1.2 - - - -
1708A PHE* 5.5 0.7 - - - -
1712A ILE* 3.6 23.8 - - + -
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Residues in contact with TRP1673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1669A PHE 2.7 25.4 + - - +
1670A SER* 3.7 5.2 - - - +
1672A TYR* 1.3 74.1 - - - +
1674A LYS* 1.3 71.8 + - + +
1676A VAL* 3.4 2.4 + - - +
1677A ASP* 3.0 49.7 + - + +
1709A ASN* 3.3 35.2 + - - +
1712A ILE* 3.8 11.4 - - + +
1713A GLY* 3.3 40.7 - - - -
1716A LYS* 4.1 26.8 - - - +
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Residues in contact with LYS1674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1670A SER* 3.0 38.4 + - - +
1671A LYS* 4.0 15.3 - - + +
1673A TRP* 1.3 88.2 - - + +
1675A GLU* 1.3 66.3 + - - +
1677A ASP* 3.2 6.7 + - - +
1678A MET* 3.1 26.0 + - - +
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Residues in contact with GLU1675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659A LEU* 5.8 1.7 - - - +
1671A LYS* 3.0 22.1 + - - +
1672A TYR* 3.6 24.8 - - + +
1674A LYS* 1.3 77.0 - - - +
1676A VAL* 1.3 63.6 + - - +
1678A MET* 3.1 11.0 + - - +
1679A LYS* 3.1 35.1 + - + +
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Residues in contact with VAL1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1656A TRP* 5.6 0.2 - - + -
1672A TYR* 3.0 48.3 + - + +
1673A TRP 3.9 3.6 - - - +
1675A GLU* 1.3 72.5 - - - +
1677A ASP* 1.3 67.3 + - - +
1679A LYS* 3.0 12.3 + - + +
1680A ILE* 2.9 40.1 + - + +
1705A TYR* 4.0 24.0 - - + +
1708A PHE* 4.6 5.4 - - + -
1709A ASN* 3.9 20.0 - - + +
1712A ILE* 3.9 14.1 - - + -
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Residues in contact with ASP1677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1673A TRP* 3.0 38.1 + - + +
1674A LYS* 3.4 11.6 - - - +
1676A VAL* 1.3 78.0 - - - +
1678A MET* 1.3 63.5 + - - +
1680A ILE* 3.3 9.5 + - - +
1681A LYS* 3.0 61.2 + - - +
1709A ASN* 4.0 17.6 + - - +
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Residues in contact with MET1678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674A LYS 3.1 16.8 + - - +
1675A GLU* 3.1 11.0 + - - +
1677A ASP* 1.3 74.8 - - - +
1679A LYS* 1.3 55.5 + - - +
1681A LYS* 2.9 30.8 + - + +
1682A GLY* 2.7 34.2 + - - +
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Residues in contact with LYS1679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630A LEU* 6.5 0.9 - - - -
1635A ASP* 5.3 9.0 - - - +
1636A ILE* 3.9 33.1 - - + +
1637A GLU* 4.8 3.1 - - - +
1655A MET* 4.5 15.0 - - - +
1659A LEU* 6.0 0.4 - - - +
1672A TYR* 5.3 7.5 + - - -
1675A GLU* 3.1 30.6 + - + +
1676A VAL* 3.0 18.9 + - - +
1678A MET* 1.3 75.8 - - - +
1680A ILE* 1.3 56.0 + - - +
1682A GLY* 3.1 3.3 + - - -
1683A LEU* 2.8 35.0 + - - +
1705A TYR* 3.3 38.4 + - + +
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Residues in contact with ILE1680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676A VAL* 2.9 16.4 + - + +
1677A ASP* 3.6 9.4 - - - +
1679A LYS* 1.3 73.1 - - - +
1681A LYS* 1.3 62.2 + - + +
1683A LEU* 3.4 2.9 + - - +
1684A LEU* 3.0 40.5 + - + +
1702A LEU* 3.7 21.8 - - + -
1705A TYR* 3.7 29.6 - - + +
1706A LEU* 3.9 26.0 - - + -
1709A ASN* 3.6 37.2 - - + +
1935A GLN* 6.0 0.9 - - + +
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Residues in contact with LYS1681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1677A ASP* 3.0 40.9 + - - +
1678A MET* 2.9 31.7 + - + +
