Contacts of the helix formed by residues 1681 - 1698 (chain A) in PDB entry 3CLY
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 THR1681 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1623A ILE* 3.5 16.8 - - - +
1651A ILE* 4.5 4.9 - - - -
1655A ASP 4.1 7.4 - - - +
1656A PTR 3.6 20.6 - - + -
1673A GLU* 4.8 3.7 + - + -
1679A VAL* 4.2 11.9 + - + +
1680A TYR* 1.3 81.9 - - - +
1682A HIS* 1.3 65.5 + - - +
1683A GLN* 3.0 27.8 + - - +
1684A SER* 2.7 27.0 + - - -
1685A ASP* 3.2 5.0 + - - +
1744A PRO* 5.4 1.9 - - - +
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Residues in contact with HIS1682 (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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1618A ALA* 3.6 38.9 + - + +
1621A LYS* 3.6 22.4 + - - +
1622A CYS 3.4 37.0 + - - -
1623A ILE* 3.7 5.8 - - - +
1651A ILE* 3.8 16.4 - - + +
1655A ASP 5.7 1.6 - - - -
1681A THR* 1.3 75.3 - - - +
1683A GLN* 1.3 64.8 + - - +
1685A ASP* 3.0 10.8 + - - +
1686A VAL* 3.0 30.5 + - + +
1750A PHE* 3.9 5.3 - - + -
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Residues in contact with GLN1683 (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 THR* 3.0 16.3 + - - +
1682A HIS* 1.3 91.1 + - - +
1684A SER* 1.3 60.3 + - - +
1686A VAL* 3.3 12.0 + - + +
1687A TRP 3.2 13.2 + - - -
1744A PRO* 3.1 39.1 - - + +
1745A SER* 4.0 20.8 - - - +
1747A ARG* 3.0 23.2 + - + +
1748A PRO 5.5 0.9 - - - +
1749A THR* 6.3 4.7 - - + +
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Residues in contact with SER1684 (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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1623A ILE* 5.4 0.5 - - - +
1625A ARG* 5.9 0.3 - - - +
1669A TRP 4.9 0.2 - - - +
1671A ALA* 4.0 15.4 + - - +
1673A GLU* 3.8 17.9 + - - -
1674A ALA* 4.6 6.3 - - - -
1679A VAL 4.4 3.8 - - - -
1680A TYR* 3.3 19.2 - - - +
1681A THR* 2.7 36.8 + - - -
1683A GLN* 1.3 77.0 - - - +
1685A ASP* 1.3 67.0 + - - +
1687A TRP* 3.3 5.4 + - - +
1688A SER* 3.1 19.4 + - - -
1747A ARG* 4.0 2.6 - - - +
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Residues in contact with ASP1685 (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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1614A MET* 3.5 16.8 - - + +
1622A CYS 4.5 1.0 - - - +
1623A ILE* 3.3 17.0 - - - +
1624A HIS* 2.8 26.4 + - - +
1625A ARG* 3.0 27.5 + - - +
1627A LEU* 4.1 5.4 - - + +
1681A THR 3.2 4.6 + - - +
1682A HIS* 3.0 13.1 + - - +
1684A SER* 1.3 79.2 + - - +
1686A VAL* 1.3 54.2 + - - +
1688A SER* 3.1 10.3 + - - -
1689A PHE* 2.7 33.6 + - - +
1750A PHE* 3.7 17.9 - - + -
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Residues in contact with VAL1686 (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 HIS* 3.0 19.0 + - + +
1683A GLN* 3.4 14.6 - - + +
1684A SER 3.2 0.2 - - - -
1685A ASP* 1.3 74.8 - - - +
1687A TRP* 1.3 65.2 + - - +
1689A PHE* 2.9 13.4 + - - +
1690A GLY 3.0 10.2 + - - -
1739A CYS* 3.6 33.0 - - - +
1747A ARG* 4.0 9.4 - - + -
1748A PRO* 3.3 29.6 - - + +
1749A THR* 4.5 1.1 - - - -
1750A PHE* 3.7 33.4 - - + +
1753A LEU* 4.4 3.8 - - + -
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Residues in contact with TRP1687 (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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1668A LYS 5.2 0.6 + - - -
