Contacts of the strand formed by residues 1841 - 1850 (chain A) in PDB entry 2H03
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 TRP1841 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1838A LEU* 2.9 60.1 + - + +
1840A GLU* 1.3 114.4 - - + +
1842A THR* 1.3 64.7 + - - +
1843A ILE* 4.1 14.5 - - + +
1863A PHE* 5.4 1.3 - + - -
1864A HIS 3.1 17.9 - - - +
1865A TYR* 3.8 13.9 - + - -
1866A THR* 4.1 3.4 - - - -
1879A SER* 3.6 17.5 - - - -
1882A GLN* 3.7 17.0 - - + -
1883A PHE* 3.4 53.4 - + + -
1886A THR* 4.1 26.4 - - + +
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Residues in contact with THR1842 (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 GLU* 4.0 18.2 - - + -
1836A SER 3.3 13.9 - - - +
1837A VAL* 3.7 23.1 - - + +
1838A LEU 4.8 0.2 + - - -
1841A TRP* 1.3 77.4 + - - +
1843A ILE* 1.3 65.3 + - - +
1844A ARG* 3.6 37.0 + - + +
1862A HIS 3.6 1.9 - - - +
1863A PHE* 3.8 0.5 - - - -
1864A HIS* 2.8 36.9 + - - +
1866A THR* 4.3 11.3 - - - +
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Residues in contact with ILE1843 (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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1834A SER* 4.2 2.3 + - - +
1835A GLU* 3.6 1.0 + - - -
1836A SER* 2.9 46.2 + - - +
1838A LEU* 4.0 21.3 - - + -
1841A TRP* 4.1 16.2 - - + +
1842A THR* 1.3 76.5 - - - +
1844A ARG* 1.3 66.2 + - - +
1861A ARG* 3.4 36.1 - - - +
1862A HIS 3.3 9.0 - - - +
1863A PHE* 3.9 31.0 - - + -
1886A THR* 5.3 2.5 - - + -
1890A TYR* 4.2 12.8 - - + +
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Residues in contact with ARG1844 (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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1814A HIS* 5.8 0.4 + - - -
1816A TRP* 3.5 39.3 - - - +
1832A MET* 4.0 6.7 - - - -
1834A SER* 3.2 9.0 - - - +
1835A GLU* 2.9 42.0 + - + -
1837A VAL* 6.1 0.2 - - - +
1842A THR* 3.6 19.2 - - + +
1843A ILE* 1.3 84.2 - - - +
1845A GLU* 1.3 60.6 + - - +
1846A PHE* 3.9 21.3 - - + -
1861A ARG* 3.5 3.1 - - - -
1862A HIS* 2.8 42.3 + - + +
1864A HIS* 3.4 36.8 + - - +
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Residues in contact with GLU1845 (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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1832A MET* 3.6 5.2 - - - +
1833A LEU* 2.7 45.0 + - + -
1834A SER* 3.0 26.9 + - - +
1844A ARG* 1.3 74.4 - - - +
1846A PHE* 1.3 65.1 + - - +
1859A LEU* 3.4 31.0 - - + +
1860A ILE 3.3 9.6 - - - +
1861A ARG* 3.2 37.4 + - + +
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Residues in contact with PHE1846 (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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1787A TRP* 4.6 7.4 - + - -
1816A TRP* 3.6 45.1 - + + -
1817A PRO* 4.0 7.0 - - + -
1830A LEU* 4.0 21.1 - - + -
1831A GLN 3.2 8.7 - - - +
1832A MET* 3.6 35.7 - - + -
1833A LEU* 4.1 4.9 - - - +
1844A ARG* 3.9 17.5 - - + -
1845A GLU* 1.3 77.3 - - - +
1847A LYS* 1.3 60.8 + - - +
1859A LEU* 3.4 5.4 - - - +
1860A ILE* 2.9 52.2 + - + -
1862A HIS* 3.6 34.3 - + + -
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Residues in contact with LYS1847 (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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1829A ILE 3.8 0.7 - - - +
1830A LEU* 3.5 4.9 - - - +
1831A GLN* 2.9 48.5 + - + +
1833A LEU* 3.9 28.7 - - + +
1846A PHE* 1.3 75.6 - - - +
1848A ILE* 1.3 62.5 + - - +
1849A CYS* 4.3 13.8 - - - -
1857A HIS* 3.8 45.7 + - + +
1858A ARG 3.4 4.3 - - - -
1859A LEU* 4.4 5.2 - - + -
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Residues in contact with ILE1848 (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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1787A TRP* 4.1 22.0 - - + +
1790A VAL* 4.9 4.0 - - + -
1791A TRP* 3.7 23.4 - - + -
1828A LEU* 4.0 26.9 - - + -
1829A ILE 3.3 3.4 - - - +
1830A LEU* 3.4 34.5 - - + -
1847A LYS* 1.3 76.3 - - - +
1849A CYS* 1.3 63.2 + - - +
1857A HIS* 3.3 3.3 - - - -
1858A ARG* 2.9 50.8 + - + +
1860A ILE* 3.7 24.0 - - + -
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Residues in contact with CYS1849 (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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1791A TRP* 4.3 2.7 - - - -
1828A LEU* 3.4 8.9 - - - +
1829A ILE* 2.9 46.0 + - + +
1847A LYS* 4.3 17.0 - - - -
1848A ILE* 1.3 76.7 - - - +
1850A GLY* 1.3 66.1 + - - +
1854A LEU* 4.1 35.0 - - + +
1856A ALA 4.7 1.1 - - - -
1857A HIS* 4.0 19.7 - - - +
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Residues in contact with GLY1850 (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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1791A TRP* 3.7 24.1 - - - -
1827A ASP 3.9 0.9 - - - -
1828A LEU* 3.7 15.5 - - - -
1849A CYS* 1.3 72.3 - - - +
1851A GLU* 1.3 65.7 + - - -
1852A GLU 3.1 2.9 - - - -
1853A GLN* 3.0 29.1 + - - +
1854A LEU* 3.7 3.5 + - - +
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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