Contacts of the helix formed by residues 947 - 952 (chain A) in PDB entry 3AVS
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 ASN 947 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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946A GLU* 1.3 91.9 + - - +
948A LYS* 1.3 66.3 + - - +
949A ARG* 3.5 45.4 - - + +
950A ASP* 3.0 31.9 + - - +
951A ALA 3.7 1.2 + - - -
976A ALA* 3.6 11.7 - - - +
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Residues in contact with LYS 948 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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947A ASN* 1.3 72.2 - - - +
949A ARG* 1.3 63.7 + - - +
951A ALA* 3.2 13.5 + - - +
952A PHE* 3.2 41.9 - - + -
976A ALA 3.2 24.3 + - - +
977A LEU* 4.0 19.3 - - + +
978A LYS* 6.2 2.5 - - - -
1105A LYS 5.5 0.8 + - - -
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Residues in contact with ARG 949 (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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947A ASN* 3.5 31.7 - - + +
948A LYS* 1.3 80.4 - - - +
950A ASP* 1.3 78.3 + - - +
952A PHE* 3.2 18.2 + - - +
953A PHE* 3.3 10.7 + - - +
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Residues in contact with ASP 950 (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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944A TYR 4.7 2.3 - - - +
945A LEU* 3.7 19.0 - - + +
946A GLU* 3.1 16.0 + - - +
947A ASN* 3.0 42.0 + - - +
949A ARG* 1.3 99.4 + - - +
951A ALA* 1.3 61.1 + - - +
953A PHE* 3.3 21.8 + - - +
956A LEU* 3.7 13.5 - - - +
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Residues in contact with ALA 951 (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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945A LEU* 3.9 20.1 - - + +
947A ASN 3.7 2.3 + - - +
948A LYS* 3.2 13.8 + - - +
949A ARG 3.1 0.6 - - - -
950A ASP* 1.3 78.9 - - - +
952A PHE* 1.3 60.9 + - + +
953A PHE 3.4 1.1 - - - +
956A LEU* 3.4 25.2 - - - +
973A LEU* 4.8 1.6 - - + -
976A ALA* 5.4 0.9 - - + -
977A LEU* 3.6 25.8 - - + -
1107A PRO* 3.6 24.5 - - + +
1109A PHE* 4.6 1.0 - - - -
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Residues in contact with PHE 952 (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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948A LYS* 3.2 46.0 - - + -
949A ARG* 3.2 10.9 + - - +
951A ALA* 1.3 78.7 - - + +
953A PHE* 1.3 63.8 + - - +
954A PRO* 3.2 11.3 - - - +
977A LEU* 3.7 23.1 - - + -
1105A LYS 3.5 21.3 - - - -
1106A LEU 4.3 2.2 - - - -
1107A PRO* 3.6 29.2 - - + -
1108A ALA 4.9 1.8 - - - -
1111A ARG* 5.1 4.5 - - - -
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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