Contacts of the helix formed by residues 1686 - 1694 (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 ILE1686 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662A TRP* 3.8 22.9 - - + -
1663A PHE* 3.9 26.9 - - + -
1672A THR* 3.6 17.0 - - + -
1675A GLN* 3.4 40.2 - - - +
1676A VAL* 4.2 19.1 - - + -
1681A SER 3.4 2.6 + - - +
1682A TRP 3.3 13.1 + - - +
1683A SER 3.6 0.2 + - - -
1685A GLY* 1.4 79.1 - - - +
1687A VAL* 1.3 71.7 + - + +
1688A ARG 3.4 1.6 - - - -
1689A PRO* 3.2 10.2 - - - +
1690A LEU* 3.3 20.6 + - + +
1701A PHE* 4.8 2.7 - - + -
1684B MET* 3.8 8.1 - - + -
1688B ARG* 4.2 2.9 - - - +
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Residues in contact with VAL1687 (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* 4.8 3.4 - - + -
1682A TRP* 2.8 41.8 + - + +
1686A ILE* 1.3 77.3 - - + +
1688A ARG* 1.4 59.1 + - - +
1690A LEU* 3.5 7.5 - - - +
1691A MET* 3.3 32.5 + - - +
1697A ALA* 4.9 0.9 - - + -
1698A TRP* 4.1 15.3 - - + +
1701A PHE* 3.7 44.2 - - + -
1702A ILE* 5.8 0.2 - - + -
1671D TYR* 3.4 23.3 - - + +
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Residues in contact with ARG1688 (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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1683A SER* 3.0 29.0 + - - +
1684A MET* 3.9 25.1 - - - +
1687A VAL* 1.4 72.7 - - - +
1689A PRO* 1.4 67.2 - - + +
1691A MET* 3.0 24.6 + - + +
1692A GLU* 3.7 12.6 + - - +
1661D GLU 3.5 22.2 + - - -
1662D TRP* 3.5 19.4 - - - +
1668D GLU* 3.9 8.5 + - - -
1671D TYR* 3.3 28.6 - - + -
1672D THR* 2.8 31.9 + - - +
1675D GLN* 3.0 22.2 - - - +
1801D PX4 5.3 3.0 - - - -
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Residues in contact with PRO1689 (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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1659A PHE* 3.7 16.2 - - + -
1662A TRP* 4.4 12.3 - - + -
1683A SER 3.8 4.7 - - - +
1684A MET 4.3 6.7 - - - +
1685A GLY 3.4 20.4 - - - +
1686A ILE 3.2 15.9 - - - +
1688A ARG* 1.4 92.6 - - + +
1690A LEU* 1.4 58.1 + - - +
1692A GLU* 3.1 28.3 + - + +
1693A VAL* 4.7 0.5 - - - +
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Residues in contact with LEU1690 (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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1655A PHE* 3.7 28.0 - - + -
1659A PHE* 3.6 27.4 - - + -
1662A TRP* 3.5 23.3 - - + -
1663A PHE* 3.6 20.0 - - + -
1686A ILE* 3.3 22.4 + - + +
1687A VAL* 3.5 7.4 - - - +
1688A ARG 3.2 0.2 - - - -
1689A PRO* 1.4 78.1 - - - +
1691A MET* 1.3 56.4 + - - +
1692A GLU 3.3 1.1 - - - -
1693A VAL* 3.7 1.4 + - - +
1694A TYR* 3.0 33.9 + - - +
1697A ALA* 4.0 4.7 - - + +
1701A PHE* 3.5 32.5 - - + -
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Residues in contact with MET1691 (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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1687A VAL* 3.3 23.9 + - - +
1688A ARG* 3.0 17.5 + - + +
1690A LEU* 1.3 73.6 - - - +
1692A GLU* 1.3 64.0 + - - +
1693A VAL 3.5 0.2 - - - -
1694A TYR 3.3 10.3 - - - +
1695A PRO* 3.3 36.9 - - - +
1697A ALA* 4.3 5.6 - - + -
1698A TRP* 3.7 37.0 - - + -
1671D TYR* 4.2 19.3 - - + -
1801D PX4 3.6 42.0 - - - -
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Residues in contact with GLU1692 (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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1688A ARG* 4.0 11.3 - - - +
1689A PRO* 3.1 19.0 + - + +
1691A MET* 1.3 81.6 - - - +
1693A VAL* 1.3 67.2 + - + +
1695A PRO* 4.7 2.4 - - - +
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Residues in contact with VAL1693 (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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1658A ARG* 3.6 46.8 + - + +
1659A PHE* 3.6 29.6 - - + -
1689A PRO 4.0 1.9 + - - +
1690A LEU 3.7 0.6 + - - -
1692A GLU* 1.3 82.8 - - + +
1694A TYR* 1.4 90.2 + - + +
1695A PRO* 3.3 9.2 - - - +
1801A PX4 4.8 0.9 + - - -
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Residues in contact with TYR1694 (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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1654A LEU 3.8 14.7 + - - -
1655A PHE* 3.7 39.3 - + + -
1657A GLU* 4.7 4.2 + - - +
1658A ARG* 3.3 30.5 + - + +
1659A PHE* 3.9 12.3 - + - -
1690A LEU 3.0 23.2 + - - +
1691A MET* 3.3 2.2 - - - -
1693A VAL* 1.4 95.9 - - + +
1695A PRO* 1.4 66.4 - - - +
1696A TYR 3.3 1.8 - - - -
1697A ALA* 3.2 14.6 + - + +
1801A PX4 3.3 26.0 - - + +
1596D THR* 4.3 4.9 - - - -
1599D ARG* 3.3 35.9 - - - -
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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