Contacts of the helix formed by residues 1618 - 1628 (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 GLN1618 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1617C PRO* 1.3 76.3 + - + +
1619C MET* 1.4 60.2 + - + +
1620C ARG 3.5 1.6 - - - +
1621C LYS* 3.4 20.7 - - + +
1622C ILE* 3.1 34.2 + - + +
1803C PX4 3.3 33.1 - - - +
1634D LEU 5.6 0.5 - - - +
1635D SER* 5.0 16.2 + - - +
1638D ALA* 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1619 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1612C LEU 3.5 17.7 - - - +
1613C VAL* 3.9 11.4 - - + +
1616C VAL* 3.5 29.2 - - + +
1617C PRO 2.8 9.9 + - - +
1618C GLN* 1.4 70.9 - - + +
1620C ARG* 1.4 65.0 + - - +
1622C ILE* 3.0 8.8 + - - +
1623C VAL* 2.9 25.4 + - - +
1803C PX4 4.9 16.6 - - + -
1635D SER 5.1 1.8 - - - +
1638D ALA* 4.2 11.7 - - - +
1639D LEU* 3.9 42.4 - - + -
1642D LEU* 3.8 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1620 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1507C THR* 5.8 2.0 - - - +
1567C TRP* 3.7 49.3 - - + +
1613C VAL 3.4 10.5 + - - +
1614C THR 2.8 18.5 + - - +
1615C ALA* 2.9 31.3 + - - +
1616C VAL 3.0 15.6 + - - +
1617C PRO* 3.3 38.2 - - + +
1619C MET* 1.4 74.4 - - - +
1621C LYS* 1.4 54.1 + - - +
1623C VAL* 3.5 4.1 + - - +
1624C SER* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1621 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618C GLN* 3.4 24.1 - - + +
1620C ARG* 1.4 77.3 - - - +
1622C ILE* 1.4 63.3 + - + +
1624C SER* 3.3 6.2 + - - -
1625C ALA* 2.9 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1622 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1618C GLN* 3.1 18.2 - - + +
1619C MET* 3.0 9.4 + - - +
1621C LYS* 1.4 82.8 - - + +
1623C VAL* 1.3 64.1 + - - +
1625C ALA* 4.0 8.0 - - + +
1626C LEU* 3.1 36.9 + - + +
1635D SER* 3.6 34.1 - - - +
1636D VAL* 4.3 23.3 - - + -
1639D LEU* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1623 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1613C VAL* 3.8 31.6 - - + +
1619C MET 2.9 21.2 + - - +
1620C ARG* 3.8 5.4 - - - +
1622C ILE* 1.3 74.9 - - - +
1624C SER* 1.4 58.0 + - - +
1626C LEU* 3.7 3.3 - - - +
1627C ILE* 3.0 48.2 + - + +
1639D LEU* 3.6 32.8 - - + -
1643D PHE* 5.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1624 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1567C TRP* 5.0 12.3 - - - -
1620C ARG* 3.1 17.9 + - - -
1621C LYS* 3.3 5.4 + - - -
1623C VAL* 1.4 71.3 - - - +
1625C ALA* 1.4 58.9 + - - +
1626C LEU 3.1 1.6 - - - -
1627C ILE* 3.1 11.7 + - - +
1628C SER* 3.0 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1625 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1621C LYS* 2.9 24.6 + - + +
1622C ILE* 4.2 9.6 - - + +
1624C SER* 1.4 70.5 - - - +
1626C LEU* 1.3 57.6 + - + +
1628C SER* 2.7 22.1 + - - -
1629C VAL* 4.0 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1626 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622C ILE* 3.1 25.4 + - + +
1623C VAL* 3.7 4.7 - - - +
1624C SER 3.1 0.4 - - - -
1625C ALA* 1.3 75.9 - - + +
1627C ILE* 1.4 63.5 + - - +
1628C SER 3.2 0.4 - - - -
1629C VAL* 3.3 12.0 + - + +
1636D VAL* 4.5 16.4 - - + -
1639D LEU* 4.7 9.2 - - + -
1643D PHE* 6.3 0.2 - - + -
1710D PHE* 3.1 42.4 - - + -
1711D VAL* 3.7 32.3 - - + -
1714D ASN* 3.6 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1627 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1623C VAL* 3.0 41.0 + - + +
1624C SER* 3.1 8.9 + - - +
1626C LEU* 1.4 74.6 - - + +
1628C SER* 1.4 57.8 + - - +
1629C VAL 3.1 5.8 + - - -
1630C ILE* 3.3 30.7 + - + +
1631C PRO* 3.7 3.3 - - - +
1710D PHE* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1628 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1624C SER 3.0 11.5 + - - -
1625C ALA* 2.7 29.2 + - - -
1627C ILE* 1.4 77.3 - - - +
1629C VAL* 1.3 60.0 + - - +
1630C ILE 3.5 0.2 - - - -
1631C PRO* 3.2 16.6 - - - +
1632C GLY 4.9 0.7 + - - -
----------------------------------------------------------
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