Contacts of the helix formed by residues 1665 - 1679 (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 THR1665 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524B GLU 4.3 8.4 + - - -
1525B LYS* 5.1 10.3 - - - +
1652C THR* 3.3 8.8 - - - +
1664C GLY* 1.3 74.7 - - - +
1666C LEU* 1.4 66.8 + - - +
1667C GLY 3.0 6.4 + - - -
1668C GLU* 3.2 23.5 + - + +
1669C SER* 3.0 22.5 + - - -
1802C PX4 3.2 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1666 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1521B MET 4.6 1.1 - - - +
1522B MET* 3.8 45.1 - - + +
1524B GLU* 4.2 5.9 + - + +
1645C TYR* 4.4 1.8 - - + -
1648C ALA* 3.9 17.7 - - + +
1649C ILE* 3.5 34.3 - - + +
1652C THR* 3.6 12.7 - - + +
1665C THR* 1.4 73.9 + - - +
1667C GLY* 1.3 59.1 + - - +
1669C SER* 3.8 2.9 - - - -
1670C PHE* 2.9 56.5 + - + +
1802C PX4 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1667 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1665C THR* 3.0 6.0 + - - -
1666C LEU* 1.3 77.4 - - - +
1668C GLU* 1.4 62.7 + - - +
1670C PHE 3.5 0.2 + - - -
1671C TYR* 3.4 16.5 + - - +
1802C PX4 2.8 64.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1668 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1660C PRO 3.0 21.6 - - - +
1661C GLU* 3.3 16.9 - - - +
1662C TRP 2.9 26.0 - - - +
1664C GLY* 3.8 6.1 + - - +
1665C THR* 3.2 29.4 + - + +
1667C GLY* 1.4 72.1 - - - +
1669C SER* 1.4 62.9 + - - +
1671C TYR* 3.4 4.9 + - - +
1672C THR* 3.0 20.3 + - - -
1802C PX4 3.4 31.3 - - - -
1688D ARG* 4.8 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1669 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1648C ALA* 3.5 22.7 - - - -
1651C ALA* 3.4 8.0 - - - +
1652C THR* 3.1 33.3 + - - +
1662C TRP 3.6 5.1 + - - -
1663C PHE* 3.6 12.0 - - - +
1665C THR 3.0 12.4 + - - -
1666C LEU 3.6 5.6 - - - -
1668C GLU* 1.4 76.8 - - - +
1670C PHE* 1.4 60.4 + - - +
1672C THR* 3.6 1.7 + - - -
1673C LEU* 3.3 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1670 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1641C THR* 4.3 2.5 - - + -
1644C PHE* 3.4 49.8 - + + -
1645C TYR* 3.6 50.0 - + - -
1648C ALA* 3.5 25.1 - - + -
1666C LEU* 2.9 26.8 + - + +
1667C GLY 3.8 1.1 - - - +
1668C GLU 3.4 0.2 - - - -
1669C SER* 1.4 75.7 - - - +
1671C TYR* 1.3 56.4 - - - +
1673C LEU* 4.7 2.5 - - - -
1674C PHE* 3.1 27.7 + - - +
1802C PX4 3.7 59.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1671 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1667C GLY 3.4 10.4 + - - +
1668C GLU* 3.4 8.5 + - - +
1669C SER 3.3 0.6 - - - -
1670C PHE* 1.3 76.0 - - - +
1672C THR* 1.4 58.8 + - - +
1674C PHE* 3.2 6.1 + + - +
1675C GLN* 3.0 26.7 + - + +
1802C PX4 3.8 28.4 - - + +
1682D TRP* 3.6 15.2 - + - -
1683D SER* 2.9 17.6 + - - -
1687D VAL* 3.4 26.2 - - + +
1688D ARG* 3.2 49.8 - - + +
1691D MET* 3.5 20.2 - - + +
1698D TRP* 4.0 11.0 - - + -
1702D ILE* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1672 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1662C TRP* 2.8 29.3 + - + -
1663C PHE* 3.6 34.5 - - + -
1668C GLU 3.0 5.0 + - - -
1669C SER 4.2 0.4 - - - -
1671C TYR* 1.4 73.5 - - - +
1673C LEU* 1.3 52.5 + - - +
1675C GLN* 3.3 3.6 + - - +
1676C VAL* 2.8 38.4 + - + +
