Contacts of the helix formed by residues 1813 - 1823 (chain r) in PDB entry 6FF7
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 LEU1813 (chain r).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1800r LYS* 3.9 20.6 - - + +
1801r CYS 3.1 14.5 + - - +
1802r ILE* 4.2 8.1 - - - +
1803r SER* 5.0 3.6 - - - +
1811r ALA 3.7 0.2 + - - -
1812r PRO* 1.3 74.1 - - - +
1814r ASN* 1.3 69.2 + - - +
1815r LEU 3.4 0.8 + - - -
1816r GLY 3.5 1.8 + - - -
1817r MET* 2.9 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1814 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1813r LEU* 1.3 77.3 - - - +
1815r LEU* 1.3 66.7 + - - +
1817r MET* 3.0 7.1 + - - +
1818r ILE* 3.0 19.2 + - - +
1932r SER* 5.5 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1815 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1799r SER 4.6 5.6 - - - +
1800r LYS* 3.3 25.9 + - + +
1801r CYS* 4.2 2.2 - - + -
1813r LEU 3.4 0.2 - - - -
1814r ASN* 1.3 76.8 - - - +
1816r GLY* 1.3 65.2 + - - +
1818r ILE* 2.8 20.7 + - - +
1819r ALA* 2.9 13.5 + - - +
1829r ILE* 5.5 14.1 - - + +
1830r GLU* 6.5 0.2 - - - -
1833r SER* 6.1 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1816 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737r ASN* 5.4 9.4 - - - +
1741r VAL* 5.7 2.0 - - - -
1801r CYS* 3.6 34.8 - - - +
1812r PRO* 5.5 2.5 - - - -
1813r LEU 3.5 2.8 + - - -
1815r LEU* 1.3 77.8 - - - +
1817r MET* 1.3 56.6 - - - +
1819r ALA* 3.4 8.3 - - - +
1820r ALA* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1817 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1741r VAL* 5.4 4.3 - - - -
1812r PRO* 5.1 7.8 - - + +
1813r LEU 2.9 16.0 + - - +
1814r ASN* 3.0 12.8 + - - +
1816r GLY* 1.3 77.3 - - - +
1818r ILE* 1.3 62.3 + - - +
1820r ALA* 3.8 4.5 - - - +
1821r TYR* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1818 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814r ASN 3.0 9.7 + - - +
1815r LEU* 2.8 12.4 + - - +
1817r MET* 1.3 72.7 - - - +
1819r ALA* 1.3 69.6 + - - +
1821r TYR* 2.9 17.2 + - - +
1822r TYR* 3.0 15.3 + - - +
1829r ILE* 5.8 5.8 - - + -
1925r ALA* 5.6 12.1 - - + +
1928r ASP* 5.3 13.5 - - + -
1929r VAL 6.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1819 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737r ASN* 6.0 3.6 - - + -
1801r CYS* 6.2 0.2 - - + -
1815r LEU 2.9 8.2 + - - +
1816r GLY* 3.4 13.2 - - - +
1818r ILE* 1.3 81.7 - - - +
1820r ALA* 1.3 64.7 + - - +
1822r TYR* 3.2 0.7 + - - +
1823r TYR* 2.9 21.1 + - - -
1824r ILE* 3.3 31.7 + - - +
1825r ASN 5.1 0.9 - - - +
1826r TYR* 4.9 16.2 - - + -
1829r ILE* 5.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1820 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737r ASN* 5.1 2.0 - - + +
1738r ALA* 4.0 34.9 - - + +
1741r VAL* 4.1 15.5 - - + -
1816r GLY 2.9 15.0 + - - +
1817r MET 3.8 3.6 - - - +
1819r ALA* 1.3 78.2 - - - +
1821r TYR* 1.3 62.3 + - - +
1823r TYR* 3.7 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1821 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1817r MET 3.0 14.7 + - - +
1818r ILE* 2.9 13.0 + - - +
1820r ALA* 1.3 79.3 - - - +
1822r TYR* 1.3 59.0 + - + +
1823r TYR* 3.6 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1822 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1818r ILE 3.0 13.4 + - - +
1819r ALA 4.3 1.3 - - - +
1821r TYR* 1.3 77.0 - - + +
1823r TYR* 1.3 71.4 + - - +
1824r ILE* 4.7 10.0 - - + +
1921r ARG* 4.4 33.3 - - + +
1925r ALA* 5.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1823 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1434r ILE* 4.3 24.2 - - + -
1819r ALA 2.9 8.9 + - - -
1820r ALA* 3.7 7.9 + - - +
1821r TYR 3.3 3.8 - - - +
1822r TYR* 1.3 82.9 - - - +
1824r ILE* 1.3 56.4 + - - +
----------------------------------------------------------
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