Contacts of the helix formed by residues 1830 - 1840 (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 GLY1830 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1826A GLU* 2.7 21.5 + - - -
1829A SER* 1.3 75.2 - - - +
1831A LEU* 1.3 64.0 + - - +
1832A GLU 3.3 2.7 - - - -
1833A VAL* 3.2 14.9 + - - +
1834A ILE* 3.2 16.5 + - - +
1855A TYR* 4.2 0.9 + - - -
1865A ARG* 3.6 16.3 - - - +
1938A GLN* 3.3 13.5 - - - -
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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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1826A GLU 3.5 2.3 + - - -
1827A ILE* 3.4 40.5 + - + +
1828A THR 4.7 2.4 + - - +
1829A SER 3.9 1.8 + - - -
1830A GLY* 1.3 75.2 - - - +
1832A GLU* 1.3 54.9 + - - +
1834A ILE* 3.5 11.6 + - + -
1835A SER* 2.6 60.7 + - - +
1938A GLN* 3.7 1.8 + - - +
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Residues in contact with GLU1832 (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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1831A LEU* 1.3 76.0 - - - +
1833A VAL* 1.3 55.0 + - - +
1835A SER* 4.1 9.1 - - - -
1836A SER* 2.8 47.3 + - - -
1840A ILE* 6.0 0.2 - - - +
1902A ARG* 4.6 6.7 - - - +
1938A GLN* 3.1 34.8 + - + +
1939A GLU* 4.2 18.3 - - + +
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Residues in contact with VAL1833 (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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1830A GLY 3.2 8.5 + - - +
1832A GLU* 1.3 72.0 - - - +
1834A ILE* 1.3 60.1 + - - +
1836A SER* 3.2 3.3 + - - -
1837A LEU* 2.9 36.6 + - + +
1855A TYR* 3.3 20.4 - - + +
1865A ARG* 3.9 20.6 - - - +
1899A GLU* 4.5 0.7 - - - +
1938A GLN* 3.1 43.4 + - + +
1941A THR* 4.4 4.3 - - + -
1942A ALA* 3.8 12.2 - - - +
1945A LEU* 3.6 26.2 - - + -
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Residues in contact with ILE1834 (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* 3.8 29.2 - - + -
1826A GLU* 3.4 33.9 - - + +
1827A ILE* 3.8 17.9 - - + +
1830A GLY 3.2 9.5 + - - +
1831A LEU* 3.9 12.3 - - + +
1833A VAL* 1.3 73.9 - - - +
1835A SER* 1.3 62.0 + - - +
1837A LEU* 3.4 11.4 + - - +
1838A ARG* 3.1 23.9 + - + +
1845A VAL* 3.9 25.7 - - + +
1847A VAL* 5.0 7.9 - - + -
1855A TYR* 4.5 7.0 - - + +
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Residues in contact with SER1835 (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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1831A LEU* 2.6 44.0 + - - +
1832A GLU* 3.7 13.2 - - - -
1834A ILE* 1.3 78.3 - - - +
1836A SER* 1.3 55.7 + - - +
1838A ARG* 3.4 3.6 + - - +
1839A ALA* 2.9 37.8 + - - +
1840A ILE* 5.0 0.2 - - - +
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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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1832A GLU* 2.8 34.7 + - - -
1835A SER* 1.3 70.2 - - - +
1837A LEU* 1.3 63.9 + - - +
1840A ILE* 3.2 43.2 + - - +
1841A HIS* 3.2 9.2 + - - -
1939A GLU* 3.0 28.5 + - - -
1942A ALA* 3.6 18.0 - - - +
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Residues in contact with LEU1837 (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 19.7 - - + -
1822A VAL* 5.0 3.4 - - + -
1833A VAL* 2.9 22.4 + - + +
1834A ILE* 3.5 12.8 - - - +
1836A SER* 1.3 77.1 - - - +
1838A ARG* 1.3 56.9 + - - +
1841A HIS* 3.6 5.9 - - + -
1842A GLY 3.2 20.1 + - - -
1843A LEU* 3.3 39.2 + - + +
1845A VAL* 4.1 4.5 - - + -
1855A TYR* 4.3 8.7 - - + -
1942A ALA* 3.6 27.6 - - + +
1945A LEU* 3.9 32.1 - - + -
1946A LYS* 4.1 8.3 - - + +
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Residues in contact with ARG1838 (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 ILE* 3.1 17.8 + - + +
1835A SER* 4.0 3.1 - - - +
1837A LEU* 1.3 78.2 - - - +
1839A ALA* 1.3 61.3 + - + +
1840A ILE 3.6 0.2 - - - -
1842A GLY* 3.2 23.7 - - - -
1843A LEU 3.5 19.8 + - - -
1844A GLN* 4.9 11.9 + - - +
1845A VAL* 3.9 21.9 + - + +
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Residues in contact with ALA1839 (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 SER* 2.9 20.5 + - - +
1838A ARG* 1.3 75.1 - - + +
1840A ILE* 1.3 71.3 + - + +
1842A GLY* 4.5 1.5 + - - -
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Residues in contact with ILE1840 (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 LYS* 6.0 0.3 - - - +
1832A GLU* 6.0 0.2 - - - +
1836A SER* 3.2 32.8 + - - +
1839A ALA* 1.3 84.5 - - + +
1841A HIS* 1.3 80.6 + - + +
1842A GLY* 3.2 5.4 + - - -
1939A GLU* 4.6 12.6 - - - +
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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