Contacts of the helix formed by residues 5032 - 5037 (chain o) in PDB entry 3A0B
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 THR5032 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5372c PRO* 4.4 0.9 - - - -
5031o LEU* 1.3 72.4 - - - +
5033o TYR* 1.3 66.3 + - - +
5034o ASP* 2.6 23.1 + - + +
5035o ASP* 2.5 57.3 + - - +
5036o ILE* 2.9 15.1 - - - +
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Residues in contact with TYR5033 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5348c GLU* 2.8 30.9 + - - -
5349c ILE 5.6 0.2 - - - -
5359c TRP* 4.2 17.7 + - - -
5360c ASP* 5.6 0.9 - - - -
5362c ARG* 3.5 43.4 - - - +
5370c ARG* 3.3 34.4 + - - -
5371c GLY 3.2 17.0 + - - +
5372c PRO* 3.2 19.7 + - - +
5373c ASN 4.4 0.4 - - - -
5374c GLY* 3.4 34.8 - - - -
5032o THR* 1.3 76.8 + - - +
5034o ASP* 1.3 57.2 + - - +
5036o ILE* 3.5 2.1 + - - +
5037o VAL* 2.8 44.1 + - + +
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Residues in contact with ASP5034 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5228c ASN* 6.0 2.1 - - - -
5362c ARG* 2.9 37.5 + - - -
5032o THR* 2.6 19.7 + - + +
5033o TYR* 1.3 72.4 - - - +
5035o ASP* 1.3 69.6 + - - +
5036o ILE 2.8 2.4 + - - -
5037o VAL* 2.8 31.6 + - + +
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Residues in contact with ASP5035 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5030o THR 4.2 2.8 - - - +
5031o LEU* 3.2 17.5 - - + +
5032o THR* 2.5 47.3 + - - +
5034o ASP* 1.3 71.7 - - - +
5036o ILE* 1.3 59.2 + - + +
5039o THR* 3.0 17.5 - - - +
5041o LEU* 5.5 0.7 - - - +
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Residues in contact with ILE5036 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5346c THR* 3.5 3.0 - - - +
5348c GLU* 5.2 0.2 - - - -
5372c PRO* 3.3 26.9 - - + +
5373c ASN* 5.0 4.5 - - - +
5031o LEU* 4.6 16.6 - - + +
5032o THR 2.9 36.6 - - - +
5033o TYR* 4.0 1.1 - - - +
5034o ASP 2.8 3.2 + - - -
5035o ASP* 1.3 79.5 - - + +
5037o VAL* 1.3 68.1 + - - +
5038o GLY 3.1 0.9 + - - -
5039o THR* 2.3 48.8 + - - +
5041o LEU* 3.1 35.0 - - + -
5042o ALA* 3.3 24.7 - - + +
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Residues in contact with VAL5037 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5348c GLU* 3.1 27.4 - - - +
5359c TRP* 4.4 7.6 - - + -
5360c ASP* 5.8 1.6 - - - +
5362c ARG* 5.8 3.1 - - - +
5033o TYR* 2.8 38.5 + - + +
5034o ASP* 2.8 30.8 + - + +
5036o ILE* 1.3 73.2 - - - +
5038o GLY* 1.3 59.4 + - - +
5039o THR* 2.8 11.3 + - - +
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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