Contacts of the helix formed by residues 1856 - 1868 (chain D) in PDB entry 6X34
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 GLY1856 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1809D ARG* 4.6 4.9 - - - +
1854D ILE 3.3 5.9 + - - -
1855D PHE* 1.3 76.2 - - - +
1857D ASP* 1.3 66.4 + - - -
1858D GLU 3.4 2.0 - - - -
1859D ASP* 3.6 8.9 - - - +
1860D VAL* 3.1 22.6 + - - +
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Residues in contact with ASP1857 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1765D GLY 5.6 1.1 - - - -
1766D VAL* 5.6 9.9 - - + +
1856D GLY* 1.3 68.7 - - - -
1858D GLU* 1.3 61.4 + - - +
1860D VAL* 3.2 11.3 - - - +
1861D LYS* 2.9 45.3 + - - +
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Residues in contact with GLU1858 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856D GLY 3.4 0.2 - - - -
1857D ASP* 1.3 79.4 - - - +
1859D ASP* 1.3 57.2 + - - +
1861D LYS* 3.3 11.9 + - - +
1862D GLN* 2.9 30.7 + - - +
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Residues in contact with ASP1859 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1809D ARG* 4.1 13.4 - - - +
1813D LEU* 4.7 15.5 - - + +
1855D PHE* 3.6 24.2 - - + -
1856D GLY* 3.4 23.6 + - - +
1857D ASP 3.2 0.6 - - - -
1858D GLU* 1.3 79.0 - - - +
1860D VAL* 1.3 58.9 + - - +
1862D GLN* 3.3 7.0 + - - +
1863D ILE* 2.9 33.6 + - - +
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Residues in contact with VAL1860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1764D PRO 4.8 7.5 - - - +
1765D GLY* 3.6 27.1 - - - +
1766D VAL* 4.0 15.7 - - + -
1850D LEU* 3.9 26.5 - - + -
1855D PHE* 3.9 12.3 - - + +
1856D GLY 3.1 15.3 + - - +
1857D ASP* 3.2 15.3 - - - +
1859D ASP* 1.3 75.1 - - - +
1861D LYS* 1.3 61.3 + - - +
1863D ILE* 3.6 9.8 - - + +
1864D LEU* 2.9 30.1 + - - +
1947D PHE* 6.1 3.3 - - + -
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Residues in contact with LYS1861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763D LEU* 3.9 27.0 - - + +
1766D VAL* 4.2 22.0 - - + +
1857D ASP* 2.9 32.0 + - - +
1858D GLU* 3.6 9.0 - - - +
1860D VAL* 1.3 77.7 - - - +
1862D GLN* 1.3 56.0 + - - +
1864D LEU* 3.3 6.1 + - - +
1865D LYS* 2.9 30.1 + - - +
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Residues in contact with GLN1862 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813D LEU* 5.1 13.5 - - + -
1858D GLU 2.9 17.4 + - - +
1859D ASP* 3.7 5.8 - - - +
1861D LYS* 1.3 76.3 - - - +
1863D ILE* 1.3 58.1 + - - +
1865D LYS* 3.3 6.4 + - - +
1866D MET* 2.9 30.5 + - - +
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Residues in contact with ILE1863 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813D LEU* 4.6 13.2 - - + -
1846D VAL* 4.1 17.9 - - + -
1850D LEU* 4.2 13.2 - - + -
1855D PHE* 3.6 38.1 - - + -
1859D ASP 2.9 21.1 + - - +
1860D VAL* 3.6 7.6 - - - +
1861D LYS 3.2 0.2 - - - -
1862D GLN* 1.3 77.1 - - - +
1864D LEU* 1.3 56.8 + - - +
1866D MET* 3.2 8.1 + - - +
1867D ILE* 2.9 43.7 + - + +
1943D LEU* 5.8 4.3 - - + -
1947D PHE* 4.0 25.1 - - + -
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Residues in contact with LEU1864 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763D LEU* 5.6 6.7 - - + -
1764D PRO* 5.3 17.7 - - + +
1860D VAL 2.9 17.4 + - - +
1861D LYS* 3.8 6.1 - - - +
1863D ILE* 1.3 77.8 - - - +
1865D LYS* 1.3 58.6 + - - +
1867D ILE* 4.0 6.0 - - - +
1868D GLU 2.9 26.0 + - - +
1871D VAL* 3.8 25.6 - - + +
1947D PHE* 5.9 5.4 - - + -
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Residues in contact with LYS1865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861D LYS 2.9 16.8 + - - +
1862D GLN* 3.7 7.4 - - - +
1864D LEU* 1.3 77.2 - - - +
1866D MET* 1.3 62.0 + - - +
1868D GLU 3.4 17.8 - - - +
1869D PRO* 4.1 6.6 - - - +
1871D VAL 5.3 2.2 - - - -
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Residues in contact with MET1866 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1816D LEU* 3.7 45.5 - - + +
1817D GLY* 4.8 1.3 - - - -
1819D ALA* 5.9 1.1 - - + -
1820D VAL* 4.1 29.1 - - + +
1843D LEU* 5.4 8.1 - - + -
1862D GLN 2.9 17.5 + - - +
1863D ILE* 3.2 7.6 + - - +
1865D LYS* 1.3 76.5 - - - +
1867D ILE* 1.3 71.9 + - + +
1868D GLU* 4.6 0.3 - - - -
1925D GLU 4.8 6.8 - - - +
1926D GLY* 5.7 0.2 - - - -
1927D LEU* 4.4 31.8 + - + +
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Residues in contact with ILE1867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1843D LEU* 6.1 1.1 - - + -
1863D ILE* 2.9 32.9 + - + +
1864D LEU* 4.0 6.7 - - - +
1865D LYS 3.4 0.2 - - - -
1866D MET* 1.3 86.0 - - + +
1868D GLU* 1.3 65.7 + - + +
1869D PRO* 4.9 0.2 - - - +
1871D VAL* 6.0 2.5 - - + -
1926D GLY* 5.5 1.4 - - - -
1927D LEU* 4.5 14.1 + - + -
1928D LEU* 3.4 35.3 + - + +
1929D GLN* 5.2 1.7 - - - +
1940D MET* 3.6 29.2 - - + -
1943D LEU* 4.8 8.5 - - + -
1944D LEU* 5.4 13.5 - - + -
1947D PHE* 4.8 12.8 - - + -
2098D LEU* 6.0 4.7 - - + -
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Residues in contact with GLU1868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864D LEU 2.9 17.3 + - - +
1865D LYS* 3.4 8.8 - - - +
1866D MET 3.4 0.2 - - - -
1867D ILE* 1.3 86.9 - - + +
1869D PRO* 1.3 75.3 - - + +
1870D GLU* 3.5 3.1 + - + +
1871D VAL* 3.5 27.6 + - + +
1928D LEU* 5.8 2.2 - - + -
1929D GLN* 6.1 0.7 - - - +
2098D LEU* 5.3 11.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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