Contacts of the helix formed by residues 79 - 83 (chain O) in PDB entry 3KYM
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 GLN 79 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO* 3.1 32.8 - - + +
78A LEU 4.5 1.3 - - - +
79A GLN* 3.4 32.3 - - + +
80A SER* 3.1 30.2 + - - +
83A PHE* 4.9 0.2 - - - -
15O PRO* 6.1 0.7 - - - -
61O ARG* 3.5 25.4 + - - +
77O SER* 3.0 24.3 + - - +
78O LEU* 1.3 76.6 - - - +
80O SER* 1.3 56.9 + - - +
81O GLU 3.2 0.4 - - - -
82O ASP* 2.7 45.6 + - - +
83O PHE* 3.9 9.5 - - - -
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Residues in contact with SER 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLY* 4.1 7.7 - - - -
77A SER* 3.0 24.9 + - - -
79A GLN* 2.6 25.5 + - - -
15O PRO* 6.0 1.2 - - - +
79O GLN* 1.3 73.6 - - - +
81O GLU* 1.3 63.8 + - - +
82O ASP 3.4 0.3 + - - -
83O PHE* 3.5 29.6 + - - +
106O ILE* 5.7 0.3 - - - +
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Residues in contact with GLU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.9 28.0 - - - +
77A SER* 4.5 3.8 - - - +
79A GLN* 2.8 46.3 - - + +
81A GLU* 6.0 0.4 - - - +
37O GLN* 3.7 2.6 + - - -
39O LYS* 3.5 51.0 + - - +
61O ARG* 5.4 2.9 - - - +
80O SER* 1.3 72.8 - - - +
82O ASP* 1.3 64.9 + - - +
83O PHE 3.1 11.3 + - - +
84O ALA* 4.3 0.2 - - - +
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Residues in contact with ASP 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O GLN* 4.0 5.7 + - - +
45O ARG* 5.3 1.4 + - - -
61O ARG* 3.1 38.7 + - - -
62O PHE* 3.5 21.9 - - + -
75O ILE* 4.0 4.9 - - + +
78O LEU* 3.7 17.3 - - + -
79O GLN* 2.7 36.4 + - - +
81O GLU* 1.3 79.2 - - - +
83O PHE* 1.3 56.6 + - - -
84O ALA 3.1 6.3 + - - -
86O TYR* 2.6 34.0 + - - +
104O VAL* 4.1 5.5 - - - +
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Residues in contact with PHE 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O LEU* 3.9 13.0 - - + -
14O SER 4.4 0.2 - - - -
15O PRO* 3.9 31.4 - - + -
40O PRO* 4.0 12.8 - - - +
78O LEU* 3.5 23.3 - - + -
79O GLN 3.9 12.8 - - - -
80O SER* 3.5 29.2 - - - +
81O GLU 3.1 5.4 - - - +
82O ASP* 1.3 71.8 - - - +
84O ALA* 1.3 61.1 + - - +
104O VAL* 3.5 30.1 - - + +
105O GLU* 3.9 2.2 - - - -
106O ILE* 3.3 54.7 - - + -
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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