1686C ILE* 3.8 28.7 - - + -
1688D ARG* 2.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1673 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644C PHE* 3.6 20.6 - - + +
1647C PHE* 3.7 11.7 - - + +
1648C ALA* 3.6 34.3 - - + +
1651C ALA* 4.4 7.0 - - + -
1663C PHE* 5.0 2.7 - - + -
1669C SER 3.3 21.5 + - - +
1670C PHE 3.8 0.7 - - - +
1672C THR* 1.3 74.2 - - - +
1674C PHE* 1.4 53.3 + - - +
1676C VAL* 3.1 3.2 + - - -
1677C MET* 2.8 31.0 + - - +
1700C PHE* 3.7 27.1 - - + -
1701C PHE* 4.0 12.6 - - + -
1704C PHE* 3.1 36.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1674 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1644C PHE* 3.4 21.2 - + + -
1670C PHE 3.1 15.9 + - - +
1671C TYR* 3.5 8.3 - + - +
1673C LEU* 1.4 74.0 - - - +
1675C GLN* 1.3 56.7 + - - +
1677C MET* 3.2 16.0 - - + +
1678C THR* 2.8 41.9 + - + +
1802C PX4 3.9 20.4 - - + -
1682D TRP* 3.5 36.3 - + - -
1702D ILE* 3.9 23.6 - - + -
1705D ILE* 3.7 29.4 - - + -
1706D PHE* 3.6 28.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1675 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1671C TYR 3.0 13.0 + - - +
1672C THR* 3.4 8.4 - - - +
1673C LEU 3.2 0.2 - - - -
1674C PHE* 1.3 74.4 - - - +
1676C VAL* 1.4 58.7 + - - +
1678C THR* 2.7 19.0 + - - -
1679C LEU 3.0 14.0 + - - -
1680C GLU* 2.7 45.3 + - + +
1686C ILE* 3.2 20.5 - - - +
1682D TRP* 3.9 8.7 - - + -
1683D SER* 3.5 23.8 - - - +
1684D MET* 3.3 28.5 - - - +
1688D ARG* 2.7 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1676 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1672C THR* 2.8 21.7 + - + +
1673C LEU* 3.1 9.4 + - - +
1675C GLN* 1.4 70.1 - - - +
1677C MET* 1.4 56.4 + - - +
1679C LEU* 3.1 28.6 + - - +
1682C TRP* 3.8 30.1 - - + +
1686C ILE* 4.3 17.3 - - + -
1687C VAL* 5.0 0.7 - - + -
1701C PHE* 3.9 31.9 - - + -
1704C PHE* 3.6 24.5 - - + -
1705C ILE* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1677 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1640C MET* 4.5 4.9 - - + -
1644C PHE* 3.5 29.8 - - + -
1673C LEU 2.8 12.9 + - - +
1674C PHE* 3.2 27.1 - - + +
1676C VAL* 1.4 73.4 - - - +
1678C THR* 1.4 61.6 + - + +
1679C LEU* 3.0 18.4 + - - +
1704C PHE* 3.9 9.0 - - + -
1705C ILE* 5.8 1.3 - - - +
1708C VAL* 3.6 32.8 - - + +
1709C THR* 5.3 2.1 + - - -
1712C MET* 3.8 43.1 - - + -
1706D PHE* 5.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1678 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1674C PHE* 2.8 45.9 + - + +
1675C GLN* 2.7 21.7 + - - -
1677C MET* 1.4 74.6 - - + +
1679C LEU* 1.4 65.4 + - - +
1680C GLU* 3.2 3.9 + - - -
1679D LEU* 3.7 36.0 - - + +
1682D TRP* 3.3 20.0 + - - +
1705D ILE* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1679 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678B THR* 3.9 35.9 - - + +
1680B GLU* 3.3 9.2 - - - +
1804B PX4 4.4 21.8 - - + -
1675C GLN 3.0 2.6 + - - -
1676C VAL 3.3 15.7 - - - +
1677C MET 3.0 13.9 - - - +
1678C THR* 1.4 77.3 - - - +
1680C GLU* 1.4 63.0 + - - +
1681C SER 3.2 3.6 + - - -
1682C TRP* 3.3 39.0 - - + +
1705C ILE* 4.0 19.5 - - + -
1709C THR* 5.5 4.7 - - + +
----------------------------------------------------------
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