Contacts of the helix formed by residues 1644 - 1650 (chain B) in PDB entry 1CJY
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 ASN1644 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1582B ASP* 5.0 6.0 + - - +
1617B LEU* 5.4 0.2 - - - +
1619B GLU* 3.6 7.8 - - - +
1643B ALA* 1.3 75.2 - - - +
1645B ILE* 1.3 73.8 + - - +
1646B ASN 3.4 1.4 + - - -
1647B PHE* 3.1 38.2 + - - +
1648B ARG* 3.6 32.2 - - - +
1666B ALA 3.3 15.8 + - - +
1668B PHE* 3.3 41.1 + - - +
1670B ILE* 4.6 5.0 - - + +
1696B LEU* 3.5 16.3 - - + +
1700B ASN* 4.2 0.3 + - - -
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Residues in contact with ILE1645 (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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1617B LEU* 3.4 32.3 - - + +
1618B LYS* 3.6 5.2 - - - -
1619B GLU* 3.5 36.6 - - + +
1643B ALA* 4.1 18.4 - - + -
1644B ASN* 1.3 79.8 - - - +
1646B ASN* 1.3 87.5 + - - +
1648B ARG* 3.0 34.0 + - - +
1649B LYS* 5.3 1.9 - - - +
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Residues in contact with ASN1646 (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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1619B GLU* 3.1 19.2 + - - +
1645B ILE* 1.3 90.7 - - - +
1647B PHE* 1.3 61.7 + - - +
1649B LYS* 2.8 18.3 + - - +
1650B TYR* 3.2 38.7 + - - -
1699B PHE* 3.4 12.0 - - + -
1703B ASN* 3.5 17.8 + - - +
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Residues in contact with PHE1647 (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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1644B ASN* 3.1 28.1 + - - +
1645B ILE 3.1 0.8 + - - -
1646B ASN* 1.3 77.1 - - - +
1648B ARG* 1.3 59.9 + - - +
1649B LYS 3.1 1.2 + - - -
1650B TYR 3.2 19.1 + - - +
1652B ALA 6.0 0.9 - - - -
1665B ILE* 5.2 4.9 - - + -
1666B ALA* 3.5 29.6 - - + +
1668B PHE* 4.1 15.9 - + - -
1692B ARG* 4.3 3.1 - - - -
1695B ASP* 3.6 37.7 - - + -
1696B LEU* 3.6 31.0 - - + -
1699B PHE* 3.3 40.4 - + + -
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Residues in contact with ARG1648 (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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1582B ASP* 4.9 4.8 + - - +
1644B ASN* 3.6 32.2 - - - +
1645B ILE* 3.0 24.7 + - - +
1646B ASN 3.0 0.4 + - - -
1647B PHE* 1.3 76.1 - - - +
1649B LYS* 1.3 71.3 + - + +
1657B ARG* 5.1 2.6 - - - +
1663B LYS* 4.7 16.6 - - - +
1666B ALA* 3.6 26.4 + - - +
1667B ASP* 4.2 10.5 + - - +
1668B PHE 3.4 31.7 + - - +
1669B ASP* 3.9 14.5 + - - -
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Residues in contact with LYS1649 (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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1645B ILE 5.3 2.0 - - - +
1646B ASN* 2.8 7.0 + - - +
1648B ARG* 1.3 91.6 - - + +
1650B TYR* 1.3 83.9 + - + +
1656B PRO* 3.3 4.5 - - - +
1657B ARG* 3.0 28.5 + - - +
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Residues in contact with TYR1650 (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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1646B ASN* 3.2 34.3 + - - -
1647B PHE* 3.2 20.4 + - - -
1649B LYS* 1.3 109.4 - - + +
1652B ALA 2.4 45.9 + - - +
1654B GLY* 3.8 13.5 - - - -
1655B VAL 3.1 37.1 - - - +
1656B PRO* 3.6 25.3 - - + +
1657B ARG* 4.3 9.8 + - - +
1699B PHE* 3.6 22.2 - + + -
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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