Contacts of the helix formed by residues 1886 - 1900 (chain D) in PDB entry 6AH0
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 ASP1886 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1883D LYS 3.5 11.9 + - - +
1884D PHE 3.4 4.1 - - - +
1885D ASN* 1.3 76.9 - - - +
1887D PRO* 1.3 64.2 - - - +
1888D HIS 3.2 3.4 - - - -
1889D VAL* 3.2 8.3 + - - +
1890D LYS* 3.1 17.0 + - - -
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Residues in contact with PRO1887 (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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1855D TYR 4.1 15.6 - - - +
1856D GLU* 5.6 2.7 - - - -
1858D ILE* 4.4 18.3 - - - +
1859D PRO 5.6 4.0 - - - +
1885D ASN 3.8 4.0 - - - -
1886D ASP* 1.3 67.3 - - - +
1888D HIS* 1.3 59.3 + - - +
1890D LYS* 3.7 4.3 - - - +
1891D THR* 2.9 24.6 + - - -
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Residues in contact with HIS1888 (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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1850D SER* 4.0 26.4 - - - +
1851D ASN* 5.1 4.0 - - - +
1855D TYR 4.7 2.4 + - - -
1856D GLU* 5.8 1.4 - - - +
1886D ASP 3.2 1.2 - - - -
1887D PRO* 1.3 73.1 - - - +
1889D VAL* 1.3 65.3 + - - +
1891D THR* 3.3 1.1 + - - +
1892D ASN* 3.0 21.0 + - - -
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Residues in contact with VAL1889 (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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1883D LYS 5.1 7.2 - - - -
1886D ASP 3.2 8.1 + - - -
1888D HIS* 1.3 75.1 - - - +
1890D LYS* 1.3 61.7 + - - +
1892D ASN* 3.2 3.8 + - - +
1893D LEU* 3.0 20.4 + - - -
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Residues in contact with LYS1890 (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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1886D ASP 3.1 12.4 + - - -
1887D PRO* 3.4 5.8 + - - -
1888D HIS 3.3 0.4 - - - -
1889D VAL* 1.3 76.3 - - - +
1891D THR* 1.3 55.5 + - - +
1893D LEU* 3.4 1.9 + - - +
1894D LEU* 2.9 25.5 + - - -
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Residues in contact with THR1891 (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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1850D SER* 5.6 5.2 - - - +
1887D PRO 2.9 16.5 + - - -
1888D HIS* 3.8 1.8 - - - +
1889D VAL 3.2 0.2 - - - -
1890D LYS* 1.3 73.4 - - - +
1892D ASN* 1.3 59.5 + - - +
1894D LEU* 4.4 1.3 - - - +
1895D LEU* 2.9 26.9 + - - -
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Residues in contact with ASN1892 (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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1846D ILE 5.3 11.0 - - - -
1847D GLU* 6.0 2.2 - - - +
1850D SER* 5.2 4.2 - - - +
1888D HIS 3.0 14.8 + - - -
1889D VAL* 3.6 4.0 - - - +
1891D THR* 1.3 74.3 - - - +
1893D LEU* 1.3 56.0 + - - +
1895D LEU* 3.2 1.7 + - - -
1896D GLN* 2.9 26.3 + - - -
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Residues in contact with LEU1893 (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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1872D ALA* 6.2 4.5 - - - +
1889D VAL 3.0 13.2 + - - -
1890D LYS* 3.8 2.7 - - - +
1892D ASN* 1.3 72.8 - - - +
1894D LEU* 1.3 59.5 + - - +
1896D GLN* 3.6 1.6 + - - +
1897D ALA* 2.9 24.8 + - - -
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Residues in contact with LEU1894 (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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1890D LYS 2.9 17.4 + - - -
1891D THR* 4.0 1.6 - - - +
1893D LEU* 1.3 74.7 - - - +
1895D LEU* 1.3 57.1 + - - +
1897D ALA* 3.5 2.6 + - - +
1898D HIS* 2.9 23.4 + - - -
1912D THR* 5.5 11.0 - - - +
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Residues in contact with LEU1895 (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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1891D THR 2.9 18.2 + - - -
1892D ASN 3.6 1.1 - - - -
1894D LEU* 1.3 74.3 - - - +
1896D GLN* 1.3 58.9 + - - +
1898D HIS* 3.0 3.9 + - - +
1899D LEU* 2.9 24.3 + - - -
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Residues in contact with GLN1896 (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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1876D PRO 6.4 0.2 - - - -
1892D ASN 2.9 14.5 + - - -
1893D LEU* 4.0 1.6 - - - +
1895D LEU* 1.3 73.5 - - - +
1897D ALA* 1.3 56.8 + - - +
1899D LEU* 3.1 3.7 + - - +
1900D SER* 2.8 27.4 + - - -
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Residues in contact with ALA1897 (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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1893D LEU 2.9 19.1 + - - -
1894D LEU* 3.7 2.9 - - - +
1895D LEU 3.2 0.2 - - - -
1896D GLN* 1.3 74.4 - - - +
1898D HIS* 1.3 59.5 + - - +
1900D SER* 3.3 2.4 + - - +
1901D ARG 3.1 3.3 + - - -
1902D MET* 3.0 35.7 + - - +
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Residues in contact with HIS1898 (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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1894D LEU 2.9 15.2 + - - -
1895D LEU* 3.0 4.4 + - - +
1897D ALA* 1.3 75.1 - - - +
1899D LEU* 1.3 60.7 + - - +
1901D ARG* 3.1 14.2 + - - +
1902D MET 5.2 1.6 - - - +
1952D ALA* 4.1 14.0 - - - -
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Residues in contact with LEU1899 (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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1895D LEU 2.9 13.4 + - - -
1896D GLN* 3.1 4.9 + - - +
1898D HIS* 1.3 76.7 - - - +
1900D SER* 1.3 58.5 + - - +
1901D ARG 3.2 0.9 + - - -
1948D MET 5.4 1.1 - - - -
1952D ALA* 3.8 3.1 - - - +
1953D MET* 3.3 41.4 + - - +
1954D TRP* 3.6 4.0 + - - +
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Residues in contact with SER1900 (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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1896D GLN 2.8 13.4 + - - -
1897D ALA* 3.8 2.2 - - - +
1898D HIS 3.2 0.2 - - - -
1899D LEU* 1.3 77.1 - - - +
1901D ARG* 1.3 64.5 + - - +
1902D MET* 3.1 5.2 + - - -
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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