Contacts of the helix formed by residues 1707 - 1717 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1660A LEU* 3.6 9.6 - - - +
1661A LEU 3.4 15.4 - - - +
1662A ARG* 3.8 3.5 - - - +
1663A TYR* 2.8 40.2 + - - +
1705A PRO* 3.3 1.9 - - - +
1706A LEU* 1.3 83.3 + - - +
1708A LEU* 1.3 59.2 + - - +
1709A GLU* 3.4 5.6 + - - +
1710A GLY* 2.8 44.0 + - - -
1711A VAL* 3.1 13.9 + - - +
1713A ARG* 5.2 2.1 + - - -
1733A ILE* 3.7 11.5 - - - +
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Residues in contact with LEU1708 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1648A LEU* 4.5 4.9 - - + +
1651A LEU* 4.3 25.1 - - + +
1652A LEU* 3.8 19.4 - - + +
1657A THR* 4.0 28.3 - - + -
1660A LEU* 2.9 36.1 + - + +
1661A LEU* 4.2 8.7 - - + -
1707A ASP* 1.3 68.7 - - - +
1709A GLU* 1.3 60.0 + - - +
1710A GLY 3.0 2.0 - - - -
1711A VAL* 3.2 4.9 + - - +
1712A LYS* 2.8 29.1 + - - +
1730A ILE* 3.8 30.7 - - + -
1733A ILE* 4.4 14.4 - - + -
1734A ILE* 6.3 0.9 - - + -
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Residues in contact with GLU1709 (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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1652A LEU* 5.1 4.7 - - + -
1661A LEU* 2.9 38.5 + - + +
1662A ARG* 3.2 47.4 + - - +
1707A ASP* 3.3 4.5 - - - +
1708A LEU* 1.3 76.9 - - - +
1710A GLY* 1.3 57.8 + - - +
1712A LYS* 3.3 10.2 - - - +
1713A ARG* 3.1 43.0 + - - +
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Residues in contact with GLY1710 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1703A GLN* 5.0 1.6 - - - +
1705A PRO* 3.6 16.0 - - - +
1707A ASP* 2.8 20.2 + - - -
1709A GLU* 1.3 77.0 - - - +
1711A VAL* 1.3 58.9 + - - +
1712A LYS 3.1 0.2 - - - -
1713A ARG* 3.3 18.8 + - - +
1714A LYS* 2.9 28.6 + - - +
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Residues in contact with VAL1711 (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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1648A LEU* 4.1 8.3 - - + -
1705A PRO* 3.9 9.2 - - + -
1707A ASP 3.1 3.3 + - - +
1708A LEU* 3.2 8.5 + - - +
1710A GLY* 1.3 76.5 - - - +
1712A LYS* 1.3 58.6 + - - +
1714A LYS* 3.2 2.3 + - - +
1715A MET* 2.8 29.6 + - - +
1720A TYR* 3.3 29.8 - - + +
1726A PHE* 3.9 15.9 - - + -
1729A ASP* 4.6 4.5 - - + -
1730A ILE* 3.7 27.8 - - + -
1733A ILE* 3.5 31.9 - - + -
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Residues in contact with LYS1712 (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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1645A LYS* 6.3 2.1 - - - +
1648A LEU* 3.4 14.8 - - + +
1652A LEU* 3.5 30.7 - - + -
1708A LEU 2.8 17.8 + - - +
1709A GLU* 3.3 12.1 - - - +
1711A VAL* 1.3 77.9 - - - +
1713A ARG* 1.3 60.9 + - + +
1715A MET* 3.4 1.7 + - - +
1716A ASP* 3.0 66.1 + - - +
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Residues in contact with ARG1713 (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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1703A GLN* 5.7 1.6 - - - +
1707A ASP* 5.2 1.8 + - - -
1709A GLU* 3.1 31.4 + - - +
1710A GLY* 3.8 15.2 - - - +
1711A VAL 3.3 0.2 - - - -
1712A LYS* 1.3 80.1 - - + +
1714A LYS* 1.3 66.4 + - - +
1715A MET 3.1 0.2 - - - -
1716A ASP* 3.5 5.7 + - - +
1717A GLN* 3.0 49.5 + - - +
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Residues in contact with LYS1714 (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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1703A GLN* 2.9 49.6 + - + +
1705A PRO* 3.9 12.8 - - + -
1710A GLY 2.9 17.6 + - - +
1711A VAL 3.6 4.5 - - - +
1713A ARG* 1.3 77.1 - - - +
1715A MET* 1.3 59.4 + - - +
1717A GLN* 3.8 3.8 + - - +
1718A GLY 3.8 1.7 + - - -
1719A ASN* 3.0 53.3 + - + +
1720A TYR* 3.3 28.3 - - + +
1725A GLU* 2.8 29.6 + - - +
1729A ASP* 2.6 25.2 + - - +
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Residues in contact with MET1715 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1641A GLN* 4.5 16.3 - - - +
1644A LEU* 3.8 14.8 - - + +
1645A LYS* 3.7 35.7 - - + -
1648A LEU* 3.6 20.9 - - + -
1711A VAL 2.8 13.5 + - - +
1712A LYS* 3.6 5.4 - - - +
1714A LYS* 1.3 74.2 - - - +
1716A ASP* 1.3 65.3 + - - +
1717A GLN 3.1 1.6 - - - -
1718A GLY* 2.8 23.4 + - - -
1719A ASN 4.7 0.4 - - - +
1720A TYR* 3.6 18.1 + - + +
1726A PHE* 3.0 42.2 - - + -
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Residues in contact with ASP1716 (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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1645A LYS* 4.7 17.7 + - - +
1712A LYS* 3.0 54.1 + - - +
1713A ARG* 3.5 5.7 + - - +
1715A MET* 1.3 82.0 - - - +
1717A GLN* 1.3 59.5 + - + +
1718A GLY 3.1 3.3 + - - -
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Residues in contact with GLN1717 (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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1703A GLN* 3.5 24.9 + - - +
1713A ARG* 3.0 38.2 + - - +
1714A LYS 4.1 1.3 - - - +
1715A MET 3.1 1.6 - - - -
1716A ASP* 1.3 78.5 - - + +
1718A GLY* 1.3 63.1 + - - +
1719A ASN* 3.4 14.6 + - - +
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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