Contacts of the strand formed by residues 1819 - 1823 (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 CYS1819 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1817A GLY 3.5 2.4 + - - +
1818A THR* 1.3 84.9 - - - +
1820A ILE* 1.3 72.9 - - - +
1821A LEU* 4.2 15.9 - - - -
1844A GLN* 3.1 28.3 - - + -
1846A GLU* 4.2 16.4 - - - -
1857A VAL 4.4 3.8 - - - +
1949A SER* 4.9 0.5 + - - -
1953A GLN* 4.5 1.4 - - - +
1959A ILE* 3.0 34.9 - - + +
1960A HIS* 4.7 13.4 - - + +
1961A VAL 5.5 3.6 - - - +
1963A THR* 4.8 10.5 - - - -
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Residues in contact with ILE1820 (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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1819A CYS* 1.3 76.8 - - - +
1821A LEU* 1.3 75.2 + - - +
1822A VAL* 3.9 3.5 + - + -
1837A LEU* 4.3 17.7 - - + -
1843A LEU* 3.7 28.7 - - + -
1844A GLN 3.0 7.1 + - - +
1845A VAL* 3.4 18.0 - - + +
1846A GLU* 2.9 26.2 + - - +
1855A TYR* 4.6 10.8 - - + -
1856A ILE 3.7 14.1 - - - +
1857A VAL* 3.8 25.6 - - + -
1945A LEU* 4.3 17.7 - - + -
1949A SER* 4.2 8.7 - - - +
1959A ILE* 4.9 0.7 - - - -
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Residues in contact with LEU1821 (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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1819A CYS* 4.2 13.5 - - - -
1820A ILE* 1.3 78.1 - - - +
1822A VAL* 1.3 62.0 + - - +
1846A GLU* 3.5 10.5 - - + -
1848A CYS* 3.8 14.6 - - - -
1850A LEU* 4.1 7.2 - - + -
1855A TYR* 3.2 8.1 - - - +
1856A ILE* 2.9 66.6 + - + +
1959A ILE* 3.8 16.4 - - + -
1963A THR* 4.6 12.3 - - + -
1984A TYR* 3.7 28.7 - - + -
1985A ILE* 4.4 7.4 - - + -
1988A LEU* 4.2 9.4 - - + -
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Residues in contact with VAL1822 (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 ILE* 4.3 13.5 - - + +
1821A LEU* 1.3 81.0 - - - +
1823A GLY* 1.3 71.9 + - - +
1826A GLU* 3.7 12.8 - - + -
1834A ILE* 3.8 18.8 - - + -
1837A LEU* 5.0 2.5 - - + -
1845A VAL* 4.5 18.2 - - + -
1846A GLU 3.0 9.5 + - - +
1847A VAL* 3.3 12.1 - - + -
1848A CYS 2.8 31.7 + - - +
1850A LEU* 3.8 3.8 - - - -
1854A ASP 3.5 1.8 - - - -
1855A TYR* 3.6 34.1 - - + -
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Residues in contact with GLY1823 (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 VAL* 1.3 76.0 - - - +
1824A GLY* 1.3 59.8 + - - -
1825A HIS* 3.2 6.7 - - - -
1826A GLU* 2.9 28.4 + - - +
1827A ILE* 4.2 1.4 + - - +
1847A VAL* 4.6 1.5 - - - +
1848A CYS 3.6 5.2 - - - -
1850A LEU* 3.5 7.9 - - - +
1853A CYS 4.1 2.7 - - - -
1854A ASP 2.7 19.0 + - - -
2101A SO4 3.5 16.4 - - - -
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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