Contacts of the helix formed by residues 1841 - 1851 (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 LYS1841 (chain r).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1839r LYS 3.6 5.5 + - - +
1840r THR* 1.3 74.6 - - - +
1842r VAL* 1.3 58.1 + - - +
1843r ARG* 3.1 4.7 - - + +
1844r GLY* 2.7 29.2 + - - +
1845r LEU* 2.9 13.0 + - - -
1941r ALA* 5.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1842 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841r LYS* 1.3 74.6 - - - +
1843r ARG* 1.3 63.0 + - - +
1845r LEU* 3.6 10.3 - - - +
1846r ILE* 2.9 24.9 + - - +
1941r ALA* 4.9 16.7 - - + +
1945r LEU* 5.5 8.1 - - + -
1955r SER* 5.6 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1843 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841r LYS* 3.1 4.4 - - + +
1842r VAL* 1.3 78.7 - - - +
1844r GLY* 1.3 61.6 + - - +
1846r ILE* 3.6 13.6 + - - +
1847r GLU* 3.7 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1844 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840r THR* 5.4 6.3 - - - -
1841r LYS 2.7 16.7 + - - +
1843r ARG* 1.3 74.3 - - - +
1845r LEU* 1.3 57.5 + - - -
1847r GLU* 3.2 6.1 + - - +
1848r ILE* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1845 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1840r THR* 5.4 3.0 - - - -
1841r LYS 2.9 13.2 + - - +
1842r VAL* 3.9 13.2 - - - +
1844r GLY* 1.3 75.0 - - - +
1846r ILE* 1.3 57.0 + - - +
1848r ILE* 4.5 5.4 - - - -
1849r ILE* 2.9 33.8 + - - +
1941r ALA 6.5 0.4 - - - -
1942r ALA* 5.9 7.9 - - + -
1945r LEU* 5.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1846 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1842r VAL 2.9 17.6 + - - +
1843r ARG* 3.6 7.6 - - - +
1845r LEU* 1.3 77.7 - - - +
1847r GLU* 1.3 56.8 + - - +
1849r ILE* 3.8 2.7 - - - +
1850r SER* 3.0 28.3 + - - -
1892r ASN* 5.2 9.2 - - + +
1895r LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1847 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1843r ARG 3.7 6.6 + - - +
1844r GLY* 3.2 8.2 + - - +
1846r ILE* 1.3 76.0 - - - +
1848r ILE* 1.3 65.5 + - - +
1850r SER* 3.1 8.0 + - - -
1851r ASN* 3.0 24.8 + - - +
1892r ASN* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1848 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1831r LEU* 6.1 0.7 - - - +
1832r PHE* 5.9 4.7 - - - -
1835r SER* 4.5 22.2 - - - -
1836r LEU* 5.5 4.5 - - + +
1844r GLY 2.9 18.6 + - - +
1845r LEU* 4.2 4.9 - - - +
1847r GLU* 1.3 78.1 - - - +
1849r ILE* 1.3 60.4 + - - +
1850r SER 3.3 0.5 + - - -
1851r ASN* 3.4 13.4 + - - +
1852r ALA* 3.9 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1849 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1845r LEU 2.9 19.9 + - - +
1846r ILE* 4.1 2.7 - - - +
1848r ILE* 1.3 75.7 - - - +
1850r SER* 1.3 59.9 + - - +
1851r ASN 3.4 0.2 - - - -
1852r ALA* 3.3 19.5 - - - +
1855r TYR* 5.2 2.1 - - - +
1922r LEU* 5.2 16.3 - - + +
1923r ILE* 5.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1850 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1846r ILE 3.0 18.3 + - - -
1847r GLU* 3.1 10.7 + - - -
1849r ILE* 1.3 75.5 - - - +
1851r ASN* 1.3 58.4 + - - +
1852r ALA 3.0 10.3 + - - +
1855r TYR* 3.6 20.3 - - - +
1888r HIS* 3.7 31.4 - - - +
1891r THR* 4.7 6.1 - - - -
1892r ASN* 4.1 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1851 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1831r LEU* 5.8 10.6 - - + +
1847r GLU 3.0 13.9 + - - +
1848r ILE* 3.4 8.7 + - - +
1850r SER* 1.3 72.8 - - - +
1852r ALA* 1.3 67.0 + - - +
1853r ALA* 3.5 1.9 + - - -
1888r HIS* 4.2 15.0 - - + +
----------------------------------------------------------
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