Contacts of the helix formed by residues 1876 - 1891 (chain A) in PDB entry 4M6W
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 ASN1876 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1870A GLU* 3.0 33.7 + - - +
1871A MET* 5.5 2.8 - - - +
1873A ASN* 2.6 36.8 + - - +
1875A VAL* 1.3 79.1 - - + +
1877A LYS* 1.3 57.5 + - - +
1878A ASN 3.3 2.2 - - - -
1879A LYS* 3.9 23.1 - - + -
1880A PHE* 2.9 31.5 + - + +
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Residues in contact with LYS1877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1874A SER* 3.9 37.7 + - - +
1875A VAL 3.2 2.5 - - - +
1876A ASN* 1.3 80.1 + - - +
1878A ASN* 1.3 76.7 + - - +
1880A PHE* 3.8 4.6 - - - +
1881A ILE* 3.3 44.3 + - + +
1917A SER 5.0 2.6 + - - -
1918A TYR* 5.8 0.4 - - - +
1920A SER* 3.3 26.2 + - - -
1921A LEU* 3.9 35.0 - - + +
1924A THR* 5.7 2.5 - - - -
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Residues in contact with ASN1878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1875A VAL 4.7 4.8 + - - +
1876A ASN* 3.3 0.6 - - - +
1877A LYS* 1.3 88.4 - - - +
1879A LYS* 1.3 65.9 + - - +
1881A ILE* 3.5 13.5 + - - +
1882A GLU* 3.1 34.8 + - + +
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Residues in contact with LYS1879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1866A ARG* 6.2 0.7 - - - +
1875A VAL 5.2 1.5 + - - +
1876A ASN* 3.5 24.0 + - + +
1877A LYS 3.5 0.4 - - - -
1878A ASN* 1.3 77.2 - - - +
1880A PHE* 1.3 63.3 + - - +
1882A GLU* 3.2 9.2 + - - +
1883A GLN* 3.0 50.3 + - + +
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Residues in contact with PHE1880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864A GLU* 4.9 4.3 - - + -
1866A ARG* 3.3 40.4 - - + +
1871A MET* 3.8 31.6 - - + -
1876A ASN* 2.9 20.4 + - + +
1877A LYS* 3.8 4.3 - - - +
1879A LYS* 1.3 77.7 - - - +
1881A ILE* 1.3 62.1 + - - +
1883A GLN* 3.1 12.5 + - + +
1884A ILE* 3.0 47.4 + - + +
1896A VAL* 4.1 25.8 - - + -
1921A LEU* 3.8 20.4 - - + -
1925A LEU* 4.0 31.0 - - + -
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Residues in contact with ILE1881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1877A LYS* 3.3 43.4 + - + +
1878A ASN* 3.8 14.1 - - - +
1879A LYS 3.3 0.4 - - - -
1880A PHE* 1.3 78.3 - - + +
1882A GLU* 1.3 58.8 + - + +
1884A ILE* 3.2 11.7 + - + +
1885A GLN* 3.0 31.3 + - - +
1921A LEU* 4.3 17.0 - - + -
1924A THR* 4.8 12.1 - - + +
1925A LEU* 6.2 0.4 - - + -
144B PRO* 3.7 30.1 - - + -
145B LEU* 3.6 24.1 - - + +
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Residues in contact with GLU1882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1878A ASN* 3.1 25.4 + - - +
1879A LYS* 3.2 7.6 + - - +
1881A ILE* 1.3 77.9 - - + +
1883A GLN* 1.3 58.8 + - + +
1885A GLN* 3.4 21.3 + - - +
1886A HIS* 3.1 26.2 + - - +
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Residues in contact with GLN1883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852A GLY 5.6 6.9 + - - +
1864A GLU* 5.1 9.2 + - - +
1866A ARG* 3.2 35.5 + - - +
1879A LYS* 3.0 46.3 + - + +
1880A PHE* 3.1 13.9 + - + +
1882A GLU* 1.3 74.6 - - + +
1884A ILE* 1.3 62.0 + - + +
1886A HIS* 3.3 8.7 + - - +
1887A LEU* 3.0 35.8 + - + +
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Residues in contact with ILE1884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864A GLU* 5.4 6.1 - - + -
1880A PHE* 3.0 53.5 + - + +
