Contacts of the strand formed by residues 1828 - 1837 (chain A) in PDB entry 2H04
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 LEU1828 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1787A TRP* 3.2 37.9 - - + +
1788A LYS* 4.0 7.6 - - + +
1791A TRP* 3.6 36.3 - - + +
1824A TYR* 3.5 5.6 - - - -
1825A TYR* 2.9 40.2 + - + +
1826A GLY 4.1 1.7 - - - +
1827A ASP* 1.3 84.7 - - + +
1829A ILE* 1.3 64.3 + - - +
1848A ILE* 3.8 19.3 - - + -
1849A CYS 3.4 4.9 - - - +
1850A GLY* 3.7 23.6 - - - -
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Residues in contact with ILE1829 (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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1822A SER* 3.8 26.0 - - - +
1823A LEU 3.4 10.3 - - - +
1824A TYR* 3.7 40.4 - - + +
1827A ASP 5.9 0.2 - - - +
1828A LEU* 1.3 75.6 - - - +
1830A LEU* 1.3 64.4 + - - +
1831A GLN* 5.0 0.7 - - + +
1847A LYS 3.8 0.7 - - - +
1848A ILE* 3.2 7.2 - - - +
1849A CYS* 2.7 56.4 + - + +
1850A GLY 5.8 2.7 - - - +
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Residues in contact with LEU1830 (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* 3.5 39.0 - - + -
1817A PRO* 3.5 33.1 - - + +
1822A SER* 3.4 2.7 - - - -
1823A LEU* 2.9 32.0 + - - +
1825A TYR* 3.6 20.2 - - + -
1828A LEU* 4.2 0.6 - - + -
1829A ILE* 1.3 76.5 - - - +
1831A GLN* 1.3 61.5 + - - +
1846A PHE* 3.8 22.9 - - + -
1847A LYS 3.4 6.3 - - - +
1848A ILE* 3.6 37.7 - - + -
1860A ILE* 4.7 1.1 - - + -
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Residues in contact with GLN1831 (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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1817A PRO* 4.5 1.6 - - - -
1820A GLN* 3.1 30.3 + - - +
1821A ASP 4.7 0.2 - - - -
1822A SER* 3.7 23.8 - - - +
1829A ILE* 5.0 0.9 - - + +
1830A LEU* 1.3 75.7 - - - +
1832A MET* 1.3 66.4 + - - +
1833A LEU* 3.4 18.5 + - + +
1846A PHE* 3.3 5.5 - - - -
1847A LYS* 2.7 58.6 + - + +
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Residues in contact with MET1832 (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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1817A PRO* 3.9 19.6 - - + +
1818A ALA 4.0 3.8 - - - +
1819A ASP* 3.7 43.9 + - - +
1820A GLN* 3.1 33.6 - - - +
1831A GLN* 1.3 74.5 - - - +
1833A LEU* 1.3 60.6 + - - +
1834A SER 3.6 20.0 - - - +
1835A GLU* 3.9 23.8 - - + +
1844A ARG* 3.8 29.8 - - - -
1845A GLU 4.0 0.7 - - - +
1846A PHE* 3.6 26.0 - - + -
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Residues in contact with LEU1833 (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 GLN* 4.1 11.8 + - - +
1831A GLN* 4.0 23.1 - - - +
1832A MET* 1.3 75.1 - - - +
1834A SER* 1.3 60.8 + - - +
1845A GLU* 2.5 26.0 + - + +
1846A PHE 4.2 0.2 - - - -
1847A LYS* 3.9 31.9 - - + +
1859A LEU* 3.7 29.8 - - + -
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Residues in contact with SER1834 (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 GLN* 4.1 7.2 - - - +
1832A MET* 3.5 11.0 - - - +
1833A LEU* 1.3 79.9 - - - +
1835A GLU* 1.3 61.5 + - - +
1836A SER* 5.1 4.8 + - - -
1843A ILE 5.0 1.6 + - - -
1844A ARG* 3.2 6.5 - - - +
1845A GLU* 2.9 57.2 + - - +
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Residues in contact with GLU1835 (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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1816A TRP* 4.8 1.4 + - - -
1818A ALA 5.5 1.6 - - - +
1820A GLN* 5.1 2.4 - - - +
1832A MET* 3.9 23.4 - - + +
1834A SER* 1.3 74.8 - - - +
1836A SER* 1.3 63.3 + - - +
1837A VAL* 4.1 14.1 + - + +
1842A THR* 3.8 12.3 - - + -
1843A ILE 3.4 5.4 - - - -
1844A ARG* 2.7 42.2 + - + +
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Residues in contact with SER1836 (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* 5.1 5.4 + - - -
1835A GLU* 1.3 75.4 + - - +
1837A VAL* 1.3 62.7 + - - +
1838A LEU* 3.7 13.8 + - - +
1841A TRP 4.0 0.3 - - - +
1842A THR* 3.0 4.7 - - - -
1843A ILE* 2.7 47.2 + - - +
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Residues in contact with VAL1837 (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* 4.3 17.0 + - + +
1836A SER* 1.3 74.7 - - - +
1838A LEU* 1.3 79.4 + - - +
1842A THR* 3.7 25.1 - - + +
1844A ARG* 5.8 0.9 - - - +
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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