Contacts of the helix formed by residues 181 - 193 (chain 0) in PDB entry 5IY8
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 ASN 181 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460 TYR* 3.5 11.6 + - - -
1790 PRO 3.7 1.8 + - - -
1800 SER* 1.3 67.6 - - - +
1820 ILE* 1.3 63.3 + - - +
1830 TYR* 3.1 25.4 + - - +
1840 ASP* 3.5 36.3 + - + +
1850 LEU 3.8 2.8 + - - -
1870 LYS* 5.7 2.0 - - - +
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Residues in contact with ILE 182 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1450 LEU* 5.1 4.5 - - + -
1460 TYR* 3.8 36.8 - - + +
1490 LEU* 4.3 3.8 - - + -
1760 THR* 5.7 8.1 - - + -
1800 SER 3.0 8.7 + - - +
1810 ASN* 1.3 72.6 + - - +
1830 TYR* 1.4 81.7 + - + +
1850 LEU* 3.2 16.9 + - + +
1860 ILE* 3.0 26.4 + - + +
2070 VAL* 3.9 20.4 - - + -
2110 LEU* 4.1 28.5 - - + -
586W GLU* 6.0 2.7 - - - +
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Residues in contact with TYR 183 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810 ASN* 3.1 16.9 + - - +
1820 ILE* 1.4 82.3 - - + +
1840 ASP* 1.4 61.1 + - - +
1860 ILE* 3.2 17.4 + - + +
1870 LYS* 3.1 39.4 + - + +
2060 ARG* 5.6 5.0 + - - -
2070 VAL* 3.9 36.6 - - + +
2100 VAL* 4.2 29.6 - - + +
585W GLN* 5.8 1.7 + - - -
586W GLU* 4.5 20.0 + - - +
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Residues in contact with ASP 184 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460 TYR* 5.5 3.1 + - - -
1810 ASN* 3.5 26.8 + - + +
1820 ILE 3.4 0.8 - - - -
1830 TYR* 1.4 75.1 - - - +
1850 LEU* 1.3 62.0 + - - +
1870 LYS* 3.4 19.3 + - - +
1880 THR* 3.1 29.7 + - - -
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Residues in contact with LEU 185 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1460 TYR* 3.8 37.9 + - + +
1490 LEU* 3.6 31.0 - - + -
1500 SER* 3.2 34.8 - - - +
1530 MET* 4.2 15.9 - - + -
1810 ASN 3.8 2.0 + - - -
1820 ILE* 3.2 16.9 + - + +
1840 ASP* 1.3 76.6 + - - +
1860 ILE* 1.3 58.4 + - + +
1880 THR* 3.1 9.0 + - - -
1890 LEU* 2.9 48.1 + - + +
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Residues in contact with ILE 186 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1820 ILE* 3.0 22.0 + - + +
1830 TYR* 3.2 31.8 + - + +
1850 LEU* 1.3 73.2 - - + +
1870 LYS* 1.4 65.7 + - + +
1890 LEU* 3.2 19.2 + - + +
1900 LYS* 3.2 13.4 + - - +
2070 VAL* 4.7 3.8 - - + +
2100 VAL* 5.0 2.5 - - + -
2110 LEU* 3.7 47.8 - - + +
2140 GLU* 3.7 34.8 - - + -
2150 THR* 4.2 12.2 - - + +
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Residues in contact with LYS 187 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810 ASN* 5.7 1.6 - - - +
1830 TYR* 3.1 30.4 + - + +
1840 ASP* 3.6 20.9 - - - +
1860 ILE* 1.4 77.0 - - + +
1880 THR* 1.3 58.7 + - - +
1900 LYS* 3.5 7.6 + - - +
1910 ALA* 3.2 25.0 + - - +
2140 GLU* 5.9 5.2 - - + +
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Residues in contact with THR 188 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530 MET* 3.5 30.7 - - + -
1570 LYS* 5.7 3.8 - - + +
1840 ASP* 3.1 20.7 + - - -
1850 LEU* 3.1 12.5 + - - -
1870 LYS* 1.3 75.3 - - - +
1890 LEU* 1.4 56.3 + - - +
1910 ALA* 3.2 8.4 + - + +
1920 ALA* 2.9 33.3 + - + +
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Residues in contact with LEU 189 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490 LEU* 4.6 15.9 - - + +
1530 MET* 4.2 20.0 - - + -
1850 LEU* 2.9 40.7 + - + +
1860 ILE* 3.4 13.0 - - + +
1880 THR* 1.4 73.4 - - - +
1900 LYS* 1.3 57.4 + - - +
1920 ALA* 3.4 2.1 + - - +
1930 LYS 2.9 25.3 + - - -
1940 ILE* 3.0 47.8 + - + +
1960 VAL* 4.0 13.5 - - + -
2110 LEU* 5.3 1.6 - - + -
2150 THR* 3.6 25.8 - - + -
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Residues in contact with LYS 190 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1860 ILE 3.2 9.1 + - - +
1870 LYS* 3.8 9.9 - - - +
1890 LEU* 1.3 79.2 - - - +
1910 ALA* 1.4 61.0 + - - +
1930 LYS* 3.3 18.0 + - - +
1940 ILE 5.0 1.3 - - - -
2140 GLU* 2.9 55.2 + - + +
2150 THR* 4.8 6.5 - - - +
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Residues in contact with ALA 191 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1870 LYS 3.2 14.4 + - - +
1880 THR* 3.2 12.7 + - + +
1900 LYS* 1.4 75.1 - - - +
1920 ALA* 1.4 59.4 + - - +
1930 LYS* 3.5 8.3 + - - +
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Residues in contact with ALA 192 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1530 MET* 5.0 2.5 - - - -
1570 LYS* 4.4 15.5 - - + -
1650 ARG* 1.7 43.9 + - - +
1880 THR* 2.9 20.3 + - + +
1890 LEU* 3.6 5.4 - - - +
1910 ALA* 1.4 72.8 - - - +
1930 LYS* 1.4 61.7 + - - +
1940 ILE* 4.0 19.3 - - + -
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Residues in contact with LYS 193 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650 ARG* 3.0 25.1 + - + +
1890 LEU 2.9 6.6 + - - -
1900 LYS* 3.3 11.7 + - - +
1910 ALA 4.1 9.0 - - - +
1920 ALA* 1.4 80.2 - - - +
1940 ILE* 1.3 61.3 + - - +
1950 ARG* 3.8 5.3 + - - +
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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