Contacts of the helix formed by residues 38 - 46 (chain P) in PDB entry 5OA3
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 SER 38 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16122 G 3.4 34.1 + - - -
16132 G 3.6 9.4 - - - -
17P TYR* 5.0 2.1 + - - -
18P ARG* 4.7 3.5 + - - +
36P LEU 4.0 0.2 + - - -
37P TYR* 1.3 80.7 - - - +
39P ALA* 1.3 66.9 + - - +
40P ARG* 3.1 8.9 + - - -
41P GLN* 3.5 10.3 + - - +
42P ARG* 3.2 19.8 + - - +
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Residues in contact with ALA 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16132 G 2.8 37.7 + - + +
16142 A 3.3 38.2 + - - +
38P SER* 1.3 76.1 - - - +
40P ARG* 1.3 56.6 - - - +
42P ARG* 3.5 12.5 + - - +
43P ARG* 2.9 28.4 + - - +
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Residues in contact with ARG 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16142 A 2.8 20.5 - - - +
16152 U 2.4 28.2 + - - +
16162 U 2.7 24.7 + - - +
16172 G 4.3 3.2 - - - +
16202 A 2.9 46.6 + - - +
16212 U 3.2 29.6 + - - +
16242 U 4.4 7.7 + - - +
16252 U 4.0 7.5 + - - -
38P SER* 3.1 6.3 - - - -
39P ALA* 1.3 76.9 - - - +
41P GLN* 1.3 64.2 + - + +
43P ARG* 2.9 23.0 + - - +
44P ARG* 2.9 14.3 + - - +
115P TYR* 4.1 7.6 + - + +
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Residues in contact with GLN 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P TYR* 3.6 33.9 - - + -
38P SER* 3.5 10.5 + - - +
40P ARG* 1.3 77.8 - - + +
42P ARG* 1.3 56.2 + - - +
44P ARG* 3.4 1.7 + - - +
45P LEU* 2.9 37.4 + - + +
84P ILE* 3.1 33.7 - - + +
113P GLY* 2.3 34.0 + - - +
114P HIS* 4.4 0.2 - - - +
115P TYR* 3.2 37.9 + - - -
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Residues in contact with ARG 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16132 G 3.0 45.5 + - - -
16142 A 2.8 39.9 + - - -
34P MET* 4.2 33.1 + - + +
35P GLN* 5.0 21.8 + - - +
37P TYR* 4.6 4.4 + - - +
38P SER 3.2 15.1 + - - +
39P ALA* 3.6 7.7 - - - +
40P ARG 3.1 0.4 - - - -
41P GLN* 1.3 74.3 - - - +
43P ARG* 1.3 61.3 + - - +
45P LEU* 4.4 5.6 - - - +
46P ASN* 2.9 44.3 + - + +
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Residues in contact with ARG 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16142 A 5.6 2.0 - - + +
16152 U 3.4 45.9 + - + +
16162 U 2.4 76.1 + - - +
16172 G 3.4 10.2 + - - +
39P ALA 2.9 14.8 + - - +
40P ARG* 2.9 15.1 + - - +
42P ARG* 1.3 78.8 - - - +
44P ARG* 1.3 58.5 + - - +
46P ASN* 5.0 1.9 - - - +
47P ARG* 2.8 53.3 + - - +
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Residues in contact with ARG 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16172 G 4.6 4.3 - - - -
16192 A 4.4 18.7 + - - +
16202 A 3.4 34.2 + - - +
40P ARG 2.9 12.4 + - - +
41P GLN* 3.9 6.1 - - - +
43P ARG* 1.3 77.0 - - - +
45P LEU* 1.3 62.7 + - - +
47P ARG* 3.8 4.5 - - - +
48P GLY 3.4 18.3 + - - +
49P LEU* 3.4 25.0 - - - +
53P GLN* 2.9 31.3 + - - +
82P ASP* 2.6 35.6 + - - +
83P MET* 3.3 11.1 - - - +
84P ILE* 3.0 35.1 - - + +
115P TYR* 3.9 3.4 - - - +
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Residues in contact with LEU 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P TYR* 4.0 17.8 - - + +
33P LEU* 6.2 0.4 - - + -
34P MET* 3.7 37.2 - - + +
37P TYR* 3.9 28.9 - - + -
41P GLN* 2.9 25.2 + - + +
42P ARG 4.1 0.4 - - - +
44P ARG* 1.3 73.4 - - - +
46P ASN* 1.3 54.2 + - - +
47P ARG 3.0 4.3 - - - -
48P GLY* 2.5 31.2 + - - -
49P LEU* 3.6 36.2 + - + +
84P ILE* 3.7 21.1 - - + -
86P LEU* 5.3 4.9 - - + -
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Residues in contact with ASN 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P MET* 3.5 21.0 - - + +
42P ARG* 2.9 31.7 + - + +
43P ARG* 5.0 1.3 - - - +
45P LEU* 1.3 72.7 - - - +
47P ARG* 1.3 59.1 + - - +
48P GLY* 3.4 0.7 + - - -
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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