Contacts of the helix formed by residues 773 - 777 (chain A) in PDB entry 1YO8
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 GLY 773 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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755A ASN* 2.8 34.9 + - - +
756A CYS* 3.2 16.9 - - - -
761A ASN* 4.3 1.1 - - - -
765A ALA 3.3 10.8 - - - -
766A ASP* 4.0 2.9 - - - -
772A VAL* 1.3 76.5 - - - +
774A ASP* 1.3 66.0 + - - -
775A ARG 3.5 1.6 - - - -
777A ASP* 3.1 15.4 + - - +
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Residues in contact with ASP 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A ASN* 4.6 1.6 - - - +
765A ALA* 2.5 45.1 + - + +
766A ASP* 3.5 1.2 - - - +
767A TYR* 3.0 36.1 + - - +
772A VAL 5.3 0.2 - - - +
773A GLY* 1.3 71.1 - - - -
775A ARG* 1.3 61.2 + - + +
776A CYS 3.1 5.5 + - - -
777A ASP* 3.3 22.3 + - - +
780A PRO* 4.7 16.4 - - + +
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Residues in contact with ARG 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A CYS* 4.4 2.3 - - - -
759A LEU* 3.4 44.3 - - + +
760A PHE* 3.2 30.9 + - - +
761A ASN* 4.7 16.3 - - + +
773A GLY 3.4 0.8 + - - -
774A ASP* 1.3 78.5 - - + +
776A CYS* 1.3 57.4 + - - +
777A ASP 5.4 0.2 - - - -
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Residues in contact with CYS 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A ASN 3.8 4.7 - - - -
756A CYS* 2.0 54.9 - - + -
757A GLN 5.1 0.2 - - - -
758A LEU 5.9 0.9 - - - +
759A LEU* 4.2 17.9 - - + +
772A VAL* 3.9 10.3 - - - +
773A GLY 3.6 2.9 - - - -
774A ASP 3.1 0.2 - - - -
775A ARG* 1.3 77.5 - - - +
777A ASP* 1.3 62.1 + - - +
778A ASN* 3.5 1.7 + - - +
787A GLN* 3.2 12.5 - - - +
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Residues in contact with ASP 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ASP* 3.7 0.2 - - - +
770A ASP* 3.3 1.9 - - - +
772A VAL* 3.1 5.6 - - - +
773A GLY 3.1 17.4 + - - +
774A ASP* 3.3 12.1 + - - +
775A ARG 5.4 0.3 - - - -
776A CYS* 1.3 75.4 - - - +
778A ASN* 1.3 60.7 + - - +
779A CYS 2.8 26.2 + - - +
780A PRO* 3.8 21.0 - - + +
787A GLN* 3.0 18.8 + - - -
1202A CA 2.3 31.6 - - - -
1203A CA 2.4 23.1 - - - -
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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