Contacts of the helix formed by residues 41 - 45 (chain C) in PDB entry 3JSX
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 LEU 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C VAL* 4.0 15.5 - - + -
9C LEU 3.2 17.9 + - - +
10C ALA* 4.5 1.8 - - + -
39C SER* 3.0 24.6 + - - +
40C ASP* 1.3 68.5 - - - +
42C TYR* 1.3 63.9 + - - +
44C MET* 3.2 22.7 + - + -
45C ASN 3.1 16.3 + - - -
46C PHE* 3.1 20.6 + - + +
111C ILE* 4.0 40.3 - - + +
112C LEU* 4.0 19.1 - - + -
115C TRP* 3.7 26.9 - - + +
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Residues in contact with TYR 42 (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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9C LEU 4.7 0.8 + - - -
10C ALA 4.4 3.8 - - - -
11C HIS* 3.5 37.7 - - - +
12C SER* 3.4 34.8 - - - +
40C ASP* 3.1 1.8 + - - +
41C LEU* 1.3 77.2 - - - +
43C ALA* 1.3 58.9 + - - +
45C ASN* 3.0 21.0 + - - +
109C PRO* 6.1 2.5 - - + -
111C ILE* 4.3 25.7 - - + +
49D ILE* 3.5 21.2 - - + +
50D ILE* 2.5 47.8 + - - +
51D SER* 4.7 6.3 - - - -
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Residues in contact with ALA 43 (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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53B LYS 6.2 0.2 - - - +
56B THR* 5.5 4.9 - - + -
81B SER* 3.3 21.5 + - - +
82B PRO* 3.3 22.5 - - + +
83B ASP* 3.3 10.3 - - - +
40C ASP* 2.7 37.9 + - + +
42C TYR* 1.3 73.0 - - - +
44C MET* 1.3 56.5 + - - -
45C ASN 3.2 1.0 + - - -
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Residues in contact with MET 44 (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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82B PRO* 4.0 22.9 - - + -
83B ASP* 3.6 13.3 - - - +
39C SER* 3.7 33.4 - - - -
40C ASP 2.8 19.7 + - - +
41C LEU* 3.8 11.7 - - + +
42C TYR 3.2 0.4 - - - -
43C ALA* 1.3 76.3 - - - +
45C ASN* 1.3 70.2 + - - +
46C PHE* 3.2 35.0 + - + +
87C GLU* 4.1 19.7 - - + +
90C LYS* 4.7 4.3 - - - -
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Residues in contact with ASN 45 (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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44B MET* 3.2 16.8 + - - +
45B ASN* 2.8 34.1 + - - +
46B PHE* 4.0 7.9 - - - +
47B ASN* 4.0 8.2 - - + +
83B ASP* 4.2 18.5 + - + +
41C LEU 3.1 1.5 + - - -
42C TYR* 3.0 18.1 + - - +
43C ALA 3.2 0.6 - - - -
44C MET* 1.3 80.1 - - - +
46C PHE* 1.3 67.0 + - - +
47C ASN* 3.4 2.4 + - - +
111C ILE* 5.4 1.6 - - - -
49D ILE* 6.0 1.4 - - - +
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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