Contacts of the helix formed by residues 38 - 45 (chain C) in PDB entry 5UQ9
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 LYS 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.4 25.2 - - + +
16C GLN* 5.8 0.3 + - - -
33C ASN* 3.2 27.6 - - - +
35C THR* 3.1 23.8 + - - +
37C SER* 1.3 85.5 + - - +
39C VAL* 1.3 58.7 + - - +
41C ASP* 3.5 11.2 + - - +
42C PHE* 3.0 21.7 + - - +
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Residues in contact with VAL 39 (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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11C LEU* 3.5 11.1 - - + +
31C ALA* 3.6 28.9 - - + +
32C PHE* 4.5 5.8 - - + +
33C ASN* 4.8 5.5 - - + +
35C THR 4.3 0.8 + - - -
36C VAL* 3.1 37.9 - - + +
38C LYS* 1.3 74.8 - - - +
40C ASP* 1.3 74.8 + - - +
42C PHE* 3.0 2.9 + - - +
43C LEU* 3.0 43.7 + - + +
54C GLY* 4.4 0.7 - - - -
55C ALA 3.8 16.8 - - - +
56C GLN* 3.7 10.8 - - - +
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Residues in contact with ASP 40 (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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36C VAL 2.7 24.0 - - - +
37C SER* 3.8 10.0 - - - +
39C VAL* 1.3 72.8 - - - +
41C ASP* 1.3 66.9 + - - +
43C LEU* 3.7 7.8 + - - +
44C ALA* 3.2 24.8 + - - +
56C GLN* 3.3 23.8 + - - +
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Residues in contact with ASP 41 (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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37C SER* 3.1 21.0 + - - +
38C LYS* 3.5 14.7 + - - +
39C VAL 3.1 0.6 - - - -
40C ASP* 1.3 83.2 - - - +
42C PHE* 1.3 62.8 + - - +
44C ALA* 3.3 4.9 + - - -
45C ASN* 2.8 40.0 + - - +
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Residues in contact with PHE 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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11C LEU* 3.6 14.8 - - + -
16C GLN* 3.5 55.0 - - + +
19C ILE* 3.8 29.2 - - + -
20C LEU* 5.0 5.6 - - + -
31C ALA* 4.2 9.4 - - + -
38C LYS 3.0 14.7 + - - +
39C VAL 3.0 6.7 + - - +
41C ASP* 1.3 77.3 - - - +
43C LEU* 1.3 74.5 + - + +
44C ALA 3.3 0.9 + - - -
46C GLU* 3.4 34.1 + - + -
47C ALA* 3.1 47.4 + - + +
52C VAL* 4.3 8.5 - - + -
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Residues in contact with LEU 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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31C ALA* 4.3 6.1 - - + -
39C VAL* 3.0 45.2 + - + +
40C ASP* 4.3 7.0 - - - +
42C PHE* 1.3 91.0 - - + +
44C ALA* 1.3 58.2 + - - +
47C ALA* 3.2 19.2 - - - +
48C LYS* 4.9 2.9 - - - +
52C VAL* 4.4 16.6 - - + +
53C VAL* 3.9 4.5 - - - +
54C GLY* 3.4 32.5 - - - +
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Residues in contact with ALA 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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40C ASP 3.2 19.7 + - - +
41C ASP* 4.5 0.9 - - - -
42C PHE 3.1 1.2 - - - -
43C LEU* 1.3 80.5 - - - +
45C ASN* 1.3 69.7 + - - +
48C LYS* 3.8 19.0 - - - +
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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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41C ASP* 2.8 33.3 + - - +
44C ALA* 1.3 87.0 - - - +
46C GLU* 1.3 93.3 + - - +
47C ALA 3.6 1.6 - - - -
48C LYS* 4.4 9.9 - - - +
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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