Contacts of the helix formed by residues 1907 - 1923 (chain Q) in PDB entry 3ZWH
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 ALA1907 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASN 3.4 23.1 - - - +
62A LEU* 4.8 4.3 - - + -
64A SER* 3.7 5.4 - - - +
77A VAL* 4.0 21.1 - - + -
81A SER* 5.5 0.7 - - - -
1904Q THR* 3.2 28.0 + - - +
1905Q GLU 3.3 1.4 + - - -
1906Q THR* 1.3 77.0 - - - +
1908Q ASP* 1.3 57.4 + - - +
1910Q MET* 3.3 3.0 + - - +
1911Q ASN* 2.8 35.7 + - - +
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Residues in contact with ASP1908 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN 4.4 5.4 - - - +
64A SER* 2.7 40.7 + - - +
1905Q GLU 5.0 2.4 + - - +
1906Q THR 3.2 1.0 - - - -
1907Q ALA* 1.3 76.7 - - - +
1909Q ALA* 1.3 63.7 + - - +
1911Q ASN* 3.3 3.8 + - - +
1912Q ARG* 3.1 32.4 + - + +
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Residues in contact with ALA1909 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1906Q THR* 3.2 17.7 + - - +
1908Q ASP* 1.3 78.7 - - - +
1910Q MET* 1.3 64.3 + - + +
1912Q ARG* 3.2 14.7 + - - +
1913Q GLU* 3.0 35.2 + - - +
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Residues in contact with MET1910 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.9 20.9 - - + +
80A SER* 3.8 28.9 - - - -
81A SER* 4.2 13.7 - - - -
84A MET* 4.0 25.1 - - - +
73B GLN* 3.7 27.8 - - + +
76B CYS* 5.2 1.6 - - + -
77B VAL* 4.8 13.2 - - + +
80B SER* 5.9 0.4 - - - +
1906Q THR* 3.1 27.7 + - - +
1907Q ALA 3.7 6.5 - - - +
1909Q ALA* 1.3 78.1 - - + +
1911Q ASN* 1.3 56.5 + - - +
1913Q GLU* 3.2 10.4 + - - +
1914Q VAL* 2.9 35.2 + - + +
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Residues in contact with ASN1911 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU 4.5 1.8 + - - -
64A SER* 2.9 34.8 + - - +
73A GLN* 2.9 32.0 + - - +
74A GLU* 3.6 18.9 - - - +
77A VAL* 3.6 24.1 - - - +
1907Q ALA* 2.8 23.7 + - - +
1908Q ASP 3.3 6.0 + - - +
1910Q MET* 1.3 77.2 - - - +
1912Q ARG* 1.3 57.4 + - + +
1914Q VAL* 3.4 0.6 + - - -
1915Q SER* 2.9 34.5 + - - -
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Residues in contact with ARG1912 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1908Q ASP* 3.1 21.2 + - + +
1909Q ALA* 3.2 12.3 + - - +
1911Q ASN* 1.3 77.5 - - + +
1913Q GLU* 1.3 62.2 + - + +
1915Q SER* 3.8 6.6 - - - -
1916Q SER* 3.2 22.2 + - - -
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Residues in contact with GLU1913 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER* 5.6 12.1 - - - +
73B GLN* 3.6 24.8 + - - +
77B VAL* 3.9 24.7 - - + +
1909Q ALA* 3.0 25.8 + - - +
1910Q MET* 3.2 13.5 + - - +
1912Q ARG* 1.3 75.4 - - + +
1914Q VAL* 1.3 64.7 + - - +
1916Q SER* 3.3 7.6 + - - -
1917Q LEU* 3.1 22.2 + - - +
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Residues in contact with VAL1914 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 4.0 12.8 - - + +
77A VAL* 4.3 13.0 - - + -
77B VAL* 3.9 26.7 - - + -
80B SER* 4.1 21.1 - - - +
81B SER* 3.9 8.2 + - - +
84B MET* 3.4 33.4 - - + -
1910Q MET* 2.9 23.4 + - + +
1911Q ASN* 3.8 4.5 - - - +
1913Q GLU* 1.3 72.1 - - - +
1915Q SER* 1.3 62.0 + - - +
1917Q LEU* 3.2 2.4 + - - +
1918Q LYS* 2.8 28.1 + - - +
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Residues in contact with SER1915 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 2.8 31.2 + - - +
1911Q ASN 2.9 14.1 + - - -
