Contacts of the helix formed by residues 1663 - 1677 (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 SER1663 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1660A PHE* 2.8 31.8 + - - +
1661A PRO 3.3 1.5 - - - -
1662A GLY* 1.3 78.9 - - - +
1664A GLU* 1.3 64.7 + - - +
1665A MET* 3.3 22.5 + - - +
1666A GLU* 3.1 20.9 + - - +
1667A LYS* 3.3 19.5 + - - +
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Residues in contact with GLU1664 (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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1621A GLY* 5.8 1.1 - - - -
1626A LEU* 3.7 35.3 - - + +
1663A SER* 1.3 72.8 - - - +
1665A MET* 1.3 59.3 + - - +
1667A LYS* 3.1 15.6 + - - +
1668A TYR* 2.9 43.5 + - + -
1697A ARG* 2.8 42.1 + - - +
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Residues in contact with MET1665 (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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1620A PRO* 3.8 29.4 - - + -
1621A GLY* 3.6 24.5 - - - +
1625A ASN* 3.3 18.4 - - - +
1626A LEU* 4.2 5.8 - - + -
1629A TRP* 3.5 35.3 - - + +
1656A ILE* 3.9 14.1 - - + +
1660A PHE* 3.9 20.6 - - + -
1663A SER* 3.2 23.3 - - - +
1664A GLU* 1.3 76.1 - - - +
1666A GLU* 1.3 59.7 + - - +
1668A TYR* 3.4 2.1 + - - +
1669A ALA* 2.9 30.0 + - - +
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Residues in contact with GLU1666 (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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1656A ILE* 4.5 4.4 - - - +
1657A ARG* 2.8 64.7 + - + +
1660A PHE 3.2 23.3 + - - +
1661A PRO* 4.3 6.3 - - + -
1662A GLY* 4.8 4.1 + - - -
1663A SER* 3.1 13.7 + - - +
1665A MET* 1.3 76.6 - - - +
1667A LYS* 1.3 75.8 + - - +
1669A ALA* 3.2 3.7 + - - +
1670A LEU* 3.0 28.9 + - - +
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Residues in contact with LYS1667 (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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1662A GLY* 4.2 25.8 + - - -
1663A SER 3.5 8.5 - - - +
1664A GLU* 3.1 19.3 + - - +
1666A GLU* 1.3 86.7 + - - +
1668A TYR* 1.3 59.4 + - - +
1670A LEU* 3.4 7.3 + - - +
1671A PHE* 2.9 28.4 + - - +
1697A ARG* 3.6 35.1 - - - +
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Residues in contact with TYR1668 (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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1626A LEU* 4.4 10.8 - - + +
1629A TRP* 3.7 33.7 - + + -
1630A GLN* 2.9 37.0 + - + -
1633A THR* 3.3 22.0 + - - +
1664A GLU* 2.9 42.4 + - + +
1665A MET 3.8 2.5 - - - +
1667A LYS* 1.3 74.4 - - - +
1669A ALA* 1.3 59.6 + - - +
1671A PHE* 4.5 0.9 - - - -
1672A THR* 2.8 36.7 + - - -
1694A LEU 4.1 5.4 - - - -
1695A ILE 2.5 29.8 + - - -
1697A ARG* 3.3 35.0 + - + +
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Residues in contact with ALA1669 (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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1629A TRP* 3.9 21.9 - - + -
1653A LEU* 3.9 23.6 - - + +
1656A ILE* 4.1 2.9 - - + -
1657A ARG* 3.7 21.3 - - + -
1665A MET 2.9 18.6 + - - +
1666A GLU 3.5 4.9 - - - +
1668A TYR* 1.3 75.1 - - - +
1670A LEU* 1.3 58.5 + - - +
1672A THR* 3.6 2.0 - - - -
1673A TYR* 2.9 30.7 + - - +
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Residues in contact with LEU1670 (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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1657A ARG* 3.5 40.1 - - - +
1666A GLU* 3.0 18.4 + - - +
1667A LYS* 3.7 9.6 - - - +
1669A ALA* 1.3 73.9 - - - +
1671A PHE* 1.3 60.0 + - - +
