Contacts of the helix formed by residues 1646 - 1652 (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 PRO1646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1607A LEU* 4.7 3.1 - - + -
1614A TYR* 3.9 34.1 - - + +
1644A VAL 4.3 2.9 - - - +
1645A PHE* 1.3 90.5 - - + +
1647A GLY* 1.3 68.5 + - - +
1648A PHE* 3.3 32.1 - - + -
1649A ALA* 2.8 21.5 + - + +
1650A TYR* 3.7 2.8 - - - -
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Residues in contact with GLY1647 (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 PHE 3.5 3.2 + - - -
1646A PRO* 1.3 69.7 - - - +
1648A PHE* 1.3 64.2 + - - +
1650A TYR* 3.1 25.3 + - - +
1651A ASP* 3.7 14.7 + - - +
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Residues in contact with PHE1648 (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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1614A TYR* 3.2 48.2 - + - -
1615A ALA* 3.9 14.4 - - + -
1646A PRO* 3.4 27.1 - - + -
1647A GLY* 1.3 73.3 - - - +
1649A ALA* 1.3 68.7 + - - +
1651A ASP* 3.3 11.3 + - - +
1652A ASN* 2.8 43.7 + - - +
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Residues in contact with ALA1649 (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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1614A TYR* 3.7 43.1 - - + -
1618A TYR* 2.8 33.9 + - - +
1645A PHE* 4.3 10.3 - - + -
1646A PRO* 2.8 31.5 + - + +
1648A PHE* 1.3 77.1 - - + +
1650A TYR* 1.3 57.9 + - - +
1653A VAL* 3.4 2.9 + - - +
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Residues in contact with TYR1650 (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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701A OXN 3.9 26.9 - - - -
1641A TRP 2.8 29.2 + - - -
1642A PHE* 3.3 32.1 - + + -
1645A PHE* 3.3 48.8 + + + +
1646A PRO 3.7 3.1 - - - -
1647A GLY* 3.1 17.3 + - - +
1649A ALA* 1.3 75.7 - - - +
1651A ASP* 1.3 64.5 + - - +
1652A ASN 3.0 1.6 - - - -
1653A VAL* 2.9 17.0 + - + +
1684A ARG* 2.8 28.1 + - - +
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Residues in contact with ASP1651 (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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1647A GLY 3.7 14.5 - - - +
1648A PHE* 3.8 11.4 - - - +
1650A TYR* 1.3 79.8 - - - +
1652A ASN* 1.3 64.7 + - - +
1653A VAL 3.2 4.0 + - - +
1654A SER* 5.2 1.0 - - - -
1684A ARG* 3.8 16.4 + - - +
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Residues in contact with ASN1652 (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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1614A TYR 2.7 28.9 + - - +
1615A ALA 3.6 14.8 + - - +
1616A LYS 3.8 15.9 - - - +
1617A PRO* 3.2 17.5 - - + +
1618A TYR* 2.9 36.3 + - + -
1648A PHE* 2.8 32.6 + - - +
1649A ALA 4.0 0.2 - - - +
1650A TYR 3.0 0.4 - - - -
1651A ASP* 1.3 78.3 - - - +
1653A VAL* 1.3 58.7 + - - +
1654A SER* 2.9 6.6 + - - -
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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