Contacts of the helix formed by residues 1707 - 1717 (chain B) in PDB entry 3LQJ
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 ASP1707 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1660B LEU* 3.2 15.0 - - - +
1661B LEU 3.2 14.4 - - - +
1662B ARG* 3.6 3.9 - - - +
1663B TYR* 2.8 35.3 + - - +
1705B PRO* 3.4 1.5 - - - +
1706B LEU* 1.3 82.7 + - - +
1708B LEU* 1.3 58.5 + - - +
1709B GLU* 3.2 7.0 + - - +
1710B GLY* 2.7 44.5 + - - -
1711B VAL* 3.1 8.8 + - - +
1713B ARG* 4.9 2.6 + - - -
1733B ILE* 3.4 14.9 - - - +
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Residues in contact with LEU1708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648B LEU* 4.6 8.7 - - + +
1651B LEU* 4.4 12.8 - - + -
1652B LEU* 3.6 32.3 - - + +
1657B THR* 3.5 35.9 - - + +
1660B LEU* 2.9 36.7 + - + +
1661B LEU* 4.3 6.7 - - + -
1707B ASP* 1.3 68.7 - - - +
1709B GLU* 1.3 65.6 + - - +
1711B VAL* 3.6 9.3 - - - +
1712B LYS* 2.9 24.6 + - - +
1730B ILE* 5.1 12.1 - - + -
1733B ILE* 3.9 18.6 - - + -
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Residues in contact with GLU1709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1652B LEU* 5.8 1.1 - - - -
1661B LEU* 3.1 25.7 + - + +
1662B ARG* 2.7 51.4 + - - +
1707B ASP* 3.1 7.0 - - - +
1708B LEU* 1.3 76.8 - - - +
1710B GLY* 1.3 63.4 + - - +
1712B LYS* 3.3 11.3 + - + +
1713B ARG* 3.2 44.0 + - - +
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Residues in contact with GLY1710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703B GLN* 2.9 26.2 + - - -
1705B PRO* 3.7 14.1 - - - -
1706B LEU 5.3 0.4 - - - -
1707B ASP* 2.7 19.6 + - - -
1709B GLU* 1.3 75.6 - - - +
1711B VAL* 1.3 63.5 + - - +
1713B ARG* 3.4 16.9 + - - +
1714B LYS* 3.1 10.4 + - - +
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Residues in contact with VAL1711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1648B LEU* 4.0 21.3 - - + -
1705B PRO* 3.5 19.5 - - + -
1707B ASP 3.1 3.1 + - - +
1708B LEU* 3.6 10.8 - - - +
1710B GLY* 1.3 75.0 - - - +
1712B LYS* 1.3 57.6 + - - +
1714B LYS* 3.3 2.9 + - - +
1715B MET* 2.9 27.0 + - - +
1720B TYR* 3.5 27.8 - - + +
1726B PHE* 4.1 8.3 - - + -
1729B ASP* 4.6 4.3 - - + -
1730B ILE* 4.0 22.2 - - + -
1733B ILE* 3.6 22.0 - - + -
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Residues in contact with LYS1712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645B LYS* 5.9 2.4 - - - +
1648B LEU* 3.6 21.5 - - + +
1652B LEU* 4.4 18.6 - - + -
1708B LEU 2.9 16.6 + - - +
1709B GLU* 3.6 10.1 - - + +
1710B GLY 3.2 0.2 - - - -
1711B VAL* 1.3 78.0 - - - +
1713B ARG* 1.3 59.4 + - + +
1715B MET* 3.3 0.9 + - - +
1716B ASP* 2.7 68.2 + - - +
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Residues in contact with ARG1713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703B GLN* 4.7 7.4 + - - +
1707B ASP* 4.9 2.4 + - - -
1709B GLU* 3.2 32.7 + - - +
1710B GLY* 3.8 25.0 - - - +
1711B VAL 3.3 0.2 - - - -
1712B LYS* 1.3 77.7 - - + +
1714B LYS* 1.3 66.8 + - - +
1716B ASP* 3.4 8.3 + - - +
1717B GLN* 3.0 36.2 + - + +
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Residues in contact with LYS1714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703B GLN* 2.9 49.0 + - + +
1704B GLN* 3.8 6.3 + - - -
1705B PRO* 4.0 5.8 - - + -
1710B GLY 3.1 17.7 + - - +
1711B VAL 3.6 4.3 - - - +
1713B ARG* 1.3 76.9 - - - +
1715B MET* 1.3 60.9 + - - +
1717B GLN* 3.5 9.5 + - - +
1718B GLY 3.4 1.9 + - - -
1719B ASN* 3.0 48.1 + - + +
1720B TYR* 3.5 30.3 - - + +
1725B GLU* 2.7 30.7 + - - -
1729B ASP* 2.9 15.8 + - - +
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Residues in contact with MET1715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641B GLN* 4.5 16.5 + - - +
1644B LEU* 3.6 13.7 - - + +
1645B LYS* 3.6 40.4 - - + -
1648B LEU* 3.5 29.2 - - + -
1711B VAL 2.9 15.6 + - - +
1712B LYS 3.7 3.6 - - - +
1714B LYS* 1.3 74.0 - - - +
1716B ASP* 1.3 58.1 + - - +
1717B GLN 3.0 2.0 - - - -
1718B GLY* 2.6 27.2 + - - -
1719B ASN 4.6 0.7 - - - +
1720B TYR* 3.6 18.2 - - + +
1726B PHE* 3.1 39.7 - - + -
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Residues in contact with ASP1716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645B LYS* 4.5 16.9 + - - +
1648B LEU* 6.0 0.5 - - - +
1712B LYS* 2.7 62.5 + - - +
1713B ARG* 3.4 7.7 + - - +
1715B MET* 1.3 73.9 - - - +
1717B GLN* 1.3 60.7 + - + +
1718B GLY* 3.3 1.0 + - - -
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Residues in contact with GLN1717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1703B GLN* 3.8 17.0 - - - +
1713B ARG* 3.0 25.6 + - + +
1714B LYS* 3.6 2.1 - - - +
1715B MET 3.0 0.6 - - - -
1716B ASP* 1.3 77.3 - - + +
1718B GLY* 1.3 61.4 + - - +
1719B ASN* 3.4 29.1 + - - +
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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