Contacts of the helix formed by residues 929 - 933 (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 929 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911A ASN* 3.1 32.8 + - - -
912A CYS* 3.1 22.2 - - - -
917A ASN* 4.0 4.3 - - - -
921A GLU 3.1 12.1 - - - -
928A ARG* 1.3 74.8 - - - +
930A ASP* 1.3 62.9 + - - -
931A ILE 3.0 7.8 + - - -
932A CYS* 3.3 9.5 + - - -
933A LYS* 4.0 0.9 + - - -
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Residues in contact with ASP 930 (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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921A GLU* 2.7 21.7 + - + +
922A ASP* 3.1 6.8 - - - -
923A LEU* 2.7 37.8 + - - +
924A ASP* 3.1 8.1 + - - +
929A GLY* 1.3 70.1 - - - -
931A ILE* 1.3 60.6 + - - +
932A CYS 3.3 0.2 - - - -
933A LYS* 3.4 26.7 - - + +
1184A CA 2.4 31.4 - - - -
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Residues in contact with ILE 931 (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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912A CYS* 3.9 6.5 - - - -
915A VAL* 3.9 26.4 - - + +
916A PHE 4.6 4.5 - - - +
917A ASN* 3.5 40.4 - - + +
921A GLU* 4.6 0.8 + - - +
929A GLY 3.0 0.8 + - - -
930A ASP* 1.3 78.4 - - - +
932A CYS* 1.3 59.6 + - - +
933A LYS 3.5 1.5 + - - -
938A ASN* 5.4 3.5 - - - +
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Residues in contact with CYS 932 (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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911A ASN 4.0 1.1 - - - -
912A CYS* 2.1 49.4 - - - -
915A VAL* 3.9 12.6 - - + -
928A ARG* 2.4 51.5 + - - -
929A GLY 3.3 4.7 + - - -
931A ILE* 1.3 79.3 - - - +
933A LYS* 1.3 52.4 + - - +
934A ASP 3.3 3.4 + - - -
935A ASP* 3.5 9.3 + - - +
936A PHE* 3.8 32.1 - - - +
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Residues in contact with LYS 933 (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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673A ASP* 2.4 40.6 + - - +
924A ASP* 4.5 18.9 + - - +
926A ASP* 5.5 5.8 + - - +
928A ARG* 4.5 1.8 - - - +
929A GLY 4.5 4.3 - - - -
930A ASP* 3.4 25.3 + - + +
931A ILE 3.5 2.8 + - - -
932A CYS* 1.3 75.7 - - - +
934A ASP* 1.3 78.1 + - - +
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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