Contacts of the helix formed by residues 1561 - 1569 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546F ASP 3.5 11.4 - - - +
1547F LEU* 3.6 7.0 - - + +
1560F ASP* 1.3 95.8 + - - +
1562F PRO* 1.3 75.3 - - + +
1563F GLU* 3.4 6.2 + - + +
1564F LYS* 3.6 13.6 + - + -
1565F LEU* 3.4 18.9 + - - +
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Residues in contact with PRO1562 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1542F ILE 4.3 2.7 - - - +
1543F LEU* 4.2 33.9 - - + +
1545F ALA 3.2 19.3 - - - +
1546F ASP 3.4 15.7 - - - +
1548F VAL* 3.6 26.2 - - + -
1561F LYS* 1.3 87.9 - - + +
1563F GLU* 1.3 63.4 + - - +
1565F LEU* 3.2 5.8 + - + +
1566F LEU* 2.9 29.1 + - + +
1573F PHE* 5.3 4.7 - - + -
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Residues in contact with GLU1563 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561F LYS* 3.4 3.7 - - + -
1562F PRO* 1.3 79.7 - - + +
1564F LYS* 1.3 60.1 + - + +
1566F LEU* 3.3 17.5 - - + +
1567F SER* 2.9 33.8 + - - -
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Residues in contact with LYS1564 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1560F ASP* 3.1 38.2 + - - +
1561F LYS* 3.6 11.7 + - + +
1562F PRO 3.3 0.4 - - - -
1563F GLU* 1.3 79.2 - - + +
1565F LEU* 1.3 57.1 + - - +
1567F SER* 3.8 3.0 - - - -
1568F ARG* 2.9 35.5 + - - +
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Residues in contact with LEU1565 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1548F VAL* 3.9 23.6 - - + +
1550F VAL* 5.0 4.3 - - + -
1558F GLU 3.3 24.5 - - - +
1560F ASP* 3.6 36.6 - - + +
1561F LYS 3.4 8.7 + - - +
1562F PRO* 3.2 7.0 + - + +
1564F LYS* 1.3 77.4 - - - +
1566F LEU* 1.3 62.1 + - - +
1568F ARG* 3.3 35.0 - - - +
1569F LYS* 3.3 18.2 + - - -
1571F SER* 4.1 19.8 - - - +
1573F PHE* 4.8 12.1 - - + -
1574F ALA* 4.2 7.2 + - - +
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Residues in contact with LEU1566 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1543F LEU* 3.8 25.6 - - + -
1562F PRO* 2.9 24.6 + - + +
1563F GLU* 3.3 18.8 - - + +
1565F LEU* 1.3 79.0 - - - +
1567F SER* 1.3 68.4 + - - +
1569F LYS* 3.7 11.8 + - - +
1573F PHE* 5.3 6.0 - - + -
1574F ALA* 4.7 10.2 - - - +
1577F VAL* 5.1 14.1 - - + -
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Residues in contact with SER1567 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563F GLU 2.9 18.4 + - - -
1564F LYS* 4.3 2.9 - - - -
1566F LEU* 1.3 81.9 - - - +
1568F ARG* 1.3 63.1 + - - +
1569F LYS* 3.4 3.1 - - - +
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Residues in contact with ARG1568 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1558F GLU* 3.6 22.6 - - - +
1560F ASP* 5.0 5.5 + - - -
1564F LYS 2.9 19.3 + - - +
1565F LEU* 3.3 33.0 - - - +
1567F SER* 1.3 77.5 - - - +
1569F LYS* 1.3 61.4 + - - +
1570F ASP* 2.8 53.8 + - - +
1571F SER* 3.5 22.2 - - - +
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Residues in contact with LYS1569 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565F LEU 3.3 6.9 + - - -
1566F LEU 3.7 6.7 + - - +
1567F SER 3.4 3.9 - - - +
1568F ARG* 1.3 77.6 - - - +
1570F ASP* 1.3 72.9 + - - +
1571F SER 3.1 12.2 - - - +
1574F ALA* 3.4 24.0 - - + +
1575F SER* 5.5 1.0 + - - -
1578F 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