Contacts of the helix formed by residues 1706 - 1712 (chain A) in PDB entry 2D4Q
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 PRO1706 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1573A TYR* 3.5 13.6 - - + +
1586A TYR* 5.0 1.3 - - + -
1588A VAL* 3.5 32.1 - - + -
1590A ARG* 4.3 4.3 - - - +
1591A ARG* 3.9 25.8 - - - +
1623A ASP* 3.5 22.7 - - + +
1705A LEU* 1.3 91.4 - - + +
1707A ALA* 1.3 57.9 + - - +
1708A ALA 4.3 1.8 - - - +
1709A THR* 2.8 28.9 + - - +
1710A LEU* 3.1 9.5 + - - +
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Residues in contact with ALA1707 (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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1705A LEU 3.4 3.8 + - - -
1706A PRO* 1.3 71.2 - - - +
1708A ALA* 1.3 56.8 + - - +
1710A LEU* 3.1 12.1 + - + +
1711A ALA* 2.8 31.0 + - - +
1812B LEU* 3.7 25.4 - - + +
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Residues in contact with ALA1708 (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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1590A ARG* 3.6 26.1 + - - +
1591A ARG* 4.9 10.5 - - - +
1706A PRO* 3.1 0.8 - - - +
1707A ALA* 1.3 77.7 - - - +
1709A THR* 1.3 63.1 + - - +
1711A ALA* 3.5 7.4 + - - +
1712A LEU* 3.5 19.6 + - - +
1812B LEU* 3.6 39.2 - - + +
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Residues in contact with THR1709 (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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1590A ARG* 2.6 20.4 + - - +
1623A ASP* 2.6 25.9 + - - +
1625A THR* 3.3 21.5 + - + +
1659A TYR* 3.4 26.0 - - + +
1660A ASN* 4.4 1.3 - - - +
1705A LEU* 4.5 9.9 - - + -
1706A PRO* 2.8 17.1 + - - +
1708A ALA* 1.3 80.4 - - - +
1710A LEU* 1.3 60.7 + - + +
1712A LEU* 3.3 23.6 + - - +
1713A GLU* 3.9 7.2 + - + +
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Residues in contact with LEU1710 (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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1691A PRO* 3.9 19.1 - - + -
1703A GLN* 3.2 39.9 - - - +
1704A LYS* 5.8 0.4 - - - -
1705A LEU* 3.6 28.5 - - + +
1706A PRO 3.1 8.1 + - - +
1707A ALA* 3.1 11.4 + - - +
1709A THR* 1.3 77.6 - - + +
1711A ALA* 1.3 63.1 + - - +
1713A GLU* 3.0 22.8 + - + +
1714A GLU* 3.9 10.9 - - - +
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Residues in contact with ALA1711 (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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1707A ALA 2.8 20.8 + - - +
1708A ALA* 3.8 7.6 - - - +
1709A THR 3.3 0.4 - - - -
1710A LEU* 1.3 73.1 - - - +
1712A LEU* 1.3 62.3 + - + +
1713A GLU 3.0 1.5 + - - -
1714A GLU* 3.3 35.5 + - - +
1739A THR* 6.0 0.4 - - - -
1812B LEU* 4.3 22.4 - - + +
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Residues in contact with LEU1712 (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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1590A ARG* 5.0 3.1 - - - +
1625A THR* 3.7 29.8 - - + -
1660A ASN* 5.5 1.3 - - - +
1708A ALA 3.5 16.2 - - - +
1709A THR* 3.3 10.1 + - + +
1710A LEU 3.1 0.8 - - - -
1711A ALA* 1.3 79.5 - - + +
1713A GLU* 1.3 58.2 + - - +
1716A LEU* 3.2 15.9 - - - +
1739A THR* 3.9 21.5 - - - +
1740A ALA* 4.0 20.2 - - + -
1742A GLN* 2.9 33.3 + - - +
1761A ILE* 4.3 18.4 - - + -
1763A TYR* 4.8 11.0 - - + -
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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