Contacts of the helix formed by residues 1884 - 1890 (chain A) in PDB entry 5PCI
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 GLU1884 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1882A THR 3.6 3.5 + - - -
1883A HIS* 1.3 83.8 + - + +
1885A ASP* 1.3 73.1 + - - +
1886A ALA 3.3 0.6 + - - -
1887A TRP* 3.3 20.6 + - - +
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Residues in contact with ASP1885 (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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1883A HIS* 3.0 25.2 + - + +
1884A GLU* 1.3 91.7 - - - +
1886A ALA* 1.3 61.3 + - - +
1887A TRP* 3.3 11.4 + - - +
1888A PRO* 3.4 12.7 - - - +
1889A PHE* 3.8 0.5 - - - -
1953A ALA* 3.7 22.2 - - + +
1956A ASN* 3.1 27.8 + - + +
1957A MET* 3.6 18.8 - - + +
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Residues in contact with ALA1886 (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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1880A MET 3.3 23.3 - - - +
1881A GLU 3.9 3.1 - - - +
1883A HIS* 3.0 19.0 + - + +
1884A GLU 3.3 0.4 - - - -
1885A ASP* 1.3 78.0 - - - +
1887A TRP* 1.3 57.5 + - - +
1888A PRO* 3.3 2.0 - - - -
1889A PHE* 2.8 30.7 + - - +
1890A LEU* 3.4 30.4 + - + +
1911A PHE* 3.9 7.0 - - + -
1957A MET* 4.0 4.6 - - + -
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Residues in contact with TRP1887 (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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1883A HIS 4.8 0.2 + - - -
1884A GLU 3.3 22.7 + - - -
1885A ASP* 4.1 10.3 + - - +
1886A ALA* 1.3 76.7 - - - +
1888A PRO* 1.3 93.8 - - + +
1889A PHE 3.1 1.0 + - - -
1890A LEU* 3.9 24.1 + - + +
1891A LEU 5.3 0.7 + - - -
1949A ASP* 4.6 22.7 - - + -
1950A ILE* 3.7 29.4 - - + -
1953A ALA* 5.2 2.3 - - + +
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Residues in contact with PRO1888 (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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1885A ASP 3.4 11.9 - - - +
1886A ALA 3.3 5.4 - - - -
1887A TRP* 1.3 123.4 - - + +
1889A PHE* 1.4 82.1 + - + +
1890A LEU 3.8 0.4 - - - -
1891A LEU 4.6 6.4 - - - +
1893A VAL* 5.2 5.4 - - - +
1950A ILE* 3.9 23.6 - - + -
1953A ALA* 4.0 11.7 - - + -
2001A EDO 5.0 11.3 - - - +
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Residues in contact with PHE1889 (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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1885A ASP 3.8 16.8 - - - -
1886A ALA* 2.8 16.8 + - - +
1888A PRO* 1.4 102.3 - - + +
1890A LEU* 1.3 60.0 + - - +
1891A LEU 3.4 5.4 - - - -
1910A ASP* 3.4 6.1 - - - +
1911A PHE* 2.9 47.3 + + + -
1936A VAL* 3.5 27.4 - - + -
1937A PHE* 4.4 6.1 - + - -
1940A CYS* 3.7 30.5 - - + -
1950A ILE* 4.2 1.1 - - + -
1953A ALA 4.0 0.2 - - - -
1954A GLY* 3.6 35.0 - - - -
1957A MET* 4.0 13.9 - - + -
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Residues in contact with LEU1890 (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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1881A GLU* 3.7 32.3 - - + +
1886A ALA* 3.4 20.9 - - + +
1887A TRP* 3.9 23.2 + - + +
1888A PRO 3.8 0.8 - - - -
1889A PHE* 1.3 78.5 - - - +
1891A LEU* 1.3 69.5 + - + +
1910A ASP* 3.8 0.7 - - - -
1911A PHE* 4.0 15.4 - - + +
1912A SER* 3.2 29.6 + - - -
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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