1912Q ARG* 3.8 7.8 - - - -
1913Q GLU 3.3 0.2 - - - -
1914Q VAL* 1.3 76.3 - - - +
1916Q SER* 1.3 63.5 + - - +
1918Q LYS* 3.8 6.0 - - - +
1919Q ASN* 3.0 26.2 + - - +
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Residues in contact with SER1916 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1912Q ARG 3.2 12.6 + - - -
1913Q GLU* 3.5 10.8 - - - -
1914Q VAL 3.2 0.2 - - - -
1915Q SER* 1.3 79.6 - - - +
1917Q LEU* 1.3 62.6 + - - +
1919Q ASN* 3.4 7.2 + - - +
1920Q LYS* 3.1 45.1 + - - +
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Residues in contact with LEU1917 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 5.4 0.2 - - + -
61B ASN* 4.7 9.4 - - + +
62B LEU* 3.6 24.2 - - + -
77B VAL* 3.9 12.1 - - + +
78B PHE* 3.6 36.8 - - + +
81B SER* 3.6 14.1 - - - +
1913Q GLU 3.1 11.4 + - - +
1914Q VAL 3.8 2.9 - - - +
1916Q SER* 1.3 76.0 + - - +
1918Q LYS* 1.3 67.2 + - - +
1920Q LYS* 3.2 12.4 + - + -
1921Q LEU* 3.0 29.2 + - + +
1926Q LEU* 3.9 25.8 - - + -
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Residues in contact with LYS1918 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 3.7 21.9 + - - +
84B MET* 3.8 43.5 - - + -
85B MET* 3.9 22.7 - - + +
88B GLU* 2.9 37.9 + - - -
1914Q VAL 2.8 16.7 + - - +
1915Q SER* 3.8 6.1 - - - +
1917Q LEU* 1.3 75.7 - - - +
1919Q ASN* 1.3 56.4 + - - +
1921Q LEU* 3.3 6.7 + - - +
1922Q ARG* 2.9 42.7 + - + +
1931Q PRO 5.8 0.8 + - - -
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Residues in contact with ASN1919 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1915Q SER 3.0 19.8 + - - +
1916Q SER* 3.5 6.7 + - - +
1917Q LEU 3.2 0.2 - - - -
1918Q LYS* 1.3 74.6 - - - +
1920Q LYS* 1.3 61.5 + - - +
1922Q ARG* 2.8 36.5 + - - +
1923Q ARG* 2.9 56.6 + - - +
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Residues in contact with LYS1920 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ASN* 2.8 46.9 + - + +
1916Q SER* 3.1 31.6 + - - +
1917Q LEU* 3.2 14.7 + - + +
1919Q ASN* 1.3 80.7 - - - +
1921Q LEU* 1.3 60.7 + - - +
1923Q ARG* 3.4 3.4 + - - -
1925Q ASP* 3.0 51.2 + - + +
1926Q LEU* 4.1 13.2 - - + -
2936Q AZI 3.5 0.6 + - - -
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Residues in contact with LEU1921 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 5.3 0.2 - - + -
78B PHE* 5.1 9.9 - - + -
81B SER* 3.7 25.8 - - - -
82B ILE* 5.2 1.1 - - + -
85B MET* 3.3 36.6 - - + -
1917Q LEU* 3.0 27.8 + - + +
1918Q LYS* 3.6 6.1 - - - +
1920Q LYS* 1.3 75.8 - - - +
1922Q ARG* 1.3 62.1 + - - +
1924Q GLY* 3.2 2.3 + - - -
1926Q LEU* 4.0 25.6 - - + -
1929Q VAL* 4.0 30.1 - - + -
1931Q PRO* 4.3 9.1 - - - +
2936Q AZI 2.9 27.6 + - - +
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Residues in contact with ARG1922 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B MET* 5.2 0.4 - - - +
88B GLU* 6.2 0.2 - - - -
1918Q LYS* 2.9 32.2 + - + +
1919Q ASN* 2.8 30.8 + - - +
1921Q LEU* 1.3 78.2 - - - +
1923Q ARG* 1.3 80.7 + - - +
1924Q GLY* 3.1 4.7 + - - -
1931Q PRO* 5.2 8.9 - - - +
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Residues in contact with ARG1923 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919Q ASN* 2.9 41.3 + - - +
1920Q LYS 3.4 5.8 + - - +
1921Q LEU 3.3 0.2 - - - -
1922Q ARG* 1.3 98.0 - - - +
1924Q GLY* 1.3 59.4 + - - +
1925Q ASP* 3.6 28.3 + - - +
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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