1680A ILE* 1.3 72.9 - - + +
1682A GLY* 1.3 61.4 + - - +
1684A LEU* 3.3 10.6 + - + +
1685A ASP* 2.9 30.8 + - - +
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Residues in contact with GLY1682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637A GLU* 3.3 25.6 - - - +
1678A MET* 2.7 18.2 + - - +
1679A LYS* 3.5 2.9 - - - -
1681A LYS* 1.3 73.3 - - - +
1683A LEU* 1.3 61.3 + - - +
1684A LEU 3.2 0.3 + - - -
1685A ASP* 3.2 4.8 + - - +
1686A LYS* 3.0 24.9 + - - +
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Residues in contact with LEU1683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636A ILE* 3.6 28.3 - - + -
1637A GLU* 4.3 7.1 + - + -
1640A VAL* 4.0 22.2 - - + -
1679A LYS 2.8 24.9 + - - +
1680A ILE* 3.8 0.4 - - - +
1681A LYS 3.4 0.2 - - - -
1682A GLY* 1.3 72.2 - - - +
1684A LEU* 1.3 56.4 + - - +
1686A LYS* 3.7 6.1 + - + +
1687A LEU* 2.9 26.9 + - - +
1698A ILE* 3.3 18.3 - - + +
1701A LEU* 5.0 10.3 - - + -
1702A LEU* 3.6 28.5 - - + -
1705A TYR* 3.9 34.5 - - + -
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Residues in contact with LEU1684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1680A ILE* 3.0 34.5 + - + +
1681A LYS* 3.6 9.6 - - + +
1683A LEU* 1.3 75.5 - - - +
1685A ASP* 1.3 65.8 + - - +
1687A LEU* 3.1 17.3 + - + +
1688A ASN* 3.2 13.9 + - - +
1702A LEU* 3.5 26.5 - - + -
1935A GLN* 3.8 27.8 - - + +
1936A ILE* 3.7 19.5 - - + +
1938A GLY* 4.4 9.9 - - - -
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Residues in contact with ASP1685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1681A LYS 2.9 17.1 + - - +
1682A GLY* 3.7 5.6 - - - +
1684A LEU* 1.3 74.9 - - - +
1686A LYS* 1.3 62.9 + - - +
1688A ASN* 3.3 17.1 + - - +
1689A LYS* 3.5 15.1 + - - +
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Residues in contact with LYS1686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1637A GLU* 4.2 33.2 - - + +
1640A VAL* 4.7 6.3 - - + -
1641A SER* 3.9 21.5 + - - -
1682A GLY 3.0 16.4 + - - +
1683A LEU* 4.0 7.2 - - + +
1685A ASP* 1.3 73.1 - - - +
1687A LEU* 1.3 64.3 + - - +
1689A LYS* 3.5 7.5 + - + +
1690A SER* 3.0 40.4 + - - +
1694A VAL* 5.6 3.8 - - - +
1698A ILE* 3.8 16.2 - - + -
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Residues in contact with LEU1687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1683A LEU 2.9 20.2 + - - +
1684A LEU* 3.1 11.9 + - + +
1686A LYS* 1.3 78.8 - - - +
1688A ASN* 1.3 61.9 + - - +
1689A LYS 3.4 0.3 + - - -
1690A SER* 3.6 13.5 + - - +
1695A LYS* 3.6 29.1 - - + +
1698A ILE* 3.5 22.9 - - + -
1699A GLU* 3.6 33.2 - - + +
1702A LEU* 3.8 16.8 - - + -
1936A ILE 3.3 26.7 - - - +
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Residues in contact with ASN1688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1684A LEU 3.2 6.8 + - - +
1685A ASP* 3.3 12.1 + - - +
1687A LEU* 1.3 82.4 - - - +
1689A LYS* 1.3 61.1 - - + +
1690A SER 3.6 2.3 + - - +
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Residues in contact with LYS1689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685A ASP* 3.5 16.5 + - - +
1686A LYS* 3.5 7.9 + - + +
1687A LEU 3.2 0.6 - - - -
1688A ASN* 1.3 82.6 - - + +
1690A SER* 1.3 58.3 + - - +
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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
------------------------------------------------------------
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