Contacts of the helix formed by residues 1809 - 1816 (chain A) in PDB entry 4C6C
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 VAL1809 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1499A MET* 4.1 16.2 - - + -
1530A ASP* 3.7 30.3 - - + -
1531A PHE 2.9 22.6 + - - +
1532A ALA* 4.1 6.7 - - + -
1742A LEU* 4.0 20.0 - - + -
1743A PRO* 3.7 25.4 - - + -
1807A GLN 4.0 0.4 - - - +
1808A ASP* 1.3 72.2 - - - +
1810A ARG* 1.3 65.1 + - + +
1811A LYS 3.1 0.4 - - - -
1812A TRP* 3.2 37.3 + - + +
1815A GLY* 3.4 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1810 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1532A ALA* 4.4 10.3 - - + -
1550A GLY 3.5 19.3 + - - +
1551A SER* 3.4 30.7 - - - +
1552A ALA 2.8 18.6 + - - +
1553A ALA* 3.0 27.0 + - - +
1585A LEU* 5.9 0.2 - - - +
1586A PRO* 4.4 2.0 - - - +
1740A PHE* 2.7 22.0 + - - +
1741A HIS 2.9 27.1 + - - -
1742A LEU* 4.2 13.1 - - - +
1743A PRO* 5.1 0.6 - - - +
1808A ASP* 3.1 12.4 + - - +
1809A VAL* 1.3 79.1 - - + +
1811A LYS* 1.3 60.3 + - - +
1812A TRP 3.4 5.7 - - - +
1815A GLY* 2.9 24.6 + - - +
1816A ALA* 4.4 6.5 + - - +
1817A VAL* 3.6 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1811 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1520A GLN* 4.2 24.7 + - - +
1524A GLU* 3.5 25.1 + - - +
1551A SER* 6.1 0.8 - - - -
1808A ASP* 3.0 25.1 + - + +
1810A ARG* 1.3 77.2 - - + +
1812A TRP* 1.3 68.4 + - + +
1813A PRO* 3.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP1812 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530A ASP* 3.4 33.4 - - - -
1743A PRO* 3.5 25.1 - - + -
1744A PRO 3.4 22.4 - - - -
1745A GLN* 4.1 11.2 - - + -
1746A GLU 5.7 0.2 - - - -
1789A ARG* 3.9 18.4 - - - -
1807A GLN* 2.9 35.7 + - + +
1808A ASP 3.8 7.9 + - - -
1809A VAL* 3.2 25.5 + - + +
1810A ARG 4.0 1.6 - - - +
1811A LYS* 1.3 83.2 - - + +
1813A PRO* 1.3 73.3 - - + +
1814A GLN* 3.6 22.4 - - - +
1815A GLY* 2.9 16.5 + - - +
1816A ALA* 3.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1813 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1811A LYS 3.7 5.1 - - - +
1812A TRP* 1.3 84.0 - - + +
1814A GLN* 1.3 73.4 + - + +
1815A GLY 3.3 0.7 + - - -
1816A ALA* 3.7 14.4 + - + +
2828A FMT 4.5 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1814 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741A HIS 4.8 2.4 - - - +
1743A PRO* 3.6 22.2 - - + +
1744A PRO* 4.8 13.9 + - + +
1746A GLU* 4.9 12.5 + - - +
1812A TRP* 3.6 24.4 - - - +
1813A PRO* 1.3 98.7 - - + +
1815A GLY* 1.3 57.7 + - - +
1816A ALA 3.5 6.4 + - - +
2828A FMT 3.9 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1815 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741A HIS 4.5 1.8 - - - -
1743A PRO* 3.8 17.3 - - - +
1809A VAL 3.4 22.4 - - - -
1810A ARG* 2.9 39.6 + - - -
1812A TRP* 2.9 9.0 + - - +
1814A GLN* 1.3 78.7 - - - +
1816A ALA* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1816 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1550A GLY 5.5 1.8 - - - -
1741A HIS* 4.9 2.5 - - - +
1810A ARG* 4.4 10.3 + - - +
1812A TRP 3.6 5.2 + - - +
1813A PRO* 4.1 11.5 - - + +
1814A GLN 3.5 8.0 - - - +
1815A GLY* 1.3 79.8 - - - +
1817A VAL* 1.3 66.1 + - - +
1818A PRO* 3.4 9.9 - - - +
----------------------------------------------------------
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