Contacts of the helix formed by residues 781 - 785 (chain D) in PDB entry 5ON2
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 ASP 781 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D HIS* 3.4 29.0 + - - -
23D THR* 6.1 1.4 - - + +
770D PHE* 3.6 21.8 - - + -
773D TRP* 4.0 3.0 + - - -
774D GLN* 6.0 4.1 - - - +
779D GLU 4.4 1.2 - - - +
780D GLY* 1.3 78.7 - - - +
782D ILE* 1.3 64.1 + - - +
783D ASP* 3.3 9.6 + - + +
784D ASN* 3.5 20.5 + - + +
785D ALA* 3.6 10.4 + - - +
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Residues in contact with ILE 782 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D MET* 4.2 5.6 - - + +
758D VAL* 3.7 23.6 - - + +
759D ARG* 4.3 9.6 - - + -
762D ASN* 3.4 45.8 + - + +
769D CYS* 3.6 19.1 - - + +
770D PHE* 3.7 31.1 - - + -
773D TRP* 3.6 33.5 - - + -
781D ASP* 1.3 70.8 - - - +
783D ASP* 1.3 70.7 + - - +
785D ALA* 3.1 20.1 + - + +
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Residues in contact with ASP 783 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D TRP* 2.7 34.8 + - - -
23D THR* 4.2 18.0 - - + +
24D PHE* 4.0 11.7 - - + -
64D ARG* 2.8 31.1 + - - +
67D ARG* 3.3 24.5 - - - +
68D MET* 4.1 8.8 + - - +
762D ASN* 4.2 6.8 + - - +
770D PHE* 4.1 9.2 - - - -
781D ASP* 3.3 5.6 - - + +
782D ILE* 1.3 87.0 - - - +
784D ASN* 1.3 60.7 + - - +
785D ALA 3.4 1.4 + - - -
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Residues in contact with ASN 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D THR* 4.7 8.7 - - - +
67D ARG* 3.0 41.9 + - - +
68D MET* 5.7 0.4 - - - -
781D ASP* 3.5 15.7 + - + +
782D ILE 3.3 0.2 - - - -
783D ASP* 1.3 78.1 - - - +
785D ALA* 1.3 59.7 + - - +
786D PRO* 4.3 1.7 - - - +
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Residues in contact with ALA 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ARG 5.0 0.2 - - - +
68D MET* 3.3 27.1 - - + +
759D ARG* 4.8 3.1 - - - -
773D TRP* 4.1 21.3 - - + -
779D GLU 5.2 3.6 - - - +
781D ASP 3.8 9.6 - - - +
782D ILE* 3.1 24.8 + - + +
783D ASP 3.4 0.2 - - - -
784D ASN* 1.3 78.7 - - - +
786D PRO* 1.3 77.7 - - + +
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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