Contacts of the helix formed by residues 1886 - 1894 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A THR* 5.5 11.9 - - - -
1884X PRO 3.3 3.0 + - - -
1885X PRO* 1.3 74.0 - - - +
1887X ARG* 1.3 66.2 + - - +
1888X GLU* 3.2 20.2 + - - +
1889X GLU* 2.6 56.1 + - - +
1890X ILE* 3.0 21.9 + - - +
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Residues in contact with ARG1887 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 3.0 44.2 + - - +
36A VAL 3.6 15.8 - - - +
37A TYR* 3.4 28.8 + - + -
38A PRO* 3.9 39.2 - - + +
143A GLY* 5.5 12.3 - - - +
144A CYS 5.2 8.3 - - - +
145A THR* 5.8 2.6 - - - +
1885X PRO 3.7 1.2 + - - -
1886X SER* 1.3 69.1 - - - +
1888X GLU* 1.4 68.9 + - - +
1890X ILE* 3.1 4.8 + - - +
1891X MET* 2.8 41.4 + - + +
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Residues in contact with GLU1888 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY* 5.1 12.0 - - - +
1886X SER* 3.2 19.8 - - - +
1887X ARG* 1.4 87.0 + - + +
1889X GLU* 1.3 62.1 + - - +
1891X MET* 3.1 8.2 + - - +
1892X ALA* 3.0 23.2 + - - +
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Residues in contact with GLU1889 (chain X).
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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59A GLU* 4.7 7.4 - - - +
1884X PRO 4.6 1.2 - - - +
1885X PRO* 3.6 20.2 - - + +
1886X SER* 2.6 47.5 + - - +
1888X GLU* 1.3 79.2 - - + +
1890X ILE* 1.3 63.5 + - - +
1892X ALA* 3.3 17.6 - - - +
1893X THR* 3.7 10.6 - - - +
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Residues in contact with ILE1890 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 3.9 25.6 - - + -
38A PRO* 4.9 5.6 - - + -
41A ILE* 4.0 24.7 - - + -
57A HIS* 3.6 50.9 - - + +
60A LEU* 4.7 3.6 - - + -
1885X PRO* 4.1 20.2 - - + -
1886X SER 3.0 15.9 + - - +
1887X ARG* 3.5 6.1 - - - +
1888X GLU 3.1 0.2 - - - -
1889X GLU* 1.3 75.1 - - - +
1891X MET* 1.3 63.0 + - - +
1893X THR* 2.7 27.3 + - - -
1894X LEU* 3.5 11.4 + - + +
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Residues in contact with MET1891 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.6 31.6 - - + -
1887X ARG* 2.8 33.5 + - + +
1888X GLU* 3.1 7.8 + - - +
1890X ILE* 1.3 73.1 - - - +
1892X ALA* 1.3 62.0 + - - +
1894X LEU* 3.1 37.3 + - + +
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Residues in contact with ALA1892 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1888X GLU 3.0 11.9 + - - +
1889X GLU* 3.3 15.3 - - - +
1890X ILE 3.1 0.2 + - - -
1891X MET* 1.3 77.1 - - - +
1893X THR* 1.3 60.4 + - + +
1894X LEU 3.8 2.6 + - - +
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Residues in contact with THR1893 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A HIS* 4.0 18.3 + - - +
1889X GLU 3.7 14.4 - - - +
1890X ILE 2.7 17.8 + - - -
1892X ALA* 1.3 80.6 - - + +
1894X LEU* 1.3 72.8 + - - +
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Residues in contact with LEU1894 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO* 4.7 4.0 - - + -
40A GLY* 5.6 3.6 - - - -
41A ILE* 4.0 26.5 - - + +
57A HIS* 4.9 4.9 - - + -
1890X ILE* 3.6 15.9 - - + +
1891X MET* 3.1 44.0 + - + +
1892X ALA 4.4 2.6 - - - +
1893X THR* 1.3 98.1 - - - +
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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