Contacts of the helix formed by residues 1653 - 1671 (chain A) in PDB entry 4PY4
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 ASN1653 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1615A GLN* 2.9 27.0 + - - +
1616A ASN 2.9 16.5 + - - +
1617A PHE* 3.9 5.8 - - + +
1651A ILE* 4.8 2.5 - - + -
1652A GLN* 1.3 73.7 - - - +
1654A PRO* 1.4 54.8 - - - +
1655A ASP 3.7 0.9 + - - -
1656A LEU* 3.3 27.4 + - + +
1657A TRP* 2.7 36.6 + - - +
1693A ASN 3.0 23.1 + - - +
1694A ARG 3.1 12.9 + - - -
1792A TYR* 2.7 17.8 + - + +
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Residues in contact with PRO1654 (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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1616A ASN 3.8 11.4 - - - +
1617A PHE* 5.0 0.2 - - - -
1652A GLN* 3.6 9.4 - - + +
1653A ASN* 1.4 85.3 - - - +
1655A ASP* 1.3 63.3 + - - +
1657A TRP* 3.6 6.8 - - + +
1658A ASN* 2.8 43.7 + - - +
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Residues in contact with ASP1655 (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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1613A LYS* 3.6 18.4 - - + +
1614A GLN* 3.6 8.3 + - - +
1615A GLN* 3.0 45.5 + - + +
1616A ASN 4.6 1.3 + - - -
1653A ASN* 3.5 1.4 + - - -
1654A PRO* 1.3 81.0 - - - +
1656A LEU* 1.3 57.9 + - - +
1658A ASN* 4.0 9.7 + - - +
1659A SER* 3.0 31.7 + - - -
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Residues in contact with LEU1656 (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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1615A GLN* 3.7 23.9 - - - +
1653A ASN* 3.1 31.7 + - + +
1655A ASP* 1.3 77.8 - - - +
1657A TRP* 1.3 58.8 + - - +
1659A SER* 3.4 5.1 + - - -
1660A TYR* 2.8 30.0 + - - +
1693A ASN 4.6 2.2 - - - +
1694A ARG 4.1 0.7 - - - +
1695A ASN 4.0 15.7 - - - +
1696A GLY* 4.0 14.1 - - - +
1698A ASN* 4.8 1.3 - - - +
1789A TYR* 3.7 23.5 - - + -
1791A ALA 5.3 2.9 - - - +
1792A TYR* 3.7 25.4 - - + -
1793A PRO* 3.8 19.3 - - + -
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Residues in contact with TRP1657 (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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1653A ASN 2.7 22.2 + - - +
1654A PRO* 3.6 6.5 - - + +
1656A LEU* 1.3 73.6 - - - +
1658A ASN* 1.3 69.8 + - - +
1660A TYR* 3.1 8.7 + + - +
1661A GLN* 2.8 67.3 + - + +
1742A ARG* 4.5 22.9 - - - -
1792A TYR* 3.7 46.8 - + + +
1794A GLU* 4.7 10.1 - - - -
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Residues in contact with ASN1658 (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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1654A PRO* 2.8 32.9 + - - +
1655A ASP* 4.0 10.0 + - - +
1657A TRP* 1.3 82.8 - - - +
1659A SER* 1.3 57.6 + - - +
1661A GLN* 3.2 7.0 + - - +
1662A ALA* 2.9 30.6 + - - +
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Residues in contact with SER1659 (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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1615A GLN* 5.2 0.3 + - - -
1655A ASP 3.0 19.5 + - - -
1656A LEU 3.7 1.3 - - - -
1657A TRP 3.3 0.2 - - - -
1658A ASN* 1.3 77.7 - - - +
1660A TYR* 1.3 61.6 + - - +
1662A ALA* 3.4 7.8 + - - +
1663A LYS* 3.3 17.5 + - - +
1789A TYR* 3.4 48.7 - - - +
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Residues in contact with TYR1660 (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 LEU 2.8 14.9 + - - +
1657A TRP* 3.4 11.2 - + - +
1659A SER* 1.3 74.6 - - - +
1661A GLN* 1.3 85.9 + - + +
1663A LYS* 3.2 7.8 + - - +
1664A LYS* 3.1 22.9 + - + +
1677A GLU* 2.5 43.7 + - - +
1742A ARG* 3.4 35.0 + - + +
1744A LEU* 3.4 19.3 - - + +
1789A TYR* 3.4 25.2 - - + +
1790A GLN 3.6 14.8 - - - -
1791A ALA 3.9 3.1 - - - +
1792A TYR* 3.8 27.1 - - + -
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Residues in contact with GLN1661 (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 TRP* 2.8 64.7 + - + +
1658A ASN* 3.8 6.5 - - - +
1660A TYR* 1.3 91.6 - - - +
1662A ALA* 1.3 60.7 + - - +
1664A LYS* 3.3 22.3 + - - +
1665A LYS* 2.9 30.1 + - - +
1677A GLU* 4.7 2.4 + - - -
1742A ARG* 5.6 0.2 - - - +
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Residues in contact with ALA1662 (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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1658A ASN 2.9 17.0 + - - +
