Contacts of the helix formed by residues 1801 - 1818 (chain A) in PDB entry 3PZD
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 SER1801 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1797A VAL* 3.6 9.9 - - - +
1798A PRO* 2.9 32.5 + - - +
1799A LYS 4.4 0.5 - - - +
1800A ASP* 1.3 86.6 + - - +
1802A VAL* 1.3 64.0 + - - +
1803A GLU* 3.5 6.3 + - - +
1804A PHE* 3.2 21.0 + - - +
1805A ALA* 3.5 9.2 + - - +
1940A MET* 5.6 1.2 - - - +
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Residues in contact with VAL1802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 4.6 10.3 - - - +
1733A LEU* 4.0 31.4 - - + +
1734A ALA* 5.9 1.6 - - + -
1735A MET* 4.6 7.0 - - + -
1801A SER* 1.3 74.3 - - - +
1803A GLU* 1.3 61.8 + - - +
1805A ALA* 3.2 8.5 + - + +
1806A PHE* 3.0 42.4 + - + -
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Residues in contact with GLU1803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1735A MET* 3.9 18.3 - - + +
1738A SER* 2.7 42.8 + - - -
1739A ARG 4.2 1.3 + - - -
1740A ASN* 2.9 28.3 + - - +
1742A PHE* 4.3 13.7 - - + -
1788A LEU* 5.4 0.4 - - + -
1797A VAL* 3.8 21.5 - - + +
1798A PRO* 5.6 1.6 - - - +
1801A SER* 3.2 10.4 + - - +
1802A VAL* 1.3 78.3 - - - +
1804A PHE* 1.3 57.3 + - - +
1806A PHE* 3.3 5.3 + - - +
1807A MET* 3.0 33.7 + - + +
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Residues in contact with PHE1804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1794A THR 5.1 0.7 - - - -
1797A VAL* 3.8 21.2 - - + +
1798A PRO 3.5 15.9 - - - +
1799A LYS* 3.2 53.6 - - + +
1801A SER* 3.2 10.1 + - - +
1803A GLU* 1.3 77.3 - - - +
1805A ALA* 1.3 53.6 + - - +
1807A MET* 3.3 28.7 + - + +
1808A PHE* 2.8 34.5 + - - +
1937A GLU 5.9 0.2 - - - -
1940A MET* 3.8 34.5 - - + -
1941A ALA* 4.5 2.7 - - - -
1944A MET* 3.6 30.2 - - + +
1948A LYS* 4.5 12.6 - - - -
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Residues in contact with ALA1805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 3.4 17.9 - - - +
1801A SER 3.5 5.1 + - - +
1802A VAL* 3.2 14.7 + - + +
1804A PHE* 1.3 75.8 - - - +
1806A PHE* 1.3 53.3 + - - +
1808A PHE* 3.5 8.7 - - + +
1809A GLU* 2.8 41.1 + - + +
1837A TYR* 5.5 5.8 - - - +
1940A MET* 4.2 13.3 - - + -
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Residues in contact with PHE1806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 3.4 40.5 + - - -
1706A CYS* 3.8 11.7 - - - -
1733A LEU* 3.9 9.9 - - + -
1735A MET* 3.5 25.6 - - + -
1742A PHE* 4.2 12.1 - + + -
1786A PHE* 3.5 47.8 - + - -
1787A LYS* 5.0 3.4 - - - -
1788A LEU* 4.2 13.7 - - + -
1802A VAL* 3.0 36.5 + - + -
1803A GLU* 3.3 9.2 + - - +
1805A ALA* 1.3 71.1 - - - +
1807A MET* 1.3 60.1 + - - +
1808A PHE 3.3 0.2 + - - -
1809A GLU* 3.3 2.1 + - - +
1810A GLN* 2.8 33.8 + - - +
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Residues in contact with MET1807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740A ASN* 4.7 2.7 - - - -
1788A LEU* 3.8 27.8 - - + +
1791A PHE* 5.0 1.3 - - + -
1794A THR* 3.5 44.6 - - + +
1797A VAL* 3.7 27.6 - - + -
1803A GLU* 3.0 23.0 + - - +
1804A PHE* 3.5 24.9 - - + +
1806A PHE* 1.3 73.2 - - - +
1808A PHE* 1.3 53.8 + - - +
1810A GLN* 3.8 2.2 - - - +
1811A ALA* 2.8 37.6 + - - +
1944A MET* 4.1 11.8 - - + +
1948A LYS* 4.6 1.1 - - - -
1953A TYR* 3.8 17.7 + - - +
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Residues in contact with PHE1808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1804A PHE 2.8 20.3 + - - +
1805A ALA* 3.5 5.8 - - + +
1807A MET* 1.3 69.8 - - - +
1809A GLU* 1.3 79.9 + - - +
1811A ALA* 3.4 2.1 + - - +
1812A HIS* 3.0 21.6 + - + +
1833A LEU 5.8 0.2 - - - -
1834A ARG* 3.4 33.0 - - - -
1837A TYR* 3.7 40.2 - + + -
1939A ALA 5.8 0.2 - - - -
1940A MET* 3.8 33.4 - - + -
1943A TYR* 3.5 48.9 - + + -
1944A MET* 3.6 15.6 - - + -
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Residues in contact with GLU1809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 3.5 31.9 - - - +
1707A HIS* 4.1 9.8 - - + +
1708A GLY* 3.6 24.7 + - - +
1805A ALA* 2.8 23.3 + - + +
1806A PHE 3.9 1.6 - - - +
1808A PHE* 1.3 84.0 - - - +
1810A GLN* 1.3 61.2 + - - +
1812A HIS* 3.4 5.5 + - - +
1813A GLU* 3.1 25.5 + - - +
1834A ARG* 2.8 43.1 + - - -
1837A TYR* 4.2 10.6 + - - -
