Contacts of the helix formed by residues 26 - 31 (chain S) 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 ILE 26 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S LYS* 1.3 75.9 - - + +
27S ALA* 1.3 66.2 + - + +
29S ALA* 3.2 3.1 + - - +
30S ILE* 2.9 37.4 + - + +
45S LEU* 3.5 33.4 - - + -
50S ILE* 3.6 26.7 - - + -
51S ASP 3.8 5.4 - - - +
52S LEU* 3.8 32.8 - - + +
54S LYS 3.7 20.5 + - - +
55S ARG 4.7 0.2 - - - -
56S ALA* 3.9 15.0 - - + -
59S LEU* 4.2 18.6 - - + -
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Residues in contact with ALA 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S ILE* 1.3 81.7 - - + +
28S PHE* 1.3 63.1 + - + +
30S ILE* 3.4 0.6 + - - -
31S THR* 2.4 37.7 + - - -
38S ARG* 4.9 0.4 - - - +
41S ALA* 3.5 15.9 - - + +
42S HIS* 4.2 26.7 - - + +
45S LEU* 3.5 22.7 - - + -
52S LEU* 4.4 8.3 - - + -
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Residues in contact with PHE 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15962 U 5.9 0.2 - - - -
16032 G 3.2 66.0 - + - +
24S ARG* 3.2 46.6 + - + +
25S LYS* 3.6 26.4 + - + +
26S ILE 3.2 0.2 - - - -
27S ALA* 1.3 82.7 - - + +
29S ALA* 1.3 62.0 + - - +
31S THR* 3.6 14.4 - - - -
32S ALA 4.0 2.6 + - - -
38S ARG* 3.8 36.8 - - + -
42S HIS* 4.3 15.9 - + - -
45T LEU* 5.0 2.9 - - + -
48T TYR* 4.2 7.2 - + - -
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Residues in contact with ALA 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S ILE* 3.6 19.9 - - + +
21S ASP 3.3 26.2 - - - +
24S ARG* 4.5 4.9 - - + +
25S LYS 3.0 21.6 + - - +
26S ILE 3.2 4.7 + - - +
28S PHE* 1.3 77.6 - - - +
30S ILE* 1.3 65.6 + - + +
31S THR 3.2 0.2 - - - -
32S ALA* 3.2 22.1 - - - +
56S ALA* 3.7 13.7 - - + -
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Residues in contact with ILE 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S VAL* 6.0 2.5 - - + -
20S ILE* 4.4 17.9 - - + -
26S ILE* 2.9 27.1 + - + +
27S ALA* 3.4 7.2 + - - +
29S ALA* 1.3 79.7 - - + +
31S THR* 1.3 62.5 + - - +
32S ALA 3.1 1.2 + - - -
33S ILE* 3.2 32.2 + - + +
36S VAL* 3.9 19.2 - - + +
41S ALA* 4.5 7.0 - - + -
44S VAL* 5.8 4.5 - - + -
45S LEU* 4.3 20.9 - - + -
56S ALA* 5.9 2.7 - - + -
59S LEU* 6.2 3.4 - - + -
67S VAL* 5.0 20.4 - - + -
71S MET* 5.5 4.5 - - + -
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Residues in contact with THR 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16032 G 5.9 3.1 - - - +
16312 U 4.2 3.5 + - - +
27S ALA 2.4 25.6 + - - -
28S PHE* 3.6 13.6 - - - -
29S ALA 3.2 0.2 - - - -
30S ILE* 1.3 77.2 - - - +
32S ALA* 1.3 57.4 + - - +
33S ILE 2.9 17.2 - - - +
36S VAL* 3.0 30.4 - - - +
37S GLY* 3.5 26.8 + - - -
38S ARG* 3.7 15.3 + - + +
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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