Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 1UST
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A SER 3.8 3.0 + - - -
45A LYS* 1.3 70.7 - - - +
47A TYR* 1.3 63.5 + - - +
48A ARG* 3.1 26.0 + - - +
49A GLU* 3.1 28.1 + - - +
50A LEU* 3.3 17.0 + - - +
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Residues in contact with TYR 47 (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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45A LYS 3.4 15.7 - - - -
46A SER* 1.3 73.3 + - - +
48A ARG* 1.3 56.0 + - - +
50A LEU* 4.1 9.6 - - + -
51A ILE* 2.7 43.7 + - + +
73A ILE* 5.3 0.4 - - + -
80A VAL* 3.9 16.9 - - + +
83A ALA* 4.9 3.8 - - - +
86A PHE* 3.4 42.2 - + - +
89A TYR* 3.4 43.3 