1673A TYR* 3.2 11.7 + - + +
1674A GLU* 2.8 53.6 + - + +
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Residues in contact with PHE1671 (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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1633A THR* 3.5 28.3 - - + -
1637A CYS* 4.2 4.3 - - - -
1667A LYS 2.9 17.3 + - - +
1668A TYR* 3.8 4.3 - - - +
1670A LEU* 1.3 75.7 - - - +
1672A THR* 1.3 58.2 + - - +
1674A GLU* 3.2 8.1 + - + +
1675A SER* 2.9 49.5 + - - -
1694A LEU* 4.0 25.6 - - + -
1697A ARG* 3.8 50.3 - - + -
1698A GLN 5.0 3.4 - - - -
1717A ASN* 6.2 4.7 - - + -
1719A HIS* 6.5 0.2 - + - -
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Residues in contact with THR1672 (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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1629A TRP* 4.8 1.4 - - - -
1632A LEU* 4.1 22.6 - - + +
1633A THR* 3.2 24.1 + - - +
1636A SER* 3.5 26.2 + - - -
1649A LEU* 5.0 2.2 - - + -
1653A LEU* 3.7 20.0 - - + -
1668A TYR 2.8 26.7 + - - -
1669A ALA* 3.6 5.8 - - - -
1671A PHE* 1.3 73.2 - - - +
1673A TYR* 1.3 62.8 + - - +
1675A SER* 3.2 3.6 + - - -
1676A LEU* 3.1 28.6 + - + +
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Residues in contact with TYR1673 (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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1650A LYS* 4.0 42.9 + - + +
1653A LEU* 3.9 19.9 - - + +
1654A LYS* 5.1 16.8 - - + -
1657A ARG* 5.4 7.4 - - - +
1669A ALA 2.9 19.0 + - - +
1670A LEU* 3.4 13.5 - - + +
1672A THR* 1.3 77.2 - - - +
1674A GLU* 1.3 73.4 + - - +
1676A LEU* 3.3 17.8 + - + +
1677A LYS* 3.6 41.3 + - + +
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Residues in contact with GLU1674 (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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1670A LEU* 2.8 46.6 + - + +
1671A PHE* 3.7 7.9 - - + +
1673A TYR* 1.3 77.8 - - - +
1675A SER* 1.3 61.8 + - - +
1676A LEU 3.4 0.5 + - - -
1677A LYS* 3.0 50.4 + - - +
1678A LYS* 3.9 11.8 + - + +
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Residues in contact with SER1675 (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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1636A SER* 3.2 31.2 - - - -
1637A CYS* 3.4 21.6 - - - -
1671A PHE* 2.9 29.3 + - - -
1672A THR 3.2 0.6 + - - -
1674A GLU* 1.3 77.8 - - - +
1676A LEU* 1.3 56.1 + - - +
1678A LYS* 2.9 17.6 + - - -
1679A THR* 3.0 17.8 + - - -
1719A HIS* 3.7 12.2 + - - -
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Residues in contact with LEU1676 (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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1607A TYR* 4.1 12.1 - - - +
1636A SER* 3.8 19.5 - - - -
1640A LEU* 3.6 41.8 - - + +
1641A PRO* 4.3 1.6 - - + -
1646A LEU* 3.8 24.9 - - + +
1649A LEU* 3.6 28.0 - - + -
1650A LYS* 4.7 15.5 - - + -
1653A LEU* 4.2 16.4 - - + -
1672A THR* 3.1 18.9 + - + +
1673A TYR* 3.8 9.9 - - + +
1674A GLU 3.3 0.6 - - - -
1675A SER* 1.3 76.8 - - - +
1677A LYS* 1.3 62.0 + - + +
1678A LYS 3.4 0.5 + - - -
1679A THR 4.0 2.3 + - - +
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Residues in contact with LYS1677 (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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1650A LYS* 6.1 4.5 - - - +
1673A TYR* 3.6 40.0 - - + +
1674A GLU* 3.0 40.6 + - - +
1676A LEU* 1.3 78.4 - - + +
1678A LYS* 1.3 63.8 + - + +
1679A THR 5.2 0.4 - - - +
1680A LYS* 5.5 4.5 + - - -
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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