Contacts of the helix formed by residues 80 - 85 (chain H) in PDB entry 4KYI
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 LEU 80 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLU* 4.8 5.8 - - - +
30H SER* 3.8 25.3 - - - +
52H SER* 4.5 14.8 - - - +
53H THR 5.5 2.0 - - - +
78H ALA* 3.5 3.0 - - + +
79H GLY* 1.3 83.3 - - - +
81H GLU* 1.3 65.7 + - - +
82H ARG* 3.2 5.4 - - + +
83H TYR* 3.3 41.4 + - + +
84H HIS* 3.8 7.1 + - - +
111H ARG* 5.7 0.3 + - - -
115H TRP* 5.8 1.2 - - - -
301H GNP 4.9 0.7 - - - +
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Residues in contact with GLU 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLU* 5.4 1.9 + - - +
79H GLY 3.8 0.8 + - - -
80H LEU* 1.3 74.4 - - - +
82H ARG* 1.3 63.1 + - - +
84H HIS* 3.1 34.8 + - - +
85H SER 4.7 0.2 + - - -
111H ARG* 4.2 22.5 + - - +
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Residues in contact with ARG 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431G ALA 4.0 1.4 + - - -
432G LEU 5.6 0.4 + - - -
434G ASP 2.5 32.3 + - - -
435G GLU* 3.7 29.0 + - + +
436G LYS 5.9 0.2 - - - -
437G SER 4.3 6.1 + - - +
438G GLU* 4.9 0.8 - - - +
439G LYS* 3.1 50.8 + - - +
442G PHE* 3.4 54.2 - - + +
80H LEU* 3.2 3.3 - - + +
81H GLU* 1.3 79.6 - - - +
83H TYR* 1.3 73.0 + - + +
84H HIS 3.4 3.3 + - - -
85H SER* 3.6 14.7 + - - -
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Residues in contact with TYR 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432G LEU* 3.0 24.6 + - + -
433G ILE* 5.2 0.2 - - - -
442G PHE* 3.6 28.7 - + - -
53H THR 4.6 2.2 + - - -
54H ILE* 4.0 14.1 - - - +
55H GLY* 3.5 30.1 - - - +
78H ALA* 3.6 34.2 - - + +
80H LEU* 3.3 41.0 + - + +
81H GLU 3.2 1.0 - - - -
82H ARG* 1.3 79.7 - - + +
84H HIS* 1.3 63.3 + - - +
85H SER 3.2 2.7 - - - -
86H LEU* 3.0 36.6 + - + +
87H ALA* 3.5 6.4 + - - +
90H TYR* 5.5 2.6 - - + -
115H TRP* 5.7 0.2 - - - -
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Residues in contact with HIS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU 3.8 4.2 + - - +
81H GLU* 3.1 34.9 + - - +
83H TYR* 1.3 78.9 - - - +
85H SER* 1.3 60.4 + - - +
86H LEU 3.1 1.1 + - - -
87H ALA* 3.4 12.2 + - - +
88H PRO* 3.9 3.5 - - - +
111H ARG* 4.2 22.0 + - - +
115H TRP* 3.9 22.7 - + + -
118H GLU* 3.1 39.3 + - - -
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Residues in contact with SER 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439G LYS* 5.3 4.7 + - - -
442G PHE* 4.5 5.4 - - - -
443G GLU* 4.0 23.8 + - - +
81H GLU 4.7 0.4 + - - -
82H ARG 3.6 13.7 + - - -
84H HIS* 1.3 78.3 - - - +
86H LEU* 1.3 67.9 + - - +
87H ALA 3.4 0.2 - - - -
88H PRO* 3.7 11.7 - - - +
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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