Contacts of the helix formed by residues 50 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.7 0.4 - - - -
47A ARG 2.9 16.2 + - - -
48A LYS 3.2 1.5 - - - -
49A LYS* 1.3 80.3 - - - +
51A ALA* 1.3 66.6 + - - -
52A ASP 3.3 3.3 + - - -
53A VAL* 3.4 2.4 + - - -
54A TRP* 3.0 27.1 + - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 5.0 4.7 - - + +
34A LEU* 4.1 2.6 - - + +
35A LYS* 3.7 47.8 - - + +
38A LEU* 3.7 17.0 - - + +
47A ARG 4.9 0.2 + - - -
50A GLY* 1.3 71.9 - - - -
52A ASP* 1.3 62.5 + - - +
54A TRP* 3.8 0.5 - - - +
55A PHE* 2.8 32.4 + - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.1 37.7 + - - +
50A GLY 3.3 1.0 - - - -
51A ALA* 1.3 81.3 - - - +
53A VAL* 1.3 62.8 + - + +
55A PHE* 3.4 4.8 + - - +
56A LYS* 3.0 24.1 + - - +
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 3.2 52.5 - - + +
50A GLY 3.4 2.0 + - - -
52A ASP* 1.3 78.3 - - + +
54A TRP* 1.3 62.2 + - - +
56A LYS* 3.3 7.7 + - - +
57A GLU* 3.0 24.6 + - + +
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Residues in contact with TRP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.1 5.8 - - + -
38A LEU* 3.9 27.1 - - + -
46A ILE* 2.8 55.0 + - + +
47A ARG 5.1 0.4 - - - -
49A LYS* 3.2 37.8 - - + +
50A GLY 3.0 25.5 + - - +
51A ALA 3.8 3.4 - - - +
53A VAL* 1.3 76.5 - - - +
55A PHE* 1.3 64.3 + - - +
57A GLU* 3.2 24.2 + - - +
58A LEU* 2.9 51.0 + - + +
74A LEU* 3.7 26.9 - - + -
77A LYS* 4.0 23.6 - - + -
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Residues in contact with PHE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL 3.8 2.9 - - - -
30A TYR 3.8 5.8 - - - -
31A ARG* 3.5 73.6 - - + +
34A LEU* 3.6 16.3 - - + +
51A ALA 2.8 23.3 + - - +
52A ASP 3.9 4.0 - - - +
54A TRP* 1.3 74.9 - - - +
56A LYS* 1.3 64.5 + - - +
58A LEU* 3.2 1.6 + - - +
59A ASP* 2.9 48.9 + - + +
64A GLY* 3.4 33.2 - - - -
65A ALA* 3.6 4.9 - - - -
66A VAL* 3.7 24.0 - - + -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 5.6 1.8 - - - +
52A ASP 3.0 17.4 + - - +
53A VAL* 3.7 5.6 - - - +
55A PHE* 1.3 80.6 - - - +
57A GLU* 1.3 62.0 + - - +
59A ASP* 3.8 14.5 + - - +
77B LYS* 5.2 5.7 + - - -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 2.8 35.5 + - - +
53A VAL* 3.0 19.5 + - + +
54A TRP* 3.6 22.3 - - + +
56A LYS* 1.3 78.0 - - - +
58A LEU* 1.3 62.7 + - + +
60A ILE* 3.4 18.7 - - - +
73A ILE* 4.8 5.6 - - + +
77A LYS* 3.1 28.4 + - - +
77B LYS* 5.2 2.2 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.0 28.9 - - + -
54A TRP* 2.9 37.3 + - + +
55A PHE 4.1 0.2 - - - +
57A GLU* 1.3 76.8 - - + +
59A ASP* 1.3 61.7 + - - +
60A ILE* 2.9 13.6 + - - +
66A VAL* 3.9 21.8 - - + -
70A GLU* 3.1 44.8 - - - +
71A PHE* 5.1 0.4 - - - -
73A ILE* 3.6 15.9 - - + -
74A LEU* 3.6 37.2 - - + +
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Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 2.9 31.7 + - + +
56A LYS* 3.8 9.9 + - - +
57A GLU 3.5 0.6 - - - -
58A LEU* 1.3 76.0 - - - +
60A ILE* 1.3 60.5 + - - +
61A ASN* 3.2 4.0 - - - +
62A THR* 3.1 22.2 + - + +
63A ASP* 3.1 8.7 + - - +
64A GLY* 2.8 27.0 + - - -
65A ALA 3.0 15.0 - - - +
66A VAL* 4.8 1.3 - - + -
70A GLU* 3.7 2.9 - - - -
1501A CA 2.4 28.9 - - - -
77B LYS* 5.2 1.6 - - - -
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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