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Residues in contact with GLN1810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1707A HIS* 4.8 7.2 - - + +
1745A PHE* 5.6 0.2 - - - -
1787A LYS* 3.4 31.8 - - + +
1788A LEU* 2.9 52.4 + - + +
1791A PHE* 3.7 25.4 - - + -
1806A PHE* 2.8 22.6 + - + +
1807A MET* 3.8 4.9 - - - +
1809A GLU* 1.3 71.6 - - - +
1811A ALA* 1.3 65.5 + - - +
1813A GLU* 3.2 8.9 + - + +
1814A ALA* 3.2 19.9 + - - +
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Residues in contact with ALA1811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1807A MET 2.8 21.2 + - - +
1808A PHE 3.7 3.8 - - - +
1810A GLN* 1.3 73.4 - - - +
1812A HIS* 1.3 56.5 + - - +
1814A ALA* 3.1 10.3 + - - +
1815A VAL* 2.9 31.8 + - - +
1820A HIS* 5.2 0.7 + - - +
1943A TYR* 4.4 1.3 - - + -
1944A MET* 4.1 17.5 - - - -
1947A ILE* 4.2 24.5 - - + +
1953A TYR* 4.3 13.4 - - + -
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Residues in contact with HIS1812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1808A PHE* 3.0 17.5 + - + +
1809A GLU* 3.7 5.2 - - - +
1810A GLN 3.2 0.4 - - - -
1811A ALA* 1.3 76.5 - - - +
1813A GLU* 1.3 59.4 - - + +
1815A VAL* 3.3 3.6 + - + +
1816A ILE* 3.0 52.0 + - + +
1830A LEU 5.4 0.7 - - - -
1831A ALA* 5.4 0.2 - - - -
1834A ARG* 3.4 58.8 + - + +
1853A GLU 2.8 25.4 + - - -
1854A VAL* 3.8 11.7 - - - -
1943A TYR* 2.8 33.4 + + + +
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Residues in contact with GLU1813 (chain A).
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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1707A HIS* 3.5 47.1 - - + +
1747A TYR* 3.5 12.7 + - - -
1809A GLU 3.1 12.0 + - - +
1810A GLN* 3.2 12.8 + - + +
1812A HIS* 1.3 76.2 - - + +
1814A ALA* 1.3 61.1 + - - +
1816A ILE* 3.5 18.8 + - - +
1817A HIS* 3.0 62.4 + - + -
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Residues in contact with ALA1814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1810A GLN 3.2 8.5 + - - +
1811A ALA* 3.1 12.9 + - - +
1813A GLU* 1.3 76.9 - - - +
1815A VAL* 1.3 63.1 + - - +
1817A HIS 3.3 0.7 + - - -
1818A GLY 3.2 4.5 + - - -
1819A HIS* 2.8 57.3 + - + +
1820A HIS* 4.2 7.2 - - + +
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Residues in contact with VAL1815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811A ALA 2.9 15.4 + - - +
1812A HIS* 3.4 11.4 - - + +
1814A ALA* 1.3 79.0 - - - +
1816A ILE* 1.3 69.7 + - + +
1817A HIS 3.3 0.3 + - - -
1818A GLY* 3.4 9.0 + - - -
1819A HIS 4.6 0.2 + - - -
1820A HIS* 3.8 21.3 + - + +
1827A LEU* 4.8 17.3 - - + +
1830A LEU* 4.0 19.5 - - + -
1854A VAL 4.6 7.4 - - - +
1855A TYR* 5.8 2.0 - - - -
1856A SER* 3.9 9.5 + - - +
1943A TYR* 3.6 20.4 - - - +
1947A ILE* 3.6 23.3 - - + -
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Residues in contact with ILE1816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1812A HIS* 3.0 50.8 + - + +
1813A GLU* 3.5 30.3 - - - +
1814A ALA 3.4 0.2 - - - -
1815A VAL* 1.3 77.6 - - + +
1817A HIS* 1.3 72.3 + - + +
1818A GLY 3.5 0.4 - - - -
1852A GLU 3.7 16.6 - - - +
1853A GLU* 3.6 22.2 - - + +
1854A VAL 3.6 17.9 - - - +
1855A TYR 4.7 0.7 - - - +
1856A SER* 3.4 23.0 + - - +
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Residues in contact with HIS1817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1747A TYR* 3.5 16.8 + + - -
1749A GLY* 5.1 7.8 + - - -
1813A GLU* 3.0 57.7 + - + +
1814A ALA 3.3 0.2 + - - -
1815A VAL 3.3 0.2 - - - -
1816A ILE* 1.3 91.8 + - + +
1818A GLY* 1.3 60.6 + - - +
1819A HIS* 3.6 25.6 + + + +
1856A SER* 4.4 3.4 - - - -
1858A GLN* 5.8 3.7 - - - +
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Residues in contact with GLY1818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1814A ALA 3.2 2.2 + - - -
1815A VAL 3.4 8.6 + - - -
1816A ILE 3.5 1.0 + - - -
1817A HIS* 1.3 80.5 - - - +
1819A HIS* 1.3 61.1 + - - +
1820A HIS 3.5 5.2 - - - -
1821A PRO* 5.9 0.2 - - - +
1856A SER* 4.1 10.4 + - - -
1858A GLN* 6.3 0.9 - - - -
1972A TRP* 3.2 25.3 - - - -
1986A GLY* 5.4 0.7 - - - -
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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
------------------------------------------------------------
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