Contacts of the helix formed by residues 50 - 59 (chain I) in PDB entry 1XK4
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 50 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38I LEU* 5.0 0.2 - - - -
47I ARG 2.9 14.5 + - - -
48I LYS 3.1 2.0 - - - -
49I LYS* 1.3 82.0 - - - +
51I ALA* 1.3 66.7 + - - -
52I ASP 3.3 2.9 - - - -
53I VAL* 3.3 5.2 + - - -
54I TRP* 3.0 25.0 + - - -
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Residues in contact with ALA 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ARG* 5.2 3.8 - - - +
34I LEU* 4.0 2.9 - - - +
35I LYS* 3.8 47.3 - - + +
38I LEU* 3.8 18.6 - - + +
47I ARG 4.7 1.0 + - - -
50I GLY* 1.3 71.4 - - - -
52I ASP* 1.3 61.5 + - - +
54I TRP* 3.4 1.7 + - - +
55I PHE* 2.8 28.6 + - - +
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Residues in contact with ASP 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I ARG* 3.6 31.9 + - - +
50I GLY 3.3 0.6 - - - -
51I ALA* 1.3 79.5 - - - +
53I VAL* 1.3 60.3 + - + +
55I PHE* 3.2 5.8 + - - +
56I LYS* 2.9 29.3 + - - +
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Residues in contact with VAL 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I LYS* 3.4 48.2 - - + +
50I GLY* 3.3 2.4 + - - +
52I ASP* 1.3 76.1 - - + +
54I TRP* 1.3 65.0 + - - +
56I LYS* 3.4 6.6 + - - +
57I GLU* 3.0 24.9 + - + +
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Residues in contact with TRP 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 4.2 6.7 - - + -
38I LEU* 3.8 27.1 - - + -
46I ILE* 2.9 49.1 + - + +
47I ARG 5.1 0.9 - - - -
49I LYS* 3.3 35.6 - - + +
50I GLY 3.0 21.6 + - - +
51I ALA 3.7 7.4 - - - +
53I VAL* 1.3 76.9 - - - +
55I PHE* 1.3 58.8 + - - +
57I GLU* 3.2 26.1 + - - +
58I LEU* 2.9 50.4 + - + +
74I LEU* 3.8 30.1 - - + -
77I LYS* 4.0 26.9 - - + -
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Residues in contact with PHE 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I VAL 3.9 2.7 - - - -
30I TYR 3.7 5.4 - - - -
31I ARG* 3.4 73.4 - - + +
34I LEU* 3.6 21.1 - - + -
51I ALA 2.8 18.6 + - - +
52I ASP* 3.2 8.7 + - - +
54I TRP* 1.3 75.7 - - - +
56I LYS* 1.3 59.1 + - - +
58I LEU* 3.8 1.6 - - - +
59I ASP* 2.9 47.4 + - + +
64I GLY* 3.4 31.4 - - - -
65I ALA* 3.6 5.6 - - - -
66I VAL* 3.7 17.5 - - + -
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Residues in contact with LYS 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52I ASP 2.9 15.2 + - - +
53I VAL* 3.9 5.6 - - - +
54I TRP 3.3 0.2 - - - -
55I PHE* 1.3 81.4 - - - +
57I GLU* 1.3 62.0 + - - +
59I ASP* 3.7 13.9 + - - +
62I THR* 6.0 0.7 - - - +
77J LYS* 5.3 5.4 + - - -
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Residues in contact with GLU 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LYS* 2.9 33.4 + - - +
53I VAL* 3.0 17.7 + - + +
54I TRP* 3.6 17.0 - - + +
56I LYS* 1.3 78.5 - - - +
58I LEU* 1.3 61.3 + - + +
60I ILE* 3.3 23.6 - - - +
73I ILE* 4.9 4.0 - - + +
77I LYS* 3.3 36.2 - - - +
77J LYS* 5.1 2.5 + - - +
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Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 4.1 27.8 - - + -
54I TRP* 2.9 38.2 + - + +
55I PHE 4.0 0.2 - - - +
57I GLU* 1.3 79.2 - - + +
59I ASP* 1.3 58.7 + - - +
60I ILE* 2.8 13.0 + - - +
66I VAL* 3.9 22.9 - - + -
70I GLU* 3.1 32.9 - - - +
71I PHE* 5.2 1.1 - - + -
73I ILE* 3.6 31.4 - - + +
74I LEU* 3.6 34.1 - - + +
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Residues in contact with ASP 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I PHE* 2.9 31.3 + - + +
56I LYS* 3.7 9.5 + - - +
57I GLU 3.5 1.0 - - - -
58I LEU* 1.3 73.0 - - - +
60I ILE* 1.3 62.8 + - - +
61I ASN* 3.1 4.0 - - - +
62I THR* 3.1 23.1 + - + +
63I ASP* 3.1 7.6 + - - +
64I GLY* 2.7 29.3 + - - -
65I ALA 3.3 14.4 - - - +
66I VAL* 4.6 1.1 - - + +
70I GLU* 3.7 2.7 - - - -
1521I CA 2.3 30.0 - - - -
77J LYS* 5.2 1.2 - - - -
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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