Contacts of the helix formed by residues 1886 - 1894 (chain Y) in PDB entry 3ABD
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 SER1886 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B TYR* 4.2 0.9 - - - -
145B THR* 5.7 10.8 - - - -
1884Y PRO 3.5 2.7 + - - -
1885Y PRO* 1.3 73.8 - - - +
1887Y ARG* 1.3 64.5 + - - +
1888Y GLU* 2.9 18.6 + - - +
1889Y GLU* 2.6 57.4 + - - +
1890Y ILE* 3.0 13.0 + - - +
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Residues in contact with ARG1887 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLU* 3.1 51.5 + - - +
36B VAL 3.7 17.5 + - - +
37B TYR* 3.6 27.2 - - + -
38B PRO* 3.6 42.1 - - + +
143B GLY* 6.0 7.9 - - - +
144B CYS 5.4 5.4 - - - +
145B THR* 6.0 2.2 - - - +
1885Y PRO 3.6 2.2 + - - -
1886Y SER* 1.3 70.1 - - - +
1888Y GLU* 1.4 64.3 + - - +
1890Y ILE* 2.9 5.1 + - - +
1891Y MET* 2.6 43.5 + - + +
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Residues in contact with GLU1888 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY* 5.2 9.9 - - - -
1886Y SER* 3.4 17.5 - - - +
1887Y ARG* 1.4 88.9 + - + +
1889Y GLU* 1.3 67.3 + - - +
1890Y ILE 3.1 0.7 + - - -
1891Y MET* 4.2 5.7 - - + +
1892Y ALA* 3.2 22.5 + - - +
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Residues in contact with GLU1889 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 4.5 8.7 - - - +
1885Y PRO* 3.4 18.2 - - + +
1886Y SER* 2.6 47.9 + - - +
1888Y GLU* 1.3 73.0 - - - +
1890Y ILE* 1.3 62.7 + - + +
1892Y ALA* 3.7 12.1 + - - +
1893Y THR* 3.9 12.8 + - - +
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Residues in contact with ILE1890 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR* 3.7 30.1 - - + -
38B PRO* 4.8 8.3 - - + -
41B ILE* 3.9 27.8 - - + -
57B HIS* 3.9 47.1 - - + +
60B LEU* 4.6 3.8 - - + -
1885Y PRO* 4.3 15.5 - - + -
1886Y SER 3.4 10.8 - - - +
1887Y ARG* 2.9 8.8 + - - +
1889Y GLU* 1.3 76.0 - - - +
1891Y MET* 1.3 68.1 + - - +
1893Y THR* 3.0 23.7 + - - +
1894Y LEU* 3.4 9.5 + - + +
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Residues in contact with MET1891 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 3.5 35.9 - - + -
1887Y ARG* 2.6 33.3 + - + +
1888Y GLU* 4.2 5.4 - - + +
1890Y ILE* 1.3 73.4 - - - +
1892Y ALA* 1.3 62.7 + - - +
1894Y LEU* 3.0 38.1 + - + +
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Residues in contact with ALA1892 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1888Y GLU 3.2 16.7 + - - +
1889Y GLU* 3.9 7.6 - - - +
1890Y ILE 3.1 1.2 - - - -
1891Y MET* 1.3 78.5 - - - +
1893Y THR* 1.3 63.6 + - + +
1894Y LEU 3.2 4.4 + - - +
1895Y LEU* 5.8 0.7 - - - +
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Residues in contact with THR1893 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B HIS* 4.3 16.9 + - - +
1889Y GLU 3.9 12.3 - - - +
1890Y ILE* 3.0 13.0 + - - +
1892Y ALA* 1.3 78.8 - - + +
1894Y LEU* 1.3 66.2 + - - +
1895Y LEU* 3.9 5.4 + - - +
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Residues in contact with LEU1894 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B PRO* 4.9 4.5 - - + -
40B GLY* 4.9 13.2 - - - +
41B ILE* 3.9 30.5 - - + +
57B HIS* 5.8 3.8 - - + -
1890Y ILE* 3.8 11.2 - - + +
1891Y MET* 3.0 42.9 + - + +
1892Y ALA 4.0 4.0 - - - +
1893Y THR* 1.3 86.3 + - - +
1895Y LEU* 1.3 76.8 + - - +
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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