Contacts of the helix formed by residues 1665 - 1678 (chain A) in PDB entry 5EK0
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 THR1665 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1652A THR* 3.3 12.5 + - - -
1664A GLY* 1.3 78.8 - - - +
1666A LEU* 1.3 65.5 + - - +
1667A GLY 3.7 1.7 + - - -
1668A GLU* 3.2 28.7 + - + +
1669A SER* 3.2 18.4 + - - -
1802A PX4 3.6 14.0 + - - +
1525D LYS* 4.3 23.6 - - + -
1526D GLU* 5.5 0.9 - - + +
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Residues in contact with LEU1666 (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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1645A TYR* 4.6 2.0 - - + +
1648A ALA* 3.4 37.2 - - + +
1649A ILE* 3.6 19.1 - - + +
1652A THR* 3.5 10.5 + - + +
1665A THR* 1.3 73.5 - - - +
1667A GLY* 1.3 62.3 + - - +
1669A SER* 3.2 6.2 + - - -
1670A PHE* 3.1 41.9 + - + -
1802A PX4 4.4 17.9 - - + -
1522D MET* 3.7 47.1 - - + +
1524D GLU 4.5 3.7 + - - +
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Residues in contact with GLY1667 (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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1665A THR* 3.3 4.3 + - - -
1666A LEU* 1.3 78.5 - - - +
1668A GLU* 1.3 62.2 + - - +
1670A PHE* 3.4 6.4 - - - +
1671A TYR* 3.4 18.2 + - - +
1802A PX4 3.3 55.1 + - - +
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Residues in contact with GLU1668 (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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1660A PRO 4.1 4.6 - - - +
1661A GLU* 3.2 28.4 - - - +
1662A TRP* 2.9 22.7 - - - +
1664A GLY* 3.8 4.5 - - - +
1665A THR* 3.2 35.9 + - + +
1667A GLY* 1.3 72.5 - - - +
1669A SER* 1.4 64.5 + - - +
1671A TYR* 3.3 9.4 + - - +
1672A THR* 3.2 17.5 + - - -
1802A PX4 3.3 46.9 - - - +
1688B ARG* 4.8 5.0 + - - -
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Residues in contact with SER1669 (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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1648A ALA* 3.4 14.4 - - - -
1651A ALA* 3.5 9.7 - - - +
1652A THR* 2.7 38.8 + - - -
1662A TRP 3.5 4.0 + - - -
1663A PHE* 3.4 21.1 - - - +
1665A THR 3.2 1.6 + - - -
1666A LEU 3.4 6.7 - - - -
1668A GLU* 1.4 74.2 - - - +
1670A PHE* 1.4 55.4 + - - +
1672A THR* 3.8 0.6 - - - +
1673A LEU* 2.8 42.0 + - - +
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Residues in contact with PHE1670 (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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1641A THR* 4.7 2.5 - - + -
1644A PHE* 3.7 36.4 - + + -
1645A TYR* 3.5 53.4 - + - -
1648A ALA* 3.5 27.8 - - + +
1666A LEU* 3.1 33.8 + - + +
1667A GLY* 3.4 12.3 - - - +
1668A GLU 3.3 0.2 - - - -
1669A SER* 1.4 75.1 - - - +
1671A TYR* 1.4 56.7 + - - +
1674A PHE* 3.0 28.1 + - - +
1802A PX4 3.5 51.2 - - + +
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Residues in contact with TYR1671 (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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1667A GLY 3.4 5.5 + - - +
1668A GLU* 3.3 13.5 + - - +
1670A PHE* 1.4 75.4 - - - +
1672A THR* 1.4 60.8 + - - +
1674A PHE* 3.0 5.7 + - - +
1675A GLN* 2.9 28.4 + - + +
1802A PX4 3.7 27.5 - - + +
1682B TRP* 3.8 5.3 - + - -
1683B SER* 2.7 35.0 + - - -
1687B VAL* 3.4 16.1 - - + +
1688B ARG* 3.7 34.4 - - + +
1691B MET* 3.4 29.3 - - + +
1698B TRP* 4.1 15.9 - + + -
1702B ILE* 3.7 30.5 - - + -
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Residues in contact with THR1672 (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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1662A TRP* 3.2 28.1 + - + +
