Contacts of the helix formed by residues 85 - 93 (chain S) in PDB entry 1KYO
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 85 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79S PHE* 3.5 28.8 - - - -
80S LEU* 3.4 5.1 - - - +
82S SER* 3.0 9.2 + - - -
83S LYS 3.0 1.0 - - - -
84S ALA* 1.3 80.1 - - - +
86S ARG* 1.3 54.0 + - - +
87S GLU 2.9 6.5 - - - -
88S GLU* 3.7 3.9 - - - +
89S LEU* 2.7 37.2 + - - +
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Residues in contact with ARG 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q GLU 5.0 1.6 + - - -
119Q HIS* 3.0 61.2 + - - +
80S LEU 4.3 1.3 - - - -
82S SER 3.1 9.0 + - - +
83S LYS* 3.0 29.8 + - - +
84S ALA 3.7 0.2 - - - -
85S GLY* 1.3 75.9 - - - +
87S GLU* 1.3 66.0 + - + +
89S LEU* 4.1 9.9 - - - +
90S GLU* 3.5 27.3 + - - +
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Residues in contact with GLU 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q HIS* 5.9 2.8 - - - -
83S LYS 4.7 0.2 + - - -
84S ALA 5.7 2.0 - - - +
85S GLY* 2.9 1.1 - - - -
86S ARG* 1.3 88.6 + - + +
88S GLU* 1.3 64.6 + - - +
89S LEU 3.2 1.3 - - - -
90S GLU* 3.6 14.8 + - - +
91S ARG* 3.3 37.7 + - - +
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Residues in contact with GLU 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S TYR* 3.8 18.1 + - + +
79S PHE* 3.8 23.9 - - + -
80S LEU* 3.4 22.7 - - + -
85S GLY* 3.1 8.8 + - - +
87S GLU* 1.3 78.3 - - - +
89S LEU* 1.3 57.7 + - - +
91S ARG* 2.7 49.5 + - - +
92S VAL* 2.9 38.3 + - - +
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Residues in contact with LEU 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346N VAL* 4.5 1.8 - - + -
80S LEU* 3.3 46.2 - - + +
81S TYR* 3.8 32.1 - - + +
85S GLY 2.7 18.3 + - - +
86S ARG* 4.1 7.6 - - - +
88S GLU* 1.3 72.9 - - - +
90S GLU* 1.3 58.6 + - + +
91S ARG 2.8 14.6 + - - -
92S VAL* 3.1 4.9 + - - -
93S ASN* 2.9 52.1 + - + +
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Residues in contact with GLU 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119Q HIS* 5.5 7.7 + - - -
86S ARG* 3.5 21.2 + - - +
87S GLU* 3.9 15.7 - - - +
88S GLU 3.5 0.2 - - - -
89S LEU* 1.3 83.6 - - + +
91S ARG* 1.3 60.3 + - - +
93S ASN* 4.4 7.2 + - - +
94S VAL* 4.9 5.4 + - - +
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Residues in contact with ARG 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87S GLU* 3.3 33.7 + - - +
88S GLU* 2.7 53.6 + - - +
89S LEU 2.8 1.2 + - - -
90S GLU* 1.3 81.8 - - - +
92S VAL* 1.3 64.6 + - + +
93S ASN 3.3 4.9 + - - -
94S VAL 4.1 10.9 - - - +
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Residues in contact with VAL 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346N VAL* 3.9 18.9 - - + +
76S TYR* 3.5 26.5 - - - +
80S LEU* 3.8 22.7 - - + -
88S GLU* 2.9 35.8 + - - +
89S LEU 3.8 3.1 - - - +
91S ARG* 1.3 79.3 - - + +
93S ASN* 1.3 64.3 + - - +
94S VAL 5.2 0.4 - - - -
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Residues in contact with ASN 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E ASP* 3.2 31.0 + - - +
193E LYS* 4.6 10.7 + - - +
346N VAL* 3.3 22.8 - - - +
81S TYR* 3.6 11.8 + - - -
89S LEU* 2.9 37.5 + - + +
90S GLU* 4.7 5.4 - - - +
91S ARG 3.3 2.4 - - - -
92S VAL* 1.3 80.4 - - - +
94S VAL* 1.3 73.7 + - + +
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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