1669A TRP 3.6 10.2 + - - -
1670A MET 3.5 10.9 + - - -
1671A ALA* 3.5 31.9 - - + -
1672A PRO* 3.3 32.1 - - + -
1683A GLN 3.2 8.0 + - - +
1684A SER 3.4 9.0 - - - +
1686A VAL* 1.3 79.5 - - - +
1688A SER* 1.3 66.0 + - - +
1690A GLY 3.0 10.9 + - - -
1691A VAL* 3.2 21.8 + - + +
1704A TYR* 3.9 20.0 + - - -
1716A LEU* 4.2 8.5 - - + -
1721A ARG* 3.5 32.5 - - - -
1739A CYS 3.3 12.3 - - - +
1740A TRP* 3.3 51.9 + + + -
1741A HIS 4.3 0.2 - - - -
1742A ALA* 5.4 0.2 - - - -
1747A ARG* 3.7 16.4 - - - +
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Residues in contact with SER1688 (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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1625A ARG 5.7 1.9 - - - -
1626A ASP 6.0 0.2 - - - -
1627A LEU* 2.6 46.2 + - - +
1669A TRP* 3.3 26.6 + - - +
1684A SER 3.1 8.3 + - - -
1685A ASP* 3.1 14.4 + - - -
1687A TRP* 1.3 81.4 - - - +
1689A PHE* 1.3 62.1 + - - +
1691A VAL* 3.1 6.5 + - - +
1692A LEU* 3.0 21.0 + - - +
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Residues in contact with PHE1689 (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 THR* 3.7 20.9 - - + -
1610A LEU* 3.8 12.8 - - + -
1611A ALA* 3.5 40.4 - - + -
1614A MET* 4.5 2.9 - - + -
1627A LEU* 3.7 19.5 - - + +
1685A ASP 2.7 15.8 + - - +
1686A VAL* 2.9 10.0 + - - +
1688A SER* 1.3 73.3 - - - +
1690A GLY* 1.3 58.0 + - - +
1692A LEU* 3.1 11.3 + - + +
1693A MET* 2.9 51.6 + - + +
1696A ILE* 6.3 0.4 - - + -
1739A CYS* 4.3 1.8 - - - -
1750A PHE* 3.7 23.1 - + + -
1753A LEU* 3.8 23.6 - - + -
1757A LEU* 4.3 5.8 - - + -
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Residues in contact with GLY1690 (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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1686A VAL 3.0 6.7 + - - -
1687A TRP 3.0 8.8 + - - -
1689A PHE* 1.3 78.1 - - - +
1691A VAL* 1.3 60.2 + - - +
1693A MET* 3.2 11.6 + - - +
1694A TRP 3.1 16.8 + - - -
1736A MET* 3.6 4.4 - - - +
1739A CYS* 3.7 19.9 - - - +
1740A TRP* 3.4 22.7 - - - -
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Residues in contact with VAL1691 (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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1668A LYS 4.0 13.7 - - - +
1669A TRP* 3.4 31.6 - - + +
1687A TRP* 3.2 24.4 + - + +
1688A SER 3.1 8.1 + - - +
1690A GLY* 1.3 76.7 - - - +
1692A LEU* 1.3 57.0 + - - +
1694A TRP* 3.1 5.6 + - - +
1695A GLU* 3.0 25.1 + - - +
1703A PRO* 3.5 27.6 - - + -
1704A TYR* 4.9 2.2 - - - +
1722A MET* 4.1 7.2 - - + -
1740A TRP* 3.7 23.1 - - + +
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Residues in contact with LEU1692 (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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1572A LEU* 4.0 15.7 - - + -
1610A LEU* 3.8 23.1 - - + -
1627A LEU* 3.8 33.7 - - + -
1628A ALA* 3.8 4.7 - - - +
1629A ALA* 3.5 35.9 - - + +
1632A VAL* 4.4 2.9 - - + -
1669A TRP* 4.8 0.4 - - - -
1688A SER 3.0 13.3 + - - +
1689A PHE* 3.1 21.3 + - + +
1691A VAL* 1.3 74.1 - - - +
1693A MET* 1.3 65.2 + - - +
1695A GLU* 3.1 10.8 + - - +
1696A ILE* 2.9 34.8 + - + +
