Contacts of the helix formed by residues 1561 - 1569 (chain E) in PDB entry 6C3P
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 LYS1561 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546E ASP 3.5 12.3 - - - +
1547E LEU* 3.6 6.5 - - + +
1560E ASP* 1.3 96.2 + - - +
1562E PRO* 1.3 76.1 - - + +
1563E GLU* 3.4 5.8 + - + +
1564E LYS* 3.6 13.9 + - + +
1565E LEU* 3.4 18.7 + - - +
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Residues in contact with PRO1562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542E ILE 4.3 2.5 - - - +
1543E LEU* 4.2 32.8 - - + +
1545E ALA 3.2 19.7 - - - +
1546E ASP 3.4 15.3 - - - +
1548E VAL* 3.6 26.0 - - + -
1560E ASP 3.8 0.2 - - - -
1561E LYS* 1.3 86.7 - - + +
1563E GLU* 1.3 64.2 + - - +
1565E LEU* 3.2 6.3 + - + +
1566E LEU* 2.9 28.7 + - + +
1573E PHE* 5.3 5.0 - - + -
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Residues in contact with GLU1563 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561E LYS* 3.4 3.9 - - + +
1562E PRO* 1.3 79.7 - - - +
1564E LYS* 1.3 59.5 + - + +
1566E LEU* 3.3 17.2 - - + +
1567E SER* 2.9 32.6 + - - -
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Residues in contact with LYS1564 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1560E ASP* 3.1 38.7 + - - +
1561E LYS* 3.6 11.1 + - + +
1562E PRO 3.3 0.8 - - - -
1563E GLU* 1.3 79.8 - - + +
1565E LEU* 1.3 58.1 + - - +
1567E SER* 4.3 2.9 - - - -
1568E ARG* 2.9 34.3 + - - +
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Residues in contact with LEU1565 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548E VAL* 3.9 23.6 - - + +
1550E VAL* 5.0 4.3 - - + -
1558E GLU 3.3 25.1 - - - +
1560E ASP* 3.6 37.2 - - + +
1561E LYS 3.4 8.0 + - - +
1562E PRO* 3.2 8.1 + - + +
1564E LYS* 1.3 77.0 - - - +
1566E LEU* 1.3 60.9 + - - +
1568E ARG* 3.3 33.6 - - - +
1569E LYS* 3.3 18.5 + - - -
1571E SER* 4.1 19.7 - - - +
1573E PHE* 4.8 13.0 - - + -
1574E ALA* 4.2 6.2 + - - +
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Residues in contact with LEU1566 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543E LEU* 3.8 25.4 - - + -
1562E PRO* 2.9 25.1 + - + +
1563E GLU* 3.3 19.1 - - + +
1565E LEU* 1.3 79.3 - - - +
1567E SER* 1.3 68.1 + - - +
1569E LYS* 3.7 12.3 + - - +
1573E PHE* 5.3 6.7 - - + -
1574E ALA* 4.7 10.2 - - - +
1577E VAL* 5.1 14.1 - - + -
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Residues in contact with SER1567 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563E GLU 2.9 18.1 + - - -
1564E LYS* 4.3 3.1 - - - -
1566E LEU* 1.3 83.1 - - - +
1568E ARG* 1.3 63.3 + - - +
1569E LYS* 4.5 2.8 - - - +
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Residues in contact with ARG1568 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1558E GLU* 3.6 22.8 - - - +
1560E ASP* 5.0 6.3 + - - +
1564E LYS 2.9 19.1 + - - +
1565E LEU* 3.3 33.2 - - - +
1567E SER* 1.3 78.3 - - - +
1569E LYS* 1.3 61.2 + - - +
1570E ASP* 2.8 56.0 + - - +
1571E SER* 3.5 22.4 - - - +
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Residues in contact with LYS1569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565E LEU 3.3 6.7 + - - -
1566E LEU 3.7 7.8 + - - +
1567E SER 3.4 3.3 - - - +
1568E ARG* 1.3 79.2 - - - +
1570E ASP* 1.3 72.7 + - - +
1571E SER 3.1 12.8 - - - +
1574E ALA* 3.4 24.1 - - + +
1575E SER* 5.5 0.9 + - - -
1578E ARG* 6.3 2.2 - - + -
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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