1659A SER* 3.6 9.4 - - - +
1660A TYR 3.2 0.2 - - - -
1661A GLN* 1.3 74.3 - - - +
1663A LYS* 1.3 64.5 + - - +
1665A LYS* 3.4 6.7 + - - +
1666A THR* 3.2 26.4 + - - -
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Residues in contact with LYS1663 (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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1659A SER 3.3 7.3 + - - +
1660A TYR 3.2 10.8 + - - +
1662A ALA* 1.3 78.0 - - - +
1664A LYS* 1.3 55.5 + - - +
1666A THR* 3.5 8.8 - - + +
1667A MET* 2.9 44.3 + - + +
1744A LEU* 3.7 11.9 - - + -
1787A TYR* 4.3 24.8 - - - +
1788A ASP 3.3 26.0 + - - +
1789A TYR* 3.8 16.6 - - + +
1790A GLN* 4.2 11.2 - - - -
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Residues in contact with LYS1664 (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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1660A TYR* 3.1 14.7 + - + +
1661A GLN* 3.6 29.4 - - - +
1662A ALA 3.1 0.2 - - - -
1663A LYS* 1.3 75.4 - - - +
1665A LYS* 1.3 56.8 + - - +
1667A MET* 4.2 1.3 - - - +
1668A ASP* 2.6 68.1 + - - +
1676A ASN* 5.5 0.9 - - + +
1677A GLU* 3.8 42.4 - - - +
1744A LEU* 3.8 23.6 - - + -
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Residues in contact with LYS1665 (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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1661A GLN 2.9 16.0 + - - +
1662A ALA* 3.4 7.6 + - - +
1664A LYS* 1.3 74.6 - - - +
1666A THR* 1.3 63.7 + - - +
1668A ASP* 3.4 6.5 + - - +
1669A ALA* 3.1 24.1 + - - +
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Residues in contact with THR1666 (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 ALA 3.2 11.1 + - - -
1663A LYS* 3.5 13.2 - - + +
1665A LYS* 1.3 79.0 - - - +
1667A MET* 1.3 65.6 + - - +
1669A ALA* 3.1 16.5 + - - +
1670A LYS* 3.1 21.8 + - + +
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Residues in contact with MET1667 (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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1663A LYS* 2.9 46.3 + - + +
1664A LYS* 3.0 6.7 + - - +
1666A THR* 1.3 78.1 - - + +
1668A ASP* 1.3 62.6 + - - +
1670A LYS* 3.3 9.3 + - - +
1671A ASN* 3.0 29.5 + - - +
1676A ASN* 3.0 35.4 + - + +
1744A LEU* 3.7 42.8 - - + +
1746A GLY* 4.0 4.7 - - - -
1771A ASP* 3.9 30.5 - - + +
1790A GLN* 4.6 2.0 - - - +
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Residues in contact with ASP1668 (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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1664A LYS* 2.6 54.6 + - - +
1665A LYS* 3.8 6.4 + - - +
1667A MET* 1.3 74.5 - - - +
1669A ALA* 1.3 59.4 + - - +
1670A LYS 3.3 1.0 + - - -
1671A ASN 4.4 0.5 - - - -
1672A GLY* 3.8 22.7 + - - +
1674A THR 4.6 3.6 - - - +
1676A ASN* 2.7 35.8 + - - +
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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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1665A LYS 3.1 16.2 + - - +
1666A THR* 3.1 8.1 + - - +
1668A ASP* 1.3 75.6 - - - +
1670A LYS* 1.3 58.9 + - - +
1672A GLY* 4.7 2.4 + - - -
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Residues in contact with LYS1670 (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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1666A THR* 3.1 20.6 + - + +
1667A MET* 4.0 10.8 - - - +
1668A ASP 3.2 0.2 - - - -
1669A ALA* 1.3 79.9 - - - +
1671A ASN* 1.3 79.6 + - - +
1672A GLY 3.3 7.3 + - - -
1761A LYS* 4.9 9.0 - - - +
1768A ASP* 4.7 13.9 - - - -
1769A LEU 5.2 3.2 + - - -
1771A ASP* 3.5 24.5 + - - -
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Residues in contact with ASN1671 (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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1667A MET* 3.0 13.3 + - - +
1668A ASP 4.4 1.1 - - - -
1670A LYS* 1.3 102.0 + - - +
1672A GLY* 1.3 62.3 + - - +
1673A GLN* 3.1 2.8 + - - +
1674A THR* 2.7 33.6 + - - +
1676A ASN* 3.3 27.8 + - - +
1746A GLY 4.0 0.2 - - - -
1747A ILE* 3.3 35.5 - - + +
1761A LYS* 4.6 0.7 + - - -
1771A ASP* 3.0 26.7 + - - -
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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
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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