Contacts of the helix formed by residues 950 - 954 (chain I) in PDB entry 3AOI
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 950 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885H ILE* 3.5 7.9 - - - -
889H HIS* 3.8 10.3 - - - -
969H GLN 5.1 2.0 - - - -
971H LYS* 4.6 6.3 - - - -
988H VAL* 4.5 2.5 - - - -
949I ILE* 1.3 80.5 - - - +
951I ILE* 1.3 58.0 + - - -
952I ASP* 3.1 3.8 - - - -
953I ASP* 2.6 44.6 + - - +
954I ALA* 3.7 2.3 + - - +
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Residues in contact with ILE 951 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H HIS* 5.6 1.1 - - + -
882H LEU* 4.0 42.0 - - + +
885H ILE* 3.3 8.1 - - + +
886H LEU* 3.8 28.7 - - + -
889H HIS* 3.2 24.5 + - + +
911H GLU* 3.1 33.4 - - + +
915H LYS* 4.6 2.5 - - - +
950I GLY* 1.3 70.5 - - - +
952I ASP* 1.3 81.7 + - - +
953I ASP 3.4 0.3 + - - -
954I ALA* 3.5 11.1 + - - +
1061I PHE 5.1 0.2 - - - +
1062I ARG* 3.2 26.7 + - + +
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Residues in contact with ASP 952 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915H LYS* 2.9 28.6 + - - -
969H GLN* 3.5 45.2 - - - +
950I GLY 2.9 1.0 + - - -
951I ILE* 1.3 87.3 - - - +
953I ASP* 1.3 66.3 + - - +
954I ALA 3.1 4.3 + - - +
955I VAL* 3.4 18.9 - - - +
1062I ARG* 3.6 21.1 + - - +
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Residues in contact with ASP 953 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952H LEU* 4.6 5.4 - - - +
969H GLN* 4.8 2.2 + - - +
971H LYS* 3.0 33.7 + - - -
948I THR 3.1 10.2 - - - +
949I ILE* 4.8 2.7 - - + -
950I GLY* 2.6 39.2 + - - +
952I ASP* 1.3 73.6 - - - +
954I ALA* 1.3 53.9 + - - +
955I VAL* 3.0 8.5 + - - +
1011I PHE* 4.0 0.9 - - - -
1018I ASN* 2.8 32.1 + - - +
1019I PRO* 3.2 30.0 - - + +
1020I LEU* 4.8 6.5 - - + +
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Residues in contact with ALA 954 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882H LEU* 5.1 12.8 - - + -
950I GLY 3.7 2.1 + - - +
951I ILE 3.5 12.8 + - - +
952I ASP 3.1 2.8 - - - +
953I ASP* 1.3 74.9 - - - +
955I VAL* 1.3 60.3 + - - +
956I ILE* 3.6 1.7 - - - +
1020I LEU* 3.6 29.1 - - + +
1038I LEU* 4.3 10.1 - - + -
1039I CYS* 3.9 10.1 - - - -
1062I ARG* 3.2 32.7 + - + +
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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