Contacts of the helix formed by residues 1868 - 1873 (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 GLN1868 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867A SER* 1.3 70.8 - - - +
1869A SER* 1.3 60.9 + - - +
1871A MET* 3.5 2.9 + - - +
1872A LEU* 3.0 53.2 + - + +
1898A VAL* 3.9 22.0 - - + -
1899A GLU 2.9 14.8 + - - +
1900A LYS* 3.9 24.7 - - - +
1901A ASP* 3.2 5.7 + - - +
1918A TYR* 4.8 13.5 + - + +
1934A PHE* 6.3 2.2 - - + -
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Residues in contact with SER1869 (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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1867A SER* 3.8 1.3 - - - -
1868A GLN* 1.3 74.1 - - - +
1870A GLU* 1.3 57.4 + - - +
1872A LEU* 3.1 6.7 + - - +
1873A ASN* 2.7 37.5 + - - +
1901A ASP* 3.1 31.9 + - - +
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Residues in contact with GLU1870 (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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1866A ARG* 3.1 29.3 - - + -
1867A SER* 2.8 49.6 + - - +
1869A SER* 1.3 77.0 - - - +
1871A MET* 1.3 65.5 + - + +
1873A ASN* 3.4 8.6 - - - +
1876A ASN* 3.0 40.4 - - - +
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Residues in contact with MET1871 (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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1866A ARG* 3.7 30.3 - - + +
1867A SER 3.1 17.4 + - - +
1868A GLN* 3.9 5.4 - - - +
1870A GLU* 1.3 79.7 - - + +
1872A LEU* 1.3 60.9 + - - +
1873A ASN 4.4 1.2 - - - -
1874A SER* 4.1 6.1 + - - -
1876A ASN* 5.5 3.6 - - - +
1877A LYS* 6.6 0.2 - - - -
1880A PHE* 3.8 45.1 - - + -
1896A VAL* 4.9 1.8 - - - -
1898A VAL* 4.0 26.2 - - + -
1918A TYR* 3.4 37.5 - - + +
1921A LEU* 4.1 20.9 - - + +
1922A LEU* 6.0 2.0 - - - -
1925A LEU* 5.6 2.7 - - - -
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Residues in contact with LEU1872 (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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1868A GLN* 3.0 44.1 + - + +
1869A SER* 3.8 5.6 - - - +
1871A MET* 1.3 74.8 - - - +
1873A ASN* 1.3 60.3 + - - +
1874A SER* 2.8 15.1 + - - -
1916A LYS* 4.0 35.7 - - + +
1918A TYR* 3.6 36.1 - - + +
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Residues in contact with ASN1873 (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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1869A SER 2.7 20.5 + - - +
1870A GLU* 3.4 8.5 + - - +
1871A MET 4.4 0.6 - - - +
1872A LEU* 1.3 68.4 - - - +
1874A SER* 1.3 51.3 + - - +
1875A VAL* 2.7 45.2 + - - +
1876A ASN* 2.6 37.1 - - - +
1877A LYS 4.3 0.2 + - - -
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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