Contacts of the strand formed by residues 1546 - 1550 (chain C) in PDB entry 3ZQK
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 VAL1546 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1540C LEU* 3.7 36.3 - - + -
1541C GLN 3.6 9.0 - - - +
1542C TYR* 4.2 9.6 - - + -
1545C MET* 1.3 84.3 - - - +
1547C THR* 1.3 65.4 + - - +
1548C VAL 4.3 0.5 + - - -
1580C LEU* 4.1 23.5 - - + +
1581C ALA* 3.8 23.8 - - - +
1584C TYR* 3.8 32.3 - - + -
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Residues in contact with THR1547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540C LEU* 3.3 6.9 - - - -
1541C GLN 2.8 34.5 + - - -
1545C MET* 3.2 21.3 + - + +
1546C VAL* 1.3 72.5 - - - +
1548C VAL* 1.3 68.4 + - - +
1549C GLU* 3.4 21.3 + - - +
1571C GLN* 2.9 42.8 + - - +
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Residues in contact with VAL1548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538C THR* 4.8 2.0 - - - +
1539C VAL 4.3 2.2 - - - +
1540C LEU* 3.6 12.1 - - + -
1546C VAL 4.2 1.0 + - - -
1547C THR* 1.3 76.8 - - - +
1549C GLU* 1.3 63.0 + - - +
1550C TYR 3.9 4.5 - - - +
1551C PRO* 3.8 38.7 - - + +
1564C ARG* 5.3 1.0 + - - -
1584C TYR* 3.4 40.6 - - + +
1588C HIS* 4.1 12.3 - - + +
1589C SER* 5.1 0.7 - - - +
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Residues in contact with GLU1549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539C VAL* 2.8 18.8 + - + +
1541C GLN* 2.9 43.7 + - + +
1547C THR* 3.6 23.9 - - - +
1548C VAL* 1.3 73.3 - - - +
1550C TYR* 1.3 61.4 + - - +
1551C PRO* 4.6 1.5 - - - +
1564C ARG* 3.4 44.1 + - - +
1568C ILE* 3.5 44.1 - - + +
1569C ARG 4.2 2.9 + - - +
1571C GLN* 4.1 3.6 + - - -
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Residues in contact with TYR1550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537C VAL* 3.9 12.1 - - + -
1538C THR* 2.6 28.8 + - - -
1539C VAL* 3.0 29.1 + - + +
1548C VAL* 3.5 3.1 - - - -
1549C GLU* 1.3 77.6 - - - +
1551C PRO* 1.3 71.1 - - + +
1554C GLU* 3.5 30.6 + - + +
1555C ALA* 2.6 32.7 + - - +
1556C GLN* 3.9 6.5 - - - -
1560C ASP* 3.8 16.7 - - - +
1561C ILE* 3.8 24.5 - - + -
1564C ARG* 3.5 39.0 - - + -
1565C LEU* 4.4 7.9 - - + -
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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