Contacts of the helix formed by residues 1856 - 1868 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1809H ARG* 4.6 5.2 - - - +
1854H ILE 3.3 6.3 + - - -
1855H PHE* 1.3 75.3 - - - +
1857H ASP* 1.3 67.7 + - - -
1858H GLU 3.4 2.9 - - - -
1859H ASP* 3.6 8.5 - - - +
1860H VAL* 3.1 23.0 + - - +
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Residues in contact with ASP1857 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1765H GLY 5.6 0.9 - - - -
1766H VAL* 5.6 9.0 - - + +
1856H GLY* 1.3 71.9 - - - -
1858H GLU* 1.3 59.1 + - - +
1860H VAL* 3.2 12.0 - - - +
1861H LYS* 2.9 43.8 + - - +
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Residues in contact with GLU1858 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1856H GLY* 3.4 0.4 - - - -
1857H ASP* 1.3 79.8 - - - +
1859H ASP* 1.3 58.1 + - - +
1861H LYS* 3.6 10.8 - - - +
1862H GLN* 2.9 30.5 + - - +
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Residues in contact with ASP1859 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1809H ARG* 4.1 13.9 - - - +
1813H LEU* 4.7 15.3 - - + +
1855H PHE* 3.6 24.0 - - + -
1856H GLY* 3.4 24.4 + - - +
1857H ASP 3.2 0.4 - - - -
1858H GLU* 1.3 79.6 - - - +
1860H VAL* 1.3 57.8 + - - +
1862H GLN* 3.3 6.7 + - - +
1863H ILE* 2.9 33.2 + - - +
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Residues in contact with VAL1860 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1764H PRO 4.8 7.1 - - - +
1765H GLY* 3.5 27.6 - - - +
1766H VAL* 4.0 14.8 - - + -
1850H LEU* 3.9 27.1 - - + -
1855H PHE* 3.9 11.9 - - + +
1856H GLY 3.1 16.5 + - - +
1857H ASP* 3.2 15.0 - - - +
1859H ASP* 1.3 75.3 - - - +
1861H LYS* 1.3 61.1 + - - +
1863H ILE* 3.6 9.2 - - - +
1864H LEU* 2.9 30.3 + - - +
1947H PHE* 6.3 3.1 - - + -
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Residues in contact with LYS1861 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763H LEU* 3.9 26.6 - - + +
1766H VAL* 4.2 21.7 - - + +
1857H ASP* 2.9 32.2 + - - +
1858H GLU* 3.6 9.0 - - - +
1860H VAL* 1.3 77.6 - - - +
1862H GLN* 1.3 57.1 + - - +
1864H LEU* 3.3 6.1 + - - +
1865H LYS* 2.9 29.2 + - - +
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Residues in contact with GLN1862 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813H LEU* 5.1 13.7 - - + -
1858H GLU 2.9 17.6 + - - +
1859H ASP* 3.7 6.3 - - - +
1861H LYS* 1.3 76.3 - - - +
1863H ILE* 1.3 58.0 + - - +
1865H LYS* 3.3 7.1 + - - +
1866H MET* 2.9 30.7 + - - +
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Residues in contact with ILE1863 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813H LEU* 4.6 13.7 - - + -
1846H VAL* 4.1 17.0 - - + -
1850H LEU* 4.2 12.6 - - + -
1855H PHE* 3.6 38.6 - - + -
1859H ASP 2.9 22.3 + - - +
1860H VAL* 3.6 7.4 - - - +
1862H GLN* 1.3 77.6 - - - +
1864H LEU* 1.3 58.3 + - - +
1866H MET* 3.2 8.4 + - - +
1867H ILE* 2.9 43.7 + - + +
1943H LEU* 5.8 3.6 - - + -
1947H PHE* 4.0 25.6 - - + -
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Residues in contact with LEU1864 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1763H LEU* 5.6 7.2 - - + -
1764H PRO* 5.3 17.7 - - + +
1860H VAL 2.9 17.8 + - - +
1861H LYS* 3.3 6.0 + - - +
1863H ILE* 1.3 77.0 - - - +
1865H LYS* 1.3 60.4 + - - +
1867H ILE* 4.0 6.5 - - - +
1868H GLU 2.9 26.2 + - - +
1871H VAL* 3.8 25.4 - - + +
1947H PHE* 5.9 5.2 - - + -
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Residues in contact with LYS1865 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1861H LYS 2.9 16.8 + - - +
1862H GLN* 3.7 7.9 - - - +
1864H LEU* 1.3 77.7 - - - +
1866H MET* 1.3 62.2 + - - +
1868H GLU 3.4 17.2 - - - +
1869H PRO* 4.1 6.7 - - + +
1871H VAL 5.0 2.2 - - - -
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Residues in contact with MET1866 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1816H LEU* 3.7 45.8 - - + +
1817H GLY* 4.8 1.6 - - - -
1819H ALA* 5.9 1.1 - - + -
1820H VAL* 4.1 28.2 - - + +
1843H LEU* 5.4 8.3 - - + -
1862H GLN 2.9 17.7 + - - +
1863H ILE* 3.7 7.9 - - - +
1865H LYS* 1.3 74.9 - - - +
1867H ILE* 1.3 73.1 + - + +
1868H GLU* 4.6 0.2 - - - -
1925H GLU 4.8 6.6 - - - +
1926H GLY* 5.7 0.2 - - - -
1927H LEU* 4.4 32.2 + - + +
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Residues in contact with ILE1867 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1843H LEU* 6.1 0.9 - - + -
1863H ILE* 2.9 33.2 + - + +
1864H LEU* 4.0 6.7 - - - +
1865H LYS 3.4 0.4 - - - -
1866H MET* 1.3 87.0 - - + +
1868H GLU* 1.3 65.0 + - + +
1869H PRO* 4.9 0.2 - - - +
1871H VAL* 6.0 2.7 - - + -
1926H GLY* 5.5 1.0 - - - -
1927H LEU* 4.5 13.8 + - + -
1928H LEU* 3.4 35.0 + - + +
1929H GLN* 5.2 1.9 - - - +
1940H MET* 3.6 30.3 - - + -
1943H LEU* 4.8 8.7 - - + -
1944H LEU* 5.4 13.0 - - + -
1947H PHE* 4.8 13.5 - - + -
2098H LEU* 6.0 4.9 - - + -
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Residues in contact with GLU1868 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864H LEU 2.9 17.3 + - - +
1865H LYS* 3.4 8.2 - - - +
1866H MET 3.4 0.4 - - - -
1867H ILE* 1.3 85.3 - - + +
1869H PRO* 1.3 74.6 - - + +
1870H GLU* 3.5 3.3 + - + +
1871H VAL* 3.5 27.3 + - + +
1928H LEU* 5.8 2.7 - - + -
1929H GLN* 6.1 0.9 - - - +
2098H LEU* 5.3 11.4 - - + -
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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