Contacts of the helix formed by residues 43 - 48 (chain F) in PDB entry 1S9C
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 ASP 43 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F GLY 4.6 0.3 - - - +
36F ALA* 3.3 14.3 - - + -
37F SER* 3.0 46.3 + - - +
40F ASP* 2.8 16.3 + - - +
42F LYS* 1.3 76.0 - - - +
44F LEU* 1.3 62.9 + - - +
45F LYS 2.9 7.5 + - - -
46F PHE* 2.9 29.5 + - - +
47F ILE* 3.3 15.8 + - + +
225F ARG* 4.4 10.3 + - - +
229F GLN* 4.3 12.2 + - - -
234F ASN* 4.2 4.9 + - - +
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Residues in contact with LEU 44 (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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199E ILE* 3.9 35.4 - - + +
200E ASP* 5.2 0.9 - - - +
201E PRO* 3.8 30.3 - - + -
38F ILE* 4.3 16.0 - - + +
40F ASP 3.9 1.4 + - - -
41F PRO* 3.0 19.9 + - + +
43F ASP* 1.3 78.4 - - - +
45F LYS* 1.3 55.8 + - - +
47F ILE* 3.7 4.9 - - - +
48F TYR* 2.9 53.0 + - + +
51F SER* 3.9 8.7 - - - +
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Residues in contact with LYS 45 (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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42F LYS 3.5 15.6 + - - +
44F LEU* 1.3 78.9 - - - +
46F PHE* 1.3 71.1 + - + +
51F SER* 4.0 12.7 + - - -
53F ASP* 3.4 42.6 + - + +
54F PHE* 3.2 10.6 - - - -
55F SER* 3.0 52.7 + - - +
233F ASP 4.9 0.8 + - - -
234F ASN* 2.4 40.7 + - + +
235F ASP* 4.0 8.1 + - - +
236F VAL* 4.1 5.7 - - - +
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Residues in contact with PHE 46 (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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27F ALA 5.0 0.5 - - - -
28F ILE* 3.9 13.3 - - - +
31F ALA* 3.6 29.9 - - + +
36F ALA* 4.6 7.2 - - + -
42F LYS 4.5 3.8 - - - -
43F ASP* 2.9 27.9 + - - +
45F LYS* 1.3 92.4 - - + +
47F ILE* 1.3 61.9 + - - +
48F TYR 3.8 0.2 - - - -
54F PHE* 4.0 6.4 - - - -
55F SER* 3.7 20.9 - - - +
57F LEU* 3.6 32.3 - - + +
225F ARG* 5.3 4.5 - - + -
228F LEU* 3.7 20.6 - - + -
234F ASN* 3.9 31.9 - - + -
236F VAL* 3.7 22.9 - - + -
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Residues in contact with ILE 47 (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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186E ALA* 3.8 27.4 - - + +
189E ARG* 3.7 8.5 + - - -
199E ILE* 4.0 8.0 - - + +
28F ILE* 3.3 35.6 - - + +
31F ALA* 5.1 0.7 - - + -
32F LEU* 4.1 13.0 - - + -
36F ALA* 3.9 14.6 - - + +
37F SER* 3.6 18.8 - - - +
38F ILE* 3.5 38.4 - - + +
43F ASP 3.4 15.9 - - - +
44F LEU* 3.3 3.5 + - - +
46F PHE* 1.3 84.9 - - - +
48F TYR* 1.3 57.6 + - - +
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Residues in contact with TYR 48 (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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189E ARG* 3.8 9.9 - - - -
196E PRO* 3.2 28.1 - - + +
199E ILE* 3.5 35.2 - - + -
200E ASP* 3.0 41.3 + - + -
44F LEU* 2.9 28.6 + - + +
47F ILE* 1.3 77.4 - - - +
49F GLU* 1.3 78.3 + - - +
50F GLY* 3.3 33.1 - - - -
51F SER* 3.0 31.8 + - - -
54F PHE* 3.0 15.9 - - - -
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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