Contacts of the helix formed by residues 1662 - 1672 (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 ASN1662 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1624B LEU 3.8 9.5 + - - -
1626B HIS* 4.2 7.3 - - - +
1627B THR* 3.1 36.8 + - - +
1660B ASN 4.1 0.8 + - - +
1661B CYS* 1.3 78.7 - - - +
1663B SER* 1.3 60.0 + - - +
1664B TRP* 3.1 6.5 + - - -
1665B VAL* 2.9 27.0 + - - +
1666B ARG* 3.0 27.4 + - - +
1758B LEU* 3.7 10.5 - - - +
1759B ASN 3.3 18.5 + - - +
1760B ASP* 3.2 15.4 - - - +
1761B ILE* 5.6 2.2 - - - +
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Residues in contact with SER1663 (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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1662B ASN* 1.3 67.8 - - - +
1664B TRP* 1.3 64.3 + - - -
1666B ARG* 3.3 3.8 + - - +
1667B GLU* 3.1 21.7 + - - +
1724B LYS* 5.3 4.1 + - - -
1758B LEU* 3.6 22.8 - - - +
1760B ASP* 2.7 37.0 + - - -
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Residues in contact with TRP1664 (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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702B OXN 4.4 7.0 - - + -
1627B THR* 3.5 35.0 - - + +
1628B GLY* 3.7 15.7 - - - -
1629B PRO* 3.5 44.5 - - + +
1632B ARG* 3.6 24.5 - - + -
1662B ASN* 3.1 7.9 + - - +
1663B SER* 1.3 77.9 - - - +
1665B VAL* 1.3 78.7 + - + +
1667B GLU* 3.1 11.3 + - + +
1668B TYR* 2.8 64.8 + + + +
1760B ASP* 4.5 0.8 + - - -
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Residues in contact with VAL1665 (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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702B OXN 4.5 11.2 - - + -
1624B LEU* 3.7 32.1 - - + -
1627B THR* 3.9 23.1 - - + -
1661B CYS* 3.8 13.0 - - - -
1662B ASN* 2.9 25.4 + - - +
1664B TRP* 1.3 97.2 - - + +
1666B ARG* 1.3 64.5 + - - +
1668B TYR* 3.1 4.0 + - + +
1669B THR* 3.0 35.3 + - + +
1751B VAL* 5.4 0.4 - - + -
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Residues in contact with ARG1666 (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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601B POP 3.0 48.4 + - - -
1661B CYS* 4.6 0.2 - - - -
1662B ASN 3.0 13.6 + - - +
1663B SER* 3.5 10.1 - - - +
1664B TRP 3.2 0.2 - - - -
1665B VAL* 1.3 78.0 - - - +
1667B GLU* 1.3 65.7 + - - +
1669B THR* 2.6 25.8 + - - +
1670B LYS* 3.1 27.8 + - + +
1749B THR* 3.6 24.4 - - - +
1750B LYS* 3.0 26.3 + - - +
1751B VAL* 4.0 23.3 - - + -
1758B LEU* 3.9 21.5 - - + -
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Residues in contact with GLU1667 (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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1663B SER 3.1 13.1 + - - +
1664B TRP* 3.5 13.2 - - + +
1666B ARG* 1.3 81.0 + - - +
1668B TYR* 1.3 63.6 + - - +
1670B LYS* 3.0 28.6 + - - +
1671B TYR* 3.0 32.2 + - + +
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Residues in contact with TYR1668 (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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602B POP 4.4 3.4 - - - -
702B OXN 3.6 37.4 - - + +
1632B ARG* 4.1 13.5 - - + -
1633B PHE* 2.6 33.4 + - - +
1638B LEU* 3.1 26.7 - - + +
1664B TRP* 2.8 45.3 + + + +
1665B VAL* 3.1 10.3 + - + +
1667B GLU* 1.3 79.2 - - - +
1669B THR* 1.3 63.8 + - + +
1671B TYR* 3.4 6.1 + + - +
1672B HIS* 3.0 70.3 + + + +
1676B LEU* 4.9 2.2 - - + -
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Residues in contact with THR1669 (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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702B OXN 5.2 6.3 - - + -
1665B VAL* 3.0 28.8 + - + +
1666B ARG* 2.6 22.5 + - - -
1668B TYR* 1.3 78.0 - - + +
1670B LYS* 1.3 61.3 + - - +
1672B HIS 3.6 1.4 - - - -
1673B GLU* 2.9 27.5 + - - +
1676B LEU* 3.7 26.6 - - + +
1751B VAL* 3.5 22.6 + - + +
1752B LEU* 4.2 26.9 - - + +
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Residues in contact with LYS1670 (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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601B POP 3.2 51.0 + - - -
1666B ARG* 3.1 38.0 + - + +
1667B GLU* 3.0 28.3 + - - +
1669B THR* 1.3 84.0 + - - +
1671B TYR* 1.3 63.2 + - - +
1673B GLU* 3.0 23.3 - - - +
1750B LYS 6.0 0.9 - - - +
1751B VAL 5.4 4.3 - - - +
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Residues in contact with TYR1671 (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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602B POP 2.6 35.4 + - - -
1635B THR* 4.7 0.2 - - - -
1667B GLU* 3.0 25.7 + - + +
1668B TYR* 3.8 5.6 - + - +
1670B LYS* 1.3 78.1 - - - +
1672B HIS* 1.3 88.1 + + - +
1673B GLU 3.3 1.3 + - - -
1674B ARG* 5.1 2.1 + - - +
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Residues in contact with HIS1672 (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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602B POP 3.3 13.5 + - - -
1633B PHE 4.4 0.2 + - - -
1635B THR* 3.4 40.9 - - + +
1638B LEU* 3.7 23.3 - - + +
1668B TYR* 3.0 64.3 + + - +
1669B THR 3.6 2.7 - - - -
1671B TYR* 1.3 96.8 + + - +
1673B GLU* 1.3 63.8 + - - +
1674B ARG* 3.3 2.7 - - - -
1675B LEU* 3.2 10.6 + - + +
1676B LEU* 3.1 28.1 + - + +
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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