Contacts of the helix formed by residues 1686 - 1694 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662C TRP* 3.6 22.5 - - + +
1663C PHE* 3.9 7.2 - - + -
1672C THR* 3.8 28.0 - - + -
1675C GLN* 3.2 35.0 - - - +
1676C VAL* 4.3 11.9 - - + -
1680C GLU 4.5 0.2 - - - +
1681C SER 3.3 26.7 + - - +
1682C TRP* 3.4 9.6 + - - +
1683C SER 3.5 0.4 + - - -
1685C GLY* 1.4 80.1 - - - +
1687C VAL* 1.4 67.3 + - + +
1689C PRO* 3.2 11.2 - - - +
1690C LEU* 3.3 36.3 + - + +
1701C PHE* 4.7 1.1 - - + -
1684D MET* 3.8 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1687 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671B TYR* 3.3 22.7 - - + +
1676C VAL* 5.0 0.7 - - + -
1682C TRP* 2.8 42.9 + - + +
1683C SER* 4.0 0.4 - - - -
1686C ILE* 1.4 70.9 - - + +
1688C ARG* 1.4 59.5 + - - +
1690C LEU* 3.1 10.4 + - - +
1691C MET* 3.0 35.2 + - + +
1697C ALA* 4.9 1.3 - - + -
1698C TRP* 4.3 24.9 - - - +
1701C PHE* 3.7 35.7 - - + -
1702C ILE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1688 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1661B GLU 3.9 10.5 + - - -
1662B TRP* 3.4 33.6 - - - +
1668B GLU* 4.2 7.7 + - - -
1671B TYR* 3.5 27.3 - - + +
1672B THR* 3.2 32.9 + - - +
1675B GLN* 3.1 24.7 + - - -
1686B ILE* 4.6 2.6 - - - +
1802B PX4 5.4 1.6 - - - -
1683C SER* 2.7 34.5 + - - +
1684C MET* 4.1 16.0 - - - +
1687C VAL* 1.4 70.5 - - - +
1689C PRO* 1.4 61.2 - - + +
1691C MET* 3.1 27.3 + - + +
1692C GLU* 3.6 10.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1689 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1659C PHE* 3.3 17.9 - - + -
1662C TRP* 3.9 16.2 - - + -
1684C MET 3.5 23.1 - - - +
1685C GLY* 3.7 13.2 - - - +
1686C ILE 3.2 16.6 - - - +
1688C ARG* 1.4 89.6 - - + +
1690C LEU* 1.4 57.7 + - - +
1691C MET 3.3 0.2 - - - -
1692C GLU* 3.5 22.0 - - + +
1693C VAL* 4.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1690 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1655C PHE* 3.6 31.0 - - + -
1659C PHE* 3.5 39.5 - - + -
1662C TRP* 4.5 0.7 - - + -
1663C PHE* 3.8 15.7 - - + -
1686C ILE* 3.3 28.0 + - + +
1687C VAL* 3.1 12.2 + - - +
1689C PRO* 1.4 73.0 - - - +
1691C MET* 1.3 49.0 + - - +
1692C GLU 3.1 5.8 + - - -
1693C VAL* 3.3 3.3 + - - +
1694C TYR* 2.8 42.0 + - + +
1697C ALA* 4.2 8.1 - - + -
1701C PHE* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET1691 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671B TYR* 3.5 38.1 - - + +
1802B PX4 3.6 33.2 - - - -
1687C VAL* 3.0 12.7 + - + +
1688C ARG* 3.1 26.8 + - + +
1690C LEU* 1.3 74.7 - - - +
1692C GLU* 1.3 63.8 + - - +
1694C TYR 3.1 11.7 - - - +
1695C PRO* 3.5 25.9 - - + +
1697C ALA* 3.9 11.2 - - + -
1698C TRP* 3.6 32.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1692 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1688C ARG 3.6 10.4 + - - +
1689C PRO* 3.5 16.1 + - + +
1690C LEU 3.1 0.8 - - - -
1691C MET* 1.3 83.9 - - - +
1693C VAL* 1.3 65.8 + - + +
1695C PRO* 4.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1693 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1658C ARG* 3.8 33.9 - - + +
1659C PHE* 3.5 30.1 - - + -
1689C PRO 4.6 1.8 - - - +
1690C LEU 3.3 2.0 + - - -
1692C GLU* 1.3 80.8 - - + +
1694C TYR* 1.3 84.6 + - + +
1695C PRO* 3.7 7.1 - - - +
1801C PX4 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1694 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1599B ARG* 3.5 32.0 + - - -
1654C LEU 3.9 5.4 - - - -
1655C PHE* 3.6 41.0 + + - -
1657C GLU* 3.4 17.8 + - - -
1658C ARG* 3.3 20.2 + - + +
1659C PHE* 3.8 21.5 - + - -
1690C LEU* 2.8 19.3 + - + +
1691C MET* 3.1 16.7 - - - -
1693C VAL* 1.3 88.1 - - + +
1695C PRO* 1.4 67.9 - - - +
1696C TYR 3.3 2.6 + - - -
1697C ALA* 3.4 12.9 - - + +
1801C PX4 3.5 36.8 - - - +
----------------------------------------------------------
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