Contacts of the helix formed by residues 1706 - 1712 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1573B TYR* 3.6 13.4 - - - +
1586B TYR* 5.0 1.1 - - + -
1588B VAL* 3.5 33.4 - - + -
1590B ARG* 4.3 2.2 - - - +
1591B ARG* 3.7 26.0 - - - +
1623B ASP* 3.5 22.0 - - + +
1705B LEU* 1.3 94.2 - - + +
1707B ALA* 1.3 64.5 + - - +
1708B ALA 4.3 0.4 - - - +
1709B THR* 3.0 23.4 + - - +
1710B LEU* 3.1 10.9 + - - +
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Residues in contact with ALA1707 (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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1812A LEU* 3.9 24.7 - - + +
1591B ARG* 5.5 0.4 - - - +
1705B LEU 3.5 2.1 + - - -
1706B PRO* 1.3 72.0 - - - +
1708B ALA* 1.3 52.9 + - - +
1710B LEU* 3.2 12.8 + - - +
1711B ALA* 2.8 35.9 + - - +
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Residues in contact with ALA1708 (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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1811A GLU 5.4 1.6 - - - +
1812A LEU* 3.6 34.6 - - + +
1590B ARG* 3.8 15.9 + - - +
1591B ARG* 4.7 11.8 - - - +
1706B PRO* 3.2 0.8 - - - +
1707B ALA* 1.3 79.2 - - - +
1709B THR* 1.3 61.1 + - - +
1711B ALA* 3.6 10.4 + - - +
1712B LEU* 3.7 17.2 + - - +
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Residues in contact with THR1709 (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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1590B ARG* 2.8 21.9 + - - +
1623B ASP* 2.7 25.4 + - - +
1625B THR* 3.4 25.4 - - + -
1659B TYR* 3.7 22.9 - - + +
1660B ASN* 4.5 0.9 - - - +
1705B LEU* 4.6 8.5 - - + -
1706B PRO* 3.0 17.0 + - - +
1708B ALA* 1.3 73.9 - - - +
1710B LEU* 1.3 68.7 + - + +
1712B LEU* 3.0 25.3 + - + +
1713B GLU* 4.1 5.9 + - - +
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Residues in contact with LEU1710 (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* 6.1 1.1 - - - +
1704B LYS* 6.1 0.4 - - - -
1705B LEU* 3.7 52.0 - - + +
1706B PRO 3.1 2.7 + - - +
1707B ALA* 3.5 13.5 - - - +
1709B THR* 1.3 81.3 - - + +
1711B ALA* 1.3 62.5 + - - +
1713B GLU* 3.1 36.2 + - - +
1714B GLU* 4.1 11.1 - - - +
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Residues in contact with ALA1711 (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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1812A LEU* 4.2 26.5 - - + +
1707B ALA 2.8 20.5 + - - +
1708B ALA* 3.8 9.4 - - - +
1709B THR 3.2 0.6 - - - -
1710B LEU* 1.3 75.3 - - - +
1712B LEU* 1.3 61.9 + - + +
1713B GLU 3.1 1.8 + - - -
1714B GLU* 3.2 31.0 + - - +
1739B THR* 5.8 0.6 + - - -
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Residues in contact with LEU1712 (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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1590B ARG* 5.6 1.6 - - - +
1625B THR* 4.1 21.1 - - + +
1660B ASN* 5.5 1.1 - - - +
1708B ALA 3.7 15.0 + - - +
1709B THR* 3.0 14.7 + - - +
1711B ALA* 1.3 76.2 - - - +
1713B GLU* 1.3 59.9 + - + +
1714B GLU 3.4 0.6 - - - +
1716B LEU* 3.6 9.7 - - - +
1737B GLY* 5.6 0.3 - - - -
1739B THR* 3.8 21.3 - - - +
1740B ALA* 3.9 21.3 - - + -
1742B GLN* 2.9 32.8 + - - +
1761B ILE* 4.4 23.6 - - + -
1763B TYR* 4.6 17.0 - - + +
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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