Contacts of the strand formed by residues 1553 - 1564 (chain C) in PDB entry 5ZCJ
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 PHE1553 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A PRO* 3.5 37.0 - - + -
106A HIS* 4.6 7.4 - + - -
1500C TYR* 4.2 11.2 - + - -
1545C THR* 3.8 15.3 - - + -
1546C ALA 3.5 8.5 - - - +
1547C LEU* 3.6 22.7 - - + -
1551C GLU 4.6 4.0 - - - -
1552C TYR* 1.3 90.9 - - - +
1554C SER* 1.3 68.0 + - - +
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Residues in contact with SER1554 (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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1545C THR* 4.5 5.4 - - - -
1546C ALA 3.0 27.2 + - - -
1552C TYR* 3.2 24.0 + - - -
1553C PHE* 1.3 83.3 - - - +
1555C ALA* 1.3 64.1 + - - +
1574C LYS* 2.6 40.6 + - - +
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Residues in contact with ALA1555 (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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1543C GLU* 4.6 11.9 - - + +
1544C VAL 3.3 11.2 - - - +
1545C THR* 4.5 3.1 - - - +
1554C SER* 1.3 78.7 + - - +
1556C GLY* 1.3 58.6 - - - +
1574C LYS* 3.6 17.1 - - - +
1592C GLN* 4.0 13.5 - - - +
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Residues in contact with GLY1556 (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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1543C GLU* 3.2 9.0 - - - +
1544C VAL* 2.8 32.1 + - - -
1554C SER 3.8 0.8 + - - -
1555C ALA* 1.3 76.4 - - - +
1557C VAL* 1.3 65.1 + - - -
1572C ILE* 3.7 17.7 - - - +
1573C GLU 3.3 13.5 - - - -
1574C LYS* 4.1 1.6 - - - -
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Residues in contact with VAL1557 (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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1541C ASP* 3.5 35.0 - - + +
1542C THR 3.3 3.4 - - - +
1543C GLU* 4.6 12.1 - - + +
1556C GLY* 1.3 79.1 - - - +
1558C VAL* 1.3 68.5 + - - +
1559C LYS* 3.4 23.1 + - - +
1572C ILE* 3.4 4.4 - - - +
1573C GLU* 2.8 35.8 + - + +
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Residues in contact with VAL1558 (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 ILE* 4.2 12.1 - - + -
1539C PRO 3.7 14.8 - - - +
1540C LEU* 4.1 2.9 - - - -
1541C ASP* 2.7 30.0 + - - +
1542C THR 2.9 12.5 + - - +
1544C VAL* 3.7 24.7 - - + -
1556C GLY 4.3 0.2 - - - -
1557C VAL* 1.3 73.0 - - - +
1559C LYS* 1.3 63.7 + - - +
1560C GLY 4.0 6.5 - - - +
1561C HIS* 3.4 35.2 - - + +
1570C TYR* 4.0 11.0 - - + -
1571C SER 3.5 4.9 - - - +
1572C ILE* 3.6 18.6 - - + -
1586C VAL* 5.1 0.7 - - + -
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Residues in contact with LYS1559 (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* 3.6 11.0 - - - +
1541C ASP* 3.8 21.3 - - - +
1557C VAL* 3.9 26.2 - - - +
1558C VAL* 1.3 75.0 - - - +
1560C GLY* 1.3 54.4 + - - +
1571C SER* 2.7 17.6 + - - +
1573C GLU* 3.3 35.7 + - + +
1578C ARG* 3.6 50.2 + - - +
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Residues in contact with GLY1560 (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* 3.5 12.6 - - - +
1558C VAL* 3.7 1.4 - - - +
1559C LYS* 1.3 79.6 - - - +
1561C HIS* 1.3 71.6 + - - -
1570C TYR* 3.5 1.9 - - - -
1571C SER* 2.8 36.1 + - - +
1580C TRP* 4.3 3.6 - - - -
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Residues in contact with HIS1561 (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 PRO* 3.9 19.9 - - + +
1538C ILE 2.9 29.7 + - - -
1539C PRO* 4.4 1.0 - - - +
1540C LEU* 3.5 26.8 + - + +
1558C VAL* 3.4 22.0 - - + -
1560C GLY* 1.3 73.8 + - - -
1562C ARG* 1.3 64.8 + - - +
1563C LYS* 5.5 5.3 - - - -
1568C LEU* 3.9 14.6 - - + -
1569C TYR 3.2 10.3 - - - +
1570C TYR* 3.2 22.6 - + - -
1580C TRP* 4.3 4.5 - - - -
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Residues in contact with ARG1562 (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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1561C HIS* 1.3 76.9 - - - +
1563C LYS* 1.3 66.2 + - - +
1564C GLU* 3.3 36.5 + - + +
1567C GLU 3.7 0.3 - - - +
1568C LEU* 3.6 1.8 - - - -
1569C TYR* 2.8 54.7 + - + +
1580C TRP* 3.4 67.9 - - + +
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Residues in contact with LYS1563 (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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1561C HIS* 5.5 4.0 - - - -
1562C ARG* 1.3 76.2 - - - +
1564C GLU* 1.3 64.5 + - - +
1565C SER 4.0 1.8 + - - -
1566C GLY* 4.9 6.1 - - - +
1567C GLU 3.3 8.5 - - - +
1568C LEU* 3.9 29.6 - - + +
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Residues in contact with GLU1564 (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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1562C ARG* 3.3 49.8 + - + +
1563C LYS* 1.3 74.6 - - - +
1565C SER* 1.3 73.1 + - - +
1567C GLU* 2.8 24.9 + - - +
1569C TYR* 3.7 17.2 + - + -
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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