Contacts of the helix formed by residues 1610 - 1616 (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 TYR1610 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1608B ASP* 3.1 25.2 + - - +
1609B PRO* 1.3 84.6 - - + +
1611B VAL* 1.3 55.7 + - - +
1612B PHE 2.9 6.6 + - - -
1613B ASP* 3.1 26.0 + - + +
1614B ARG* 2.9 39.8 + - + +
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Residues in contact with VAL1611 (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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1587B PHE* 4.8 4.7 - - + -
1608B ASP* 2.8 39.9 - - + +
1609B PRO 2.9 0.8 + - - +
1610B TYR* 1.3 77.2 - - - +
1612B PHE* 1.3 57.4 + - - +
1614B ARG* 3.6 24.0 - - - +
1615B GLU* 2.9 52.8 + - - +
1621B TYR* 3.8 21.5 - - + -
1622B VAL 6.1 1.8 - - - +
1623B PHE* 4.4 12.3 - - + -
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Residues in contact with PHE1612 (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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1583B SER* 3.1 34.3 - - - -
1584B SER* 3.7 2.9 - - - -
1585B PRO* 3.5 32.8 - - + -
1586B PRO* 3.7 17.3 - - + -
1587B PHE* 4.0 14.6 - - + -
1609B PRO 2.9 13.9 + - - +
1610B TYR 2.9 0.4 - - - -
1611B VAL* 1.3 76.9 - - - +
1613B ASP* 1.3 71.6 + - - +
1616B GLY* 2.4 48.0 + - - +
1617B LEU* 3.3 26.9 - - + -
1621B TYR* 3.9 4.9 - - - -
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Residues in contact with ASP1613 (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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1609B PRO 3.8 4.2 - - - +
1610B TYR* 3.1 38.9 + - + +
1612B PHE* 1.3 86.9 - - - +
1614B ARG* 1.3 64.3 + - + +
1616B GLY* 4.1 2.6 + - - -
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Residues in contact with ARG1614 (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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1608B ASP* 2.8 25.9 + - - -
1610B TYR* 2.9 23.5 + - + +
1611B VAL* 3.6 33.8 - - - +
1613B ASP* 1.3 80.9 - - + +
1615B GLU* 1.3 67.1 + - + +
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Residues in contact with GLU1615 (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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1611B VAL* 2.9 40.4 + - + +
1614B ARG* 1.3 83.7 - - + +
1616B GLY* 1.3 68.1 + - - +
1617B LEU 4.6 2.9 - - - +
1618B LYS* 5.0 6.5 - - + +
1621B TYR* 4.0 12.0 - - + +
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Residues in contact with GLY1616 (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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1612B PHE* 2.4 35.3 + - - -
1613B ASP 4.1 2.5 + - - -
1614B ARG 3.7 0.8 - - - -
1615B GLU* 1.3 77.6 - - - +
1617B LEU* 1.3 65.6 + - - -
1618B LYS* 3.1 1.6 + - - +
1621B TYR* 2.8 18.9 + - - -
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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