Contacts of the helix formed by residues 38 - 42 (chain R) 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 TYR 38 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318N PHE* 3.8 21.9 - - + -
378N PHE* 3.9 22.0 - + - -
382N ARG* 4.2 3.8 - - - -
33R ILE* 3.3 25.6 - - + +
36R ALA* 3.6 18.0 + - + -
37R GLY* 1.3 75.8 - - - +
39R LYS* 1.3 78.6 + - + +
41R LEU* 3.0 17.1 + - - +
42R GLY 3.4 0.2 + - - -
43R LEU* 2.9 42.6 + - + +
44R LYS 4.2 0.4 - - - -
45R PHE* 3.3 37.1 - - + +
48R LEU* 3.7 32.3 - - + -
99R ASP* 2.6 27.4 + - - -
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Residues in contact with LYS 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R ILE* 3.3 33.2 - - + +
34R ASN* 4.0 20.5 + - - +
37R GLY* 3.0 2.6 + - - -
38R TYR* 1.3 98.8 - - + +
40R LYS* 1.3 59.1 + - + +
42R GLY 3.0 16.8 + - - -
43R LEU 4.0 6.3 - - - +
93R TRP* 3.5 7.3 - - + -
94R ILE* 3.2 45.4 + - + +
95R LYS 4.6 1.3 - - - -
96R ALA* 4.7 15.5 - - - +
99R ASP* 3.4 22.7 + - + +
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Residues in contact with LYS 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34R ASN 3.6 21.6 + - - -
35R LEU 5.7 0.2 + - - -
37R GLY* 2.8 21.3 + - - +
39R LYS* 1.3 77.0 - - + +
41R LEU* 1.3 57.2 + - - +
42R GLY 3.3 1.3 + - - -
87R LEU* 3.8 27.3 - - + +
88R LEU* 3.2 25.1 + - - +
93R TRP* 3.3 63.6 + - + -
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Residues in contact with LEU 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210N LEU* 4.2 9.0 - - + -
317N THR* 6.5 0.2 - - + -
318N PHE* 4.2 26.2 - - + -
37R GLY 3.7 2.2 + - - +
38R TYR* 3.0 14.3 + - - +
40R LYS* 1.3 78.4 - - - +
42R GLY* 1.3 63.5 + - - +
43R LEU* 3.5 12.9 + - + +
77R ARG* 4.6 0.7 + - - -
78R ALA* 3.9 26.2 + - + +
81R THR* 4.3 11.5 + - + -
82R GLU* 3.9 24.0 - - + +
86R HIS 4.0 13.9 - - - +
87R LEU* 3.5 31.2 - - + -
88R LEU* 3.8 12.4 - - - +
51S ARG* 5.1 2.0 - - - +
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Residues in contact with GLY 42 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R LYS 3.0 11.8 + - - -
40R LYS 3.3 1.6 - - - -
41R LEU* 1.3 78.9 - - - +
43R LEU* 1.3 63.3 + - - +
74R ARG* 3.4 12.1 - - - +
77R ARG* 2.9 31.1 + - - -
88R LEU* 3.7 9.1 - - - +
92R GLU 4.6 2.0 - - - -
94R ILE* 3.7 15.9 - - - -
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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