Contacts of the helix formed by residues 1820 - 1830 (chain D) in PDB entry 1UKJ
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 GLY1820 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1785D GLN 4.7 0.2 + - - -
1818D LEU* 3.2 2.0 - - - +
1819D LYS* 1.3 77.5 - - - +
1821D GLY* 1.3 67.6 + - - +
1822D ILE 3.2 10.2 + - - +
1824D ALA* 3.6 19.3 + - - +
1827D ARG* 5.4 1.0 + - - -
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Residues in contact with GLY1821 (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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1818D LEU 3.1 15.7 + - - -
1819D LYS 3.1 4.8 + - - -
1820D GLY* 1.3 80.5 - - - +
1822D ILE* 1.3 61.3 + - - -
1824D ALA* 3.1 11.3 + - - +
1825D GLY 3.2 9.4 + - - -
1871D GLU* 3.4 10.5 - - - +
1872D GLY* 3.8 14.7 - - - -
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Residues in contact with ILE1822 (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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1820D GLY 3.2 8.1 - - - +
1821D GLY* 1.3 72.4 - - - -
1823D GLY* 1.3 63.0 + - - +
1826D ARG* 4.5 7.7 + - + +
1850D HIS* 4.1 13.7 - - + -
1852D ALA 3.4 22.9 - - - +
1853D SER* 4.9 4.7 - - - -
1861D PRO* 6.2 1.6 - - + -
1864D ARG* 3.8 20.4 - - - +
1871D GLU* 2.9 35.7 + - + +
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Residues in contact with GLY1823 (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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1821D GLY 3.4 0.2 + - - -
1822D ILE* 1.3 77.9 - - - +
1824D ALA* 1.3 57.6 + - - +
1825D GLY 3.3 3.0 - - - +
1826D ARG* 2.9 40.3 + - - +
1827D ARG* 2.9 46.9 + - - +
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Residues in contact with ALA1824 (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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1818D LEU* 3.7 14.6 - - + -
1820D GLY* 3.6 27.3 + - - +
1821D GLY 3.1 13.4 + - - +
1822D ILE 3.2 1.4 + - - -
1823D GLY* 1.3 76.2 - - - +
1825D GLY* 1.3 60.3 + - - +
1827D ARG* 3.3 15.8 - - - +
1828D PHE* 2.8 31.4 + - - +
1897D SER* 3.5 16.0 - - - +
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Residues in contact with GLY1825 (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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1818D LEU* 3.4 19.2 - - - +
1821D GLY 3.2 8.0 + - - -
1823D GLY 3.9 0.2 - - - +
1824D ALA* 1.3 78.8 - - - +
1826D ARG* 1.3 59.7 + - - +
1828D PHE* 3.6 0.8 - - - +
1829D MET* 2.9 35.5 + - - +
1850D HIS* 3.5 24.7 - - - -
1872D GLY* 5.2 0.9 - - - -
1874D VAL* 4.6 2.5 - - - -
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Residues in contact with ARG1826 (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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1043C VAL* 3.7 21.3 - - + -
1044C GLU* 3.7 17.9 - - - +
1822D ILE* 4.4 8.0 - - + +
1823D GLY* 2.9 45.1 + - - +
1824D ALA 3.3 0.4 - - - -
1825D GLY* 1.3 77.0 - - - +
1827D ARG* 1.3 77.1 + - - +
1829D MET* 3.7 2.7 - - - +
1830D ASN* 2.8 38.5 + - - +
1850D HIS* 3.5 10.4 + - - -
1853D SER* 4.3 16.4 - - - -
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Residues in contact with ARG1827 (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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1820D GLY* 5.4 1.2 + - - -
1823D GLY* 2.9 35.3 + - - +
1824D ALA* 3.3 15.5 - - - +
1826D ARG* 1.3 93.2 - - - +
1828D PHE* 1.3 67.7 + - - +
1830D ASN* 3.5 5.3 + - - +
1831D ALA* 3.2 22.2 + - - +
1896D ALA* 3.8 18.6 - - - +
1897D SER* 3.1 24.5 + - - -
1898D ALA* 3.3 24.7 + - - -
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Residues in contact with PHE1828 (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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1816D PHE* 4.1 15.0 - + - -
1818D LEU* 4.0 11.9 - - + -
1824D ALA 2.8 20.6 + - - +
1825D GLY 3.6 2.9 - - - +
1827D ARG* 1.3 76.1 - - - +
1829D MET* 1.3 105.1 + - + +
1831D ALA* 2.8 14.9 + - - +
1832D LEU* 3.2 34.0 + - + +
1874D VAL* 4.3 8.7 - - + -
1876D LEU* 4.7 5.6 - - + -
1890D VAL* 3.9 22.4 - - + -
1893D ALA* 3.8 34.0 - - + +
1894D LEU* 3.7 31.4 - - + -
1897D SER* 3.9 6.0 - - - -
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Residues in contact with MET1829 (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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1043C VAL* 3.5 19.7 - - + -
1825D GLY 2.9 28.8 + - - +
1826D ARG 3.7 0.9 - - - +
1828D PHE* 1.3 92.9 - - + +
1830D ASN* 1.3 52.2 + - - +
1831D ALA 2.9 4.0 + - - -
1832D LEU* 3.1 11.5 + - - +
1837D ARG* 2.5 36.6 + - + +
1848D ALA* 3.9 20.4 - - + +
1849D GLN* 4.0 13.9 - - - +
1850D HIS* 3.5 28.7 - - + -
1854D MET* 4.8 3.4 - - - +
1874D VAL* 3.3 41.5 - - + -
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Residues in contact with ASN1830 (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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1041C PRO 5.4 1.4 - - - +
1042C THR* 3.4 17.3 - - - +
1043C VAL* 2.6 44.4 - - - +
1044C GLU* 2.7 25.4 - - - +
1826D ARG* 2.8 24.9 + - + +
1827D ARG* 3.8 5.6 - - - +
1829D MET* 1.3 71.8 - - - +
1831D ALA* 1.3 57.2 + - - +
1837D ARG* 3.9 11.7 + - - +
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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