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Residues in contact with MET1693 (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 THR* 3.9 16.6 - - + -
1689A PHE* 2.9 47.2 + - + +
1690A GLY* 3.4 10.5 - - - +
1692A LEU* 1.3 75.4 - - - +
1694A TRP* 1.3 62.6 + - - +
1696A ILE* 3.2 10.3 + - + +
1697A PHE* 2.9 38.7 + - + -
1732A LEU* 3.7 35.7 - - + +
1735A MET* 3.9 29.8 - - - +
1736A MET* 4.0 23.8 - - + -
1739A CYS* 4.6 1.8 - - - -
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Residues in contact with TRP1694 (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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1690A GLY 3.1 9.1 + - - +
1691A VAL 3.1 11.0 + - - +
1693A MET* 1.3 80.5 - - - +
1695A GLU* 1.3 64.8 + - - +
1697A PHE 3.4 0.7 + - - -
1698A THR* 2.8 53.8 + - + +
1701A GLY* 3.7 12.3 - - - -
1702A SER 3.2 38.8 - - - -
1703A PRO* 3.5 14.1 - - + -
1705A PRO* 4.0 19.7 - - + -
1722A MET* 3.4 34.6 - - + +
1723A ASP 3.2 24.2 + - - +
1725A PRO* 3.4 24.0 - - + +
1736A MET* 4.0 17.2 - - - +
1740A TRP* 4.3 1.6 - + + -
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Residues in contact with GLU1695 (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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1573A ARG* 3.2 26.5 + - - -
1576A LEU* 4.6 1.1 - - - -
1628A ALA* 3.6 1.7 - - - -
1629A ALA* 2.9 47.9 + - + +
1630A ARG 4.8 0.7 + - - -
1669A TRP* 2.9 28.2 + - - -
1691A VAL 3.0 14.6 + - - +
1692A LEU* 3.1 11.9 + - + +
1694A TRP* 1.3 76.8 - - + +
1696A ILE* 1.3 60.1 + - - +
1698A THR* 3.1 11.1 + - - -
1700A GLY* 2.7 31.5 + - - -
1701A GLY 3.7 15.0 - - - +
1703A PRO* 4.1 10.8 - - + -
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Residues in contact with ILE1696 (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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1572A LEU* 3.8 20.2 - - + -
1576A LEU* 3.7 11.4 - - + +
1603A LEU* 3.7 38.1 - - + +
1606A CYS* 4.5 7.4 - - + -
1607A THR* 3.6 34.3 - - + +
1610A LEU* 3.8 27.8 - - + -
1689A PHE* 6.3 0.4 - - + -
1692A LEU* 2.9 26.8 + - + +
1693A MET* 3.5 9.2 - - + +
1695A GLU* 1.3 76.6 - - - +
1697A PHE* 1.3 60.5 + - + +
1699A LEU* 3.0 20.4 + - - +
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Residues in contact with PHE1697 (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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1600A PHE* 4.0 13.2 - + - -
1603A LEU* 3.6 37.2 - - + -
1604A VAL* 4.3 4.3 - - + -
1607A THR* 3.6 25.1 - - - -
1693A MET* 2.9 43.1 + - + +
1694A TRP 3.8 0.9 - - - +
1696A ILE* 1.3 78.0 - - + +
1698A THR* 1.3 59.2 + - - +
1699A LEU* 3.2 14.0 - - - +
1725A PRO* 3.9 22.3 - - + +
1726A ALA 5.3 0.2 + - - -
1727A ASN* 3.4 33.7 + - - +
1728A CYS* 4.1 12.6 - - + +
1732A LEU* 3.5 33.0 - - + -
1736A MET* 4.4 8.5 - - + -
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Residues in contact with THR1698 (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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1580A ARG* 3.2 15.2 + - - -
1694A TRP* 2.8 47.0 + - + +
1695A GLU* 3.1 5.2 + - - -
1696A ILE 3.2 0.2 - - - -
1697A PHE* 1.3 75.5 - - - +
1699A LEU* 1.3 73.1 + - - +
1701A GLY* 3.0 26.5 + - - -
1725A PRO* 3.6 26.5 - - + -
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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