1663A PHE* 3.5 33.9 - - + -
1668A GLU* 3.2 8.3 + - - -
1669A SER 4.0 1.1 - - - -
1671A TYR* 1.4 72.8 - - - +
1673A LEU* 1.3 59.8 + - - +
1675A GLN* 3.3 3.8 + - - +
1676A VAL* 2.9 29.3 + - + +
1686A ILE* 3.6 28.7 - - + -
1688B ARG* 2.8 22.1 + - - +
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Residues in contact with LEU1673 (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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1644A PHE* 3.5 12.6 - - + +
1647A PHE* 3.4 39.7 - - + +
1648A ALA* 3.7 11.4 - - + +
1651A ALA* 4.0 9.0 - - + -
1663A PHE* 4.9 2.7 - - + -
1669A SER 2.8 20.8 + - - +
1670A PHE 4.1 0.2 - - - +
1672A THR* 1.3 73.7 - - - +
1674A PHE* 1.4 60.7 + - - +
1676A VAL* 4.3 1.8 - - + -
1677A MET* 3.0 21.8 + - - +
1700A PHE* 3.9 11.2 - - + -
1701A PHE* 3.8 29.6 - - + -
1704A PHE* 3.2 43.1 - - + -
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Residues in contact with PHE1674 (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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1644A PHE* 3.4 6.0 - + - -
1670A PHE 3.0 18.7 + - - +
1671A TYR 3.0 4.4 + - - +
1673A LEU* 1.4 74.4 - - - +
1675A GLN* 1.4 58.2 + - - +
1677A MET* 3.1 16.0 + - - +
1678A THR* 2.9 44.2 + - + +
1802A PX4 3.8 29.8 - - + -
1806A PX4 3.9 15.5 - - + -
1682B TRP* 3.6 34.1 - + - -
1702B ILE* 3.7 20.0 - - + -
1705B ILE* 4.1 20.4 - - + -
1706B PHE* 3.6 36.6 - + - -
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Residues in contact with GLN1675 (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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1671A TYR* 2.9 14.0 + - + +
1672A THR* 3.5 8.7 - - - +
1674A PHE* 1.4 76.1 - - - +
1676A VAL* 1.3 56.1 + - - +
1678A THR* 3.0 18.3 + - - -
1679A LEU 3.1 13.5 + - - -
1680A GLU* 2.8 40.0 + - + +
1681A SER 4.1 0.4 + - - -
1686A ILE* 3.4 12.5 - - - +
1682B TRP* 3.8 8.5 - - + -
1683B SER* 3.1 23.4 + - - +
1684B MET* 3.3 34.2 - - - +
1688B ARG* 3.0 35.7 + - - -
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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
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1672A THR* 2.9 20.5 + - + +
1673A LEU* 3.9 5.6 - - - +
1675A GLN* 1.3 74.6 - - - +
1677A MET* 1.4 58.9 + - - +
1679A LEU* 3.1 27.4 + - - +
1682A TRP* 3.9 23.6 - - + +
1686A ILE* 4.2 28.0 - - + -
1687A VAL* 4.8 1.3 - - + -
1701A PHE* 4.1 19.1 - - + -
1704A PHE* 3.8 16.6 - - + -
1705A ILE* 3.8 30.4 - - + +
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Residues in contact with MET1677 (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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1640A MET* 3.7 33.7 - - + -
1644A PHE* 3.8 23.3 - - + -
1673A LEU 3.0 16.6 + - - +
1674A PHE* 3.3 24.5 - - - +
1676A VAL* 1.4 74.3 - - - +
1678A THR* 1.4 56.0 + - - +
1679A LEU* 3.0 18.5 + - - +
1704A PHE* 4.3 0.9 - - + -
1705A ILE* 5.6 0.2 - - - -
1708A VAL* 3.7 30.0 - - + +
1709A THR* 5.0 3.6 + - - -
1712A MET* 3.8 29.2 - - + -
1802A PX4 5.0 2.9 - - + -
1806A PX4 4.1 27.5 - - + +
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Residues in contact with THR1678 (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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1674A PHE* 2.9 44.5 + - + +
1675A GLN 3.0 11.8 + - - -
1677A MET* 1.4 71.2 - - - +
1679A LEU* 1.4 61.8 + - - +
1680A GLU* 3.2 7.0 + - - -
1806A PX4 3.9 34.6 - - + +
1679B LEU* 4.0 33.1 - - + +
1682B TRP* 2.8 29.6 + - - -
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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