Contacts of the helix formed by residues 1909 - 1919 (chain P) in PDB entry 4ETO
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 ALA1909 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLN* 5.5 1.3 - - - +
1908P ASP* 1.3 71.7 - - - +
1910P MET* 1.3 58.3 + - + +
1912P ARG* 3.3 8.3 + - - +
1913P GLU* 2.9 45.6 + - - +
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Residues in contact with MET1910 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.6 34.1 - - + +
76A CYS* 4.6 2.2 - - + -
77A VAL* 4.1 15.3 - - + -
77B VAL* 3.7 24.5 - - + +
80B SER* 3.4 35.0 - - - +
81B CYS* 4.6 12.3 - - - -
84B MET* 4.0 19.7 - - + +
1908P ASP* 3.1 6.3 - - + +
1909P ALA* 1.3 76.0 - - + +
1911P ASN* 1.3 60.4 + - - +
1913P GLU* 3.2 12.6 + - - +
1914P VAL* 2.9 34.4 + - + +
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Residues in contact with ASN1911 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B LEU* 4.5 7.9 + - - +
64B SER* 3.3 28.0 + - - +
73B GLN* 3.1 29.7 + - - +
74B GLU* 3.9 10.9 + - - +
77B VAL* 3.5 34.4 - - - +
1908P ASP* 3.3 32.6 + - + +
1910P MET* 1.3 77.9 - - - +
1912P ARG* 1.3 57.0 + - - +
1914P VAL 3.2 1.6 + - - -
1915P SER* 2.9 27.4 + - - -
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Residues in contact with ARG1912 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1908P ASP 3.3 12.4 + - - +
1909P ALA* 3.3 11.7 - - - +
1911P ASN* 1.3 77.6 - - - +
1913P GLU* 1.3 58.6 + - + +
1915P SER* 3.2 7.8 + - - +
1916P SER* 2.9 29.3 + - - -
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Residues in contact with GLU1913 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 5.2 12.3 - - - +
73A GLN* 2.9 32.0 + - - +
77A VAL* 3.6 24.8 - - + +
1909P ALA* 2.9 37.6 + - - +
1910P MET* 3.2 16.8 + - - +
1912P ARG* 1.3 74.6 - - + +
1914P VAL* 1.3 62.9 + - - +
1916P SER* 3.7 7.0 - - - -
1917P LEU* 3.0 19.8 + - - +
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Residues in contact with VAL1914 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 3.9 21.8 - - + -
80A SER* 4.0 20.4 - - - +
81A CYS* 3.6 9.1 - - - -
84A MET* 3.4 34.5 - - + -
73B GLN* 3.7 15.3 - - + +
77B VAL* 3.9 16.8 - - + -
1910P MET* 2.9 20.6 + - + +
1911P ASN 3.6 7.0 - - - +
1913P GLU* 1.3 73.5 - - - +
1915P SER* 1.3 60.8 - - - +
1917P LEU 3.3 0.7 + - - -
1918P LYS* 2.9 29.1 + - - +
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Residues in contact with SER1915 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLN* 2.9 24.7 + - - +
1911P ASN 2.9 9.9 + - - -
1912P ARG* 3.2 9.8 + - - -
1914P VAL* 1.3 77.4 - - - +
1916P SER* 1.3 60.8 + - - +
1918P LYS* 3.1 33.7 + - - +
1919P ASN* 3.1 20.3 + - - -
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Residues in contact with SER1916 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 6.1 1.0 - - - -
1912P ARG 2.9 16.9 + - - -
1913P GLU* 3.7 8.3 - - - -
1915P SER* 1.3 77.9 - - - +
1917P LEU* 1.3 63.1 + - - +
1919P ASN* 3.4 10.5 + - - +
1920P LYS* 3.3 35.0 + - - +
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Residues in contact with LEU1917 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN* 3.4 39.7 - - + +
62A LEU* 4.1 15.0 - - + +
64A SER* 6.5 0.7 - - - -
74A GLU 5.0 1.1 - - - +
77A VAL* 3.8 14.4 - - + -
78A PHE* 3.7 31.9 - - + +
81A CYS* 3.8 9.4 - - - -
1913P GLU 3.0 18.2 + - - +
1916P SER* 1.3 74.5 - - - +
1918P LYS* 1.3 60.9 + - - +
1920P LYS* 2.9 23.6 + - + +
1921P LEU* 3.1 35.1 + - + +
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Residues in contact with LYS1918 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A CYS* 3.6 18.8 - - + +
84A MET* 3.6 24.9 - - + +
85A MET* 5.8 1.8 - - - +
73B GLN* 2.6 24.5 + - - +
1914P VAL 2.9 11.5 + - - +
1915P SER* 3.1 34.4 + - - +
1917P LEU* 1.3 78.6 - - - +
1919P ASN* 1.3 73.3 + - - +
1920P LYS 3.1 1.1 + - - -
1921P LEU* 3.8 15.8 + - - +
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Residues in contact with ASN1919 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1915P SER* 3.1 23.3 + - - +
1916P SER* 3.9 6.2 - - - +
1917P LEU 3.1 0.6 - - - -
1918P LYS* 1.3 93.7 - - - +
1920P LYS* 1.3 60.9 + - + +
1921P LEU 5.3 0.4 - - - -
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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