Contacts of the helix formed by residues 1635 - 1643 (chain A) in PDB entry 4W8F
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 ASP1635 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1633A GLY 3.8 1.6 + - - -
1634A THR* 1.3 78.3 + - - +
1636A ILE* 1.3 66.4 + - - +
1637A GLU* 3.4 21.4 - - + +
1638A VAL* 3.0 33.6 + - + +
1639A VAL* 3.4 6.4 + - - +
1679A LYS* 5.3 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1630A LEU* 3.9 27.5 - - + +
1634A THR 3.6 2.0 + - - -
1635A ASP* 1.3 73.4 + - - +
1637A GLU* 1.3 76.1 + - - +
1639A VAL* 3.0 4.0 + - + +
1640A VAL* 2.9 30.4 + - + +
1648A ILE* 3.6 36.1 - - + +
1652A ALA* 5.1 0.7 - - + -
1679A LYS* 3.9 30.9 - - + +
1683A LEU* 3.6 28.5 - - + -
1701A LEU* 5.5 1.8 - - + -
1705A TYR* 3.9 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635A ASP* 3.4 25.7 - - + +
1636A ILE* 1.3 92.6 - - + +
1638A VAL* 1.3 63.8 + - + +
1639A VAL 3.3 0.3 + - - -
1640A VAL* 3.4 19.4 + - - +
1641A SER* 3.8 9.7 + - - -
1679A LYS* 5.2 3.6 - - - +
1682A GLY* 3.3 37.2 - - - +
1683A LEU* 4.6 4.7 - - + -
1686A LYS* 4.2 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1629A GLN* 4.8 12.8 - - - +
1634A THR* 3.2 27.8 - - - +
1635A ASP* 3.0 19.7 + - + +
1637A GLU* 1.3 79.5 - - + +
1639A VAL* 1.3 64.5 + - + +
1641A SER* 3.7 7.7 + - - -
1642A LYS* 3.7 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1626A CYS* 3.2 32.5 - - - -
1629A GLN* 4.7 7.2 - - + +
1630A LEU* 3.6 24.5 - - + -
1634A THR* 3.6 15.0 - - + -
1635A ASP 3.4 14.8 - - - +
1636A ILE* 3.0 6.2 + - - +
1638A VAL* 1.3 76.4 - - + +
1640A VAL* 1.3 56.5 + - - +
1641A SER 3.0 3.4 - - - -
1642A LYS* 2.7 26.5 + - - +
1643A TYR* 3.3 26.9 + - + +
1648A ILE* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636A ILE* 2.9 24.6 + - + +
1637A GLU* 3.8 9.0 - - - +
1638A VAL 3.4 0.4 - - - -
1639A VAL* 1.3 76.0 - - - +
1641A SER* 1.3 59.8 + - - +
1643A TYR 3.8 2.1 - - - +
1648A ILE* 3.4 22.4 - - + -
1683A LEU* 4.0 16.8 - - + -
1686A LYS* 4.7 6.5 - - + -
1694A VAL* 4.0 9.8 - - + +
1697A LYS* 3.2 30.3 + - - +
1698A ILE* 3.5 34.5 - - + -
1701A LEU* 3.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1637A GLU 3.8 10.9 + - - -
1638A VAL 4.0 7.1 + - - -
1639A VAL 3.0 0.6 - - - -
1640A VAL* 1.3 81.3 - - - +
1642A LYS* 1.3 65.7 + - - +
1643A TYR 3.5 3.2 + - - +
1686A LYS* 3.9 17.3 + - - -
1694A VAL* 5.3 5.6 - - - +
1697A LYS* 4.4 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622A GLN* 5.6 0.5 - - - -
1629A GLN* 5.3 10.5 - - - +
1638A VAL* 3.7 23.3 - - + +
1639A VAL* 2.7 15.1 + - - +
1641A SER* 1.3 77.7 - - - +
1643A TYR* 1.3 75.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1622A GLN* 3.5 33.2 - - + +
1625A ASP* 3.4 22.6 + - + +
1626A CYS* 3.3 35.3 + - + -
1629A GLN* 2.6 30.5 + - - -
1639A VAL* 3.3 30.2 + - + +
1640A VAL 3.8 2.6 - - - +
1641A SER 4.4 0.6 - - - +
1642A LYS* 1.3 93.4 - - + +
1644A ILE* 1.3 65.2 + - - +
1647A ALA* 4.6 4.7 - - + -
1648A ILE* 4.8 5.1 - - + +
1697A LYS* 2.7 32.2 + - - +
----------------------------------------------------------
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