1881A ILE* 3.2 9.4 + - - +
1883A GLN* 1.3 76.8 - - + +
1885A GLN* 1.3 57.9 + - - +
1887A LEU* 3.3 13.6 + - + +
1888A GLN* 2.8 33.1 + - + +
1894A ILE* 4.5 19.1 - - + -
1896A VAL* 5.2 4.3 - - + -
1925A LEU* 4.1 10.1 - - + -
1930A ILE* 3.3 30.7 - - + -
145B LEU* 3.8 15.5 - - + -
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Residues in contact with GLN1885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1881A ILE* 3.0 20.8 + - - +
1882A GLU* 3.5 29.5 - - - +
1884A ILE* 1.3 73.3 - - - +
1886A HIS* 1.3 63.8 + - - +
1888A GLN* 3.3 21.5 + - - +
1889A SER* 3.4 12.0 + - - -
144B PRO* 2.9 36.3 + - - +
145B LEU* 3.9 12.1 - - + -
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Residues in contact with HIS1886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1851A ASN* 5.0 10.6 + - - -
1852A GLY* 4.6 24.0 + - - -
1882A GLU 3.1 13.8 + - - +
1883A GLN* 3.3 10.5 + - - +
1885A GLN* 1.3 73.7 - - - +
1887A LEU* 1.3 70.2 + - + +
1889A SER* 2.6 30.0 + - - -
1890A MET* 3.5 30.7 - - + +
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Residues in contact with LEU1887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1852A GLY 3.7 10.3 - - - +
1853A CYS* 3.6 29.6 - - + -
1862A VAL* 4.2 12.1 - - + -
1864A GLU* 3.7 33.4 - - + +
1883A GLN* 3.0 24.4 + - + +
1884A ILE* 3.7 15.0 - - + +
1886A HIS* 1.3 81.6 - - + +
1888A GLN* 1.3 59.5 + - - +
1890A MET* 3.0 6.8 + - - -
1891A PHE* 2.9 45.4 + - + +
1894A ILE* 3.7 17.5 - - + -
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Residues in contact with GLN1888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1884A ILE* 2.8 16.4 + - + +
1885A GLN* 3.3 24.3 + - - +
1887A LEU* 1.3 75.9 - - - +
1889A SER* 1.3 61.9 + - - +
1890A MET 3.4 0.2 + - - -
1891A PHE 3.5 14.5 - - - +
1894A ILE* 3.5 17.7 - - + +
1928A ALA* 4.0 15.2 + - - +
1930A ILE* 4.4 4.2 - - + +
145B LEU* 3.1 50.7 + - - +
146B LEU* 5.8 0.4 - - - +
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Residues in contact with SER1889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1885A GLN 3.4 8.1 + - - -
1886A HIS* 2.6 26.2 + - - -
1888A GLN* 1.3 80.9 - - - +
1890A MET* 1.3 63.3 + - - +
1981A ASN* 3.4 39.0 + - - +
2018A LYS* 3.5 15.4 - - - +
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Residues in contact with MET1890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1851A ASN* 6.0 1.6 - - - +
1853A CYS* 5.9 2.5 - - - -
1860A ARG* 5.7 0.9 - - - -
1886A HIS* 3.5 36.3 - - + +
1887A LEU* 3.0 5.5 + - - +
1889A SER* 1.3 90.7 - - - +
1891A PHE* 1.3 82.9 + - + +
1892A GLU 4.5 0.3 + - - -
1981A ASN* 3.7 15.0 - - - +
1982A ILE 3.3 34.3 - - - +
1983A SER* 3.9 26.3 + - - +
1984A TYR 5.5 0.2 - - - +
1986A THR* 4.9 2.8 + - - -
2018A LYS* 4.3 8.0 + - - -
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Residues in contact with PHE1891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1853A CYS* 4.2 12.1 - - - -
1856A ILE* 3.8 31.4 - - + -
1860A ARG* 3.5 26.2 - - - +
1861A MET 4.2 4.0 - - - -
1862A VAL* 3.6 44.9 - - + -
1887A LEU* 2.9 23.5 + - + +
1888A GLN* 3.5 17.1 - - - +
1889A SER 3.7 0.6 - - - -
1890A MET* 1.3 93.3 - - + +
1892A GLU* 1.3 63.9 + - - +
1893A ARG 3.6 9.8 + - - +
1894A ILE* 4.2 5.9 - - + +
1983A SER* 3.5 30.1 - - - -
1985A ILE* 4.6 3.1 - - + -
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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