Contacts of the helix formed by residues 1827 - 1842 (chain A) in PDB entry 4W8F
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 ASP1827 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1825A SER 3.8 1.8 + - - -
1826A PHE* 1.3 82.1 - - - +
1828A TYR* 1.3 79.7 + - - +
1829A GLN* 3.3 28.5 + - - +
1830A VAL* 2.9 34.6 - - + +
1831A LEU 3.3 3.8 + - - -
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Residues in contact with TYR1828 (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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1826A PHE* 3.9 5.3 + - - -
1827A ASP* 1.3 78.6 + - - +
1829A GLN* 1.3 68.8 + - - +
1831A LEU* 3.1 6.9 + - + +
1832A SER* 2.7 63.6 + - - -
1856A LYS* 6.0 3.4 - - - +
1857A VAL* 4.4 22.2 - - + -
1860A ALA* 3.5 26.3 - - + +
1861A VAL* 3.8 30.7 - - + -
1864A ASN* 3.3 11.4 + - - -
1882A LEU* 3.0 30.5 - - + +
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Residues in contact with GLN1829 (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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1827A ASP* 3.7 22.2 + - - +
1828A TYR* 1.3 98.1 - - - +
1830A VAL* 1.3 57.6 + - - +
1832A SER* 3.2 7.2 + - - -
1833A ARG* 2.8 35.9 + - - +
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Residues in contact with VAL1830 (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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1826A PHE* 4.6 8.3 - - + -
1827A ASP* 2.9 43.9 - - + +
1829A GLN* 1.3 80.7 - - - +
1831A LEU* 1.3 61.8 + - - +
1833A ARG* 3.5 34.6 - - - +
1834A LEU* 3.0 44.2 + - + +
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Residues in contact with LEU1831 (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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1820A PHE* 3.5 45.0 - - + -
1822A CYS* 6.1 0.4 - - - -
1826A PHE* 3.5 36.6 - - + -
1827A ASP 3.3 5.9 + - - +
1828A TYR* 3.1 11.3 + - + +
1830A VAL* 1.3 76.0 - - - +
1832A SER* 1.3 67.2 + - - +
1834A LEU* 3.4 4.3 + - + +
1835A LEU* 3.1 25.8 + - + +
1847A PHE* 4.0 10.8 - - + -
1853A LEU* 6.3 0.7 - - + -
1861A VAL* 3.5 38.8 - - + -
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Residues in contact with SER1832 (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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1828A TYR* 2.7 57.3 + - - -
1829A GLN* 3.6 7.4 + - - -
1831A LEU* 1.3 74.6 - - - +
1833A ARG* 1.3 63.9 + - - +
1835A LEU* 3.1 9.5 + - - +
1836A VAL* 3.0 28.5 + - - +
1864A ASN* 5.4 3.6 - - - +
1882A LEU* 3.5 21.8 - - - -
1884A GLU* 5.8 1.8 - - - -
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Residues in contact with ARG1833 (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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1531A ARG* 3.9 30.5 - - - +
1538A TYR* 2.7 45.4 + - + +
1539A PHE 3.9 6.5 + - - -
1540A LEU 3.6 19.6 + - - -
1541A GLY* 3.5 17.1 - - - +
1542A ASN 5.2 0.4 - - - +
1829A GLN* 2.8 19.8 + - - +
1830A VAL* 3.5 46.4 + - - +
1832A SER* 1.3 79.2 - - - +
1834A LEU* 1.3 58.5 + - - +
1836A VAL* 3.1 8.5 + - - +
1837A GLY 3.0 23.0 + - - -
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Residues in contact with LEU1834 (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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1538A TYR 4.0 2.0 - - - +
1539A PHE* 3.3 54.2 - - + +
1818A VAL* 6.4 0.2 - - + -
1819A VAL 5.5 0.7 - - - +
1820A PHE* 3.3 41.1 - - + -
1830A VAL* 3.0 40.9 + - + +
1831A LEU* 3.8 4.7 - - + +
1832A SER 3.3 0.2 - - - -
1833A ARG* 1.3 79.5 - - - +
1835A LEU* 1.3 58.4 + - - +
1837A GLY 3.3 0.7 + - - -
1838A ILE* 2.9 28.4 + - - +
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Residues in contact with LEU1835 (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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1820A PHE* 4.3 7.4 - - + -
1831A LEU* 3.1 20.5 + - + +
1832A SER* 3.1 10.7 + - - +
1834A LEU* 1.3 76.2 - - - +
