Contacts of the helix formed by residues 40 - 43 (chain B) in PDB entry 1KO1
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 ASP 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ALA* 4.5 5.4 - - - +
21B LYS* 6.1 0.5 - - - -
22B SER* 5.6 1.4 + - - -
38B ASP* 3.0 20.6 + - - +
39B GLY* 1.3 75.3 - - - +
41B PHE* 1.3 66.7 + - + +
42B LEU 3.3 1.0 + - - -
43B HIS* 3.6 29.0 + - - +
48B ILE* 5.5 0.7 - - - +
65B TRP* 3.9 16.0 - - - +
86B VAL* 4.2 10.0 + - - +
87B CYS* 5.5 1.6 - - - -
88B SER 5.6 1.0 + - - -
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.9 11.0 - - + -
36A PHE 4.6 8.3 - - - -
37A LEU* 4.7 11.4 - - + -
71A ASP 4.9 0.2 - - - -
72A ALA* 3.5 28.5 - - + +
75A ALA* 3.8 14.8 - - - +
76A MET* 3.5 48.7 - - + -
79A THR* 5.4 2.7 - - - -
80A ASN* 3.9 27.4 - - - -
36B PHE* 6.3 0.2 - + - -
37B LEU* 5.5 0.2 - - + -
38B ASP* 2.9 47.8 + - + +
39B GLY 2.9 0.2 + - - -
40B ASP* 1.3 84.0 - - + +
42B LEU* 1.3 65.2 + - + +
43B HIS 3.4 2.1 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.8 0.9 - - + -
42A LEU* 3.4 42.4 - - + -
72A ALA* 4.7 2.5 - - + -
37B LEU* 3.9 24.0 - - + -
39B GLY* 3.0 9.8 + - - +
41B PHE* 1.3 87.1 - - + +
43B HIS* 1.3 68.4 + - - +
44B PRO* 3.3 5.7 - - - +
65B TRP* 3.8 11.9 - - + -
68B ALA* 4.0 35.4 - - + +
69B LEU* 3.8 25.1 - - + -
72B ALA* 4.0 1.8 - - + -
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Residues in contact with HIS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASP* 5.2 8.0 - - - +
75A ALA* 5.1 1.6 - - - +
40B ASP* 3.6 25.1 + - - +
41B PHE 3.4 4.7 - - - +
42B LEU* 1.3 79.7 - - - +
44B PRO* 1.3 70.8 - - + +
45B ARG 3.7 0.3 + - - -
47B ASN* 3.2 35.6 + - + -
48B ILE* 4.2 17.7 - - + +
51B MET* 4.9 16.8 - - + +
57B LEU* 4.2 17.2 - - + +
62B ARG* 5.4 0.6 - - - +
65B TRP* 3.1 62.1 + + + -
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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