Contacts of the helix formed by residues 1760 - 1772 (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 VAL1760 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1680A LYS* 6.6 0.4 - - + -
1682A ARG* 4.0 11.7 - - - +
1718A SER 3.3 28.3 - - - +
1719A HIS* 4.1 15.5 - - + +
1720A THR 3.6 10.5 - - - +
1721A THR* 4.4 3.1 - - + +
1758A ARG 4.4 6.3 - - - +
1759A THR* 1.3 75.6 - - - +
1761A VAL* 1.3 61.2 + - - +
1762A ALA 3.9 9.4 - - - +
1763A ASP* 3.0 37.6 + - + +
1764A VAL* 3.3 8.8 + - - +
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Residues in contact with VAL1761 (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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1714A ILE* 4.3 9.4 - - + -
1716A ILE* 3.7 27.1 - - + -
1720A THR 3.0 13.7 + - - +
1721A THR 3.6 5.6 - - - -
1722A ALA* 3.4 37.0 - - + +
1725A VAL* 3.7 14.4 - - + -
1744A LEU* 4.5 6.7 - - + -
1755A ILE* 6.2 0.7 - - + -
1760A VAL* 1.3 70.6 - - - +
1762A ALA* 1.3 60.4 + - - +
1764A VAL* 3.1 11.9 + - - +
1765A LEU* 3.1 18.6 + - + +
1784A PHE* 3.8 27.9 - - + -
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Residues in contact with ALA1762 (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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1682A ARG* 3.4 27.5 + - - +
1687A SER* 5.2 0.5 + - - -
1690A GLU* 3.5 16.1 - - - +
1700A MET* 4.3 4.7 - - - -
1716A ILE* 3.7 15.3 - - + +
1717A ASN 4.0 17.2 + - - +
1720A THR 4.7 0.6 + - - -
1760A VAL* 3.4 5.0 - - + +
1761A VAL* 1.3 77.0 - - - +
1763A ASP* 1.3 56.0 + - - +
1765A LEU* 3.4 8.6 + - - +
1766A ALA* 3.0 27.4 + - - +
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Residues in contact with ASP1763 (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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1681A CYS 4.9 1.0 - - - +
1682A ARG* 3.2 26.9 - - - +
1683A GLU* 3.0 28.0 + - - +
1684A PHE* 3.0 38.7 + - - +
1759A THR* 5.2 5.4 - - + +
1760A VAL* 3.0 23.7 + - + +
1762A ALA* 1.3 76.0 - - - +
1764A VAL* 1.3 64.8 + - + +
1766A ALA* 3.5 2.8 + - - +
1767A LYS* 3.1 20.8 + - - +
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Residues in contact with VAL1764 (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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1746A GLU* 4.0 13.2 - - - +
1755A ILE* 4.4 20.0 - - + -
1759A THR* 3.9 20.2 - - + -
1760A VAL 3.8 12.6 - - - +
1761A VAL* 3.1 9.1 + - - +
1763A ASP* 1.3 74.6 - - + +
1765A LEU* 1.3 60.6 + - - +
1767A LYS* 3.0 13.7 + - + +
1768A PHE* 2.9 46.0 + - + -
1784A PHE* 3.5 25.8 - - + -
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Residues in contact with LEU1765 (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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1687A SER* 4.4 9.8 - - - +
1700A MET* 3.7 29.4 - - + -
1701A THR 5.1 0.4 - - - +
1702A SER* 3.5 29.8 - - - +
1716A ILE* 3.9 20.0 - - + -
1761A VAL 3.1 8.2 + - - +
1762A ALA* 3.5 8.5 - - - +
1764A VAL* 1.3 74.3 - - - +
1766A ALA* 1.3 61.2 + - - +
1768A PHE* 3.3 19.3 + - + +
1769A GLU* 3.1 22.2 + - - +
1784A PHE* 3.8 21.5 - - + -
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Residues in contact with ALA1766 (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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1682A ARG* 4.6 0.4 - - - +
1684A PHE* 3.7 14.8 - - + +
1685A VAL 3.2 30.1 - - - +
1686A PRO* 4.5 0.7 - - + -
1687A SER* 3.9 20.1 - - - +
1762A ALA 3.0 16.6 + - - +
1763A ASP 3.6 6.5 - - - +
1765A LEU* 1.3 74.7 - - - +
1767A LYS* 1.3 58.0 + - - +
1769A GLU* 3.3 4.7 + - - +
1770A LYS* 3.0 27.9 + - - +
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Residues in contact with LYS1767 (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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1684A PHE* 3.6 41.0 - - + -
1746A GLU* 2.7 39.6 + - - +
1753A LYS* 5.0 4.0 - - - +
1763A ASP 3.1 13.3 + - - +
1764A VAL* 3.0 19.9 + - + +
1766A ALA* 1.3 73.8 - - - +
1768A PHE* 1.3 58.7 + - + +
1770A LYS* 3.2 1.6 + - - +
1771A LEU* 2.8 65.5 + - + +
1782A TRP* 6.2 1.1 - - - -
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Residues in contact with PHE1768 (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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1746A GLU* 3.7 26.9 - - + -
1764A VAL* 2.9 34.6 + - + -
1765A LEU* 3.3 25.1 - - + +
1767A LYS* 1.3 79.0 - - + +
1769A GLU* 1.3 62.3 + - - +
1771A LEU* 4.0 1.3 - - + +
1772A ALA* 3.1 23.9 + - - +
1782A TRP* 3.4 55.6 - + + +
1783A LYS* 3.7 30.7 - - - -
1784A PHE* 3.9 20.4 - + - -
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Residues in contact with GLU1769 (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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1590A GLN* 3.0 27.4 + - - +
1687A SER* 3.3 14.3 - - - -
1688A ARG* 2.9 39.5 + - - +
1689A ASP 4.7 0.2 + - - -
1765A LEU 3.1 13.1 + - - +
1766A ALA 3.5 8.9 - - - +
1767A LYS 3.2 0.4 - - - -
1768A PHE* 1.3 79.8 - - - +
1770A LYS* 1.3 66.1 + - - +
1772A ALA* 3.3 16.1 + - - +
1773A ALA* 4.2 1.0 + - - +
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Residues in contact with LYS1770 (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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1594A GLN* 3.0 41.2 + - - +
1684A PHE* 4.6 21.3 - - + -
1766A ALA 3.0 16.1 + - - +
1767A LYS* 3.8 4.9 - - - +
1769A GLU* 1.3 79.4 + - - +
1771A LEU* 1.3 63.1 + - + +
1773A ALA* 3.2 22.2 + - - +
1774A THR* 4.5 0.9 + - - -
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Residues in contact with LEU1771 (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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1684A PHE* 6.1 2.9 - - + -
1767A LYS* 2.8 53.8 + - + +
1768A PHE* 4.1 1.8 - - - +
1770A LYS* 1.3 74.0 - - + +
1772A ALA* 1.3 63.4 + - - +
1773A ALA 3.0 0.2 - - - -
1774A THR* 2.9 31.1 + - - +
1775A SER* 3.3 9.7 + - - -
1782A TRP* 3.7 42.6 + - + +
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Residues in contact with ALA1772 (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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1768A PHE 3.1 14.7 + - - +
1769A GLU* 3.4 15.5 - - - +
1770A LYS 3.2 0.2 - - - -
1771A LEU* 1.3 74.4 - - - +
1773A ALA* 1.3 60.5 + - - +
1775A SER* 3.5 22.3 + - - -
1782A TRP* 4.8 4.4 - - + -
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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