1836A VAL* 1.3 65.1 + - + +
1838A ILE* 3.2 21.0 + - + +
1839A THR* 3.1 26.0 + - - +
1847A PHE* 4.3 21.5 - - + -
1861A VAL* 4.7 2.5 - - + -
1864A ASN* 4.3 19.5 - - + +
1865A ILE* 4.2 18.2 - - + -
1868A ILE* 3.4 34.1 - - + -
1881A LEU* 6.3 2.2 - - + -
1894A VAL* 4.8 9.6 - - + -
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Residues in contact with VAL1836 (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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1528A GLU* 4.7 2.0 - - - +
1538A TYR* 3.5 20.0 - - + +
1832A SER* 3.0 22.1 + - - +
1833A ARG* 3.1 8.3 + - - +
1835A LEU* 1.3 77.4 - - + +
1837A GLY* 1.3 61.4 + - - +
1839A THR* 2.8 19.7 + - - -
1840A GLN* 3.1 36.2 + - - +
1881A LEU* 4.7 15.7 - - + -
1882A LEU* 6.1 0.4 - - + -
1884A GLU* 4.2 20.0 - - + +
1886A THR* 3.6 23.6 - - + +
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Residues in contact with GLY1837 (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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1535A PRO 4.1 3.6 - - - -
1538A TYR* 3.4 31.4 - - - +
1539A PHE* 4.3 4.7 - - - -
1833A ARG 3.0 10.3 + - - -
1834A LEU 3.3 3.3 + - - -
1835A LEU 3.2 0.2 - - - -
1836A VAL* 1.3 78.2 - - - +
1838A ILE* 1.3 53.5 + - - +
1840A GLN 3.1 1.2 + - - -
1841A ILE* 2.7 43.8 + - - +
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Residues in contact with ILE1838 (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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1539A PHE* 4.2 5.3 - - + -
1818A VAL* 3.3 23.3 - - + -
1820A PHE* 4.6 4.7 - - + -
1834A LEU 2.9 13.9 + - - +
1835A LEU* 3.2 30.5 + - + +
1837A GLY* 1.3 75.9 - - - +
1839A THR* 1.3 61.5 + - + +
1841A ILE* 4.6 0.9 - - - -
1842A GLY* 2.8 23.7 + - - -
1843A ALA* 3.0 33.6 + - + +
1844A TRP 3.4 1.1 - - - -
1845A GLY* 2.9 44.9 - - - +
1892A THR* 3.5 16.9 - - + +
1893A ALA 5.2 1.3 - - - +
1894A VAL* 5.4 1.8 - - + -
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Residues in contact with THR1839 (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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1835A LEU 3.1 13.2 + - - +
1836A VAL* 2.8 23.4 + - - -
1838A ILE* 1.3 77.3 - - + +
1840A GLN* 1.3 61.1 + - - +
1868A ILE* 3.7 45.8 - - + -
1879A ILE* 4.9 2.5 - - + -
1881A LEU* 5.5 2.9 - - + +
1886A THR* 4.0 13.1 + - - -
1887A PRO 4.0 5.9 + - - -
1888A LEU* 3.9 11.7 - - + -
1889A SER* 2.9 28.8 + - - -
1892A THR* 3.2 15.7 + - + -
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Residues in contact with GLN1840 (chain A).
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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1532A ARG* 3.8 27.0 - - - +
1535A PRO* 3.8 22.8 - - + +
1538A TYR* 2.8 43.7 + - + -
1836A VAL* 3.3 21.1 - - + +
1837A GLY 3.1 1.8 + - - +
1839A THR* 1.3 78.6 + - - +
1841A ILE* 1.3 66.6 + - - +
1886A THR* 4.1 2.4 - - - +
1887A PRO* 3.8 41.7 - - + +
1889A SER* 4.0 7.8 + - - +
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Residues in contact with ILE1841 (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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1535A PRO* 3.6 23.1 - - + +
1536A ARG* 3.7 47.6 - - + +
1539A PHE* 3.3 41.3 - - + -
1612A ASP* 5.8 0.9 - - - +
1761A GLU* 5.3 3.6 - - - +
1837A GLY 2.7 23.2 + - - +
1840A GLN* 1.3 74.5 - - - +
1842A GLY* 1.3 58.2 + - - +
1843A ALA* 4.1 17.3 - - + +
1889A SER* 4.0 5.6 + - - -
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Residues in contact with GLY1842 (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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1761A GLU* 5.3 2.1 - - - +
1815A ARG* 4.1 5.0 + - - -
1838A ILE 2.8 17.1 + - - -
1840A GLN 3.3 2.2 - - - -
1841A ILE* 1.3 77.1 - - - +
1843A ALA* 1.3 60.9 + - - +
1889A SER* 3.6 13.0 - - - -
1891A HIS* 2.9 27.3 - - - +
1892A THR* 3.5 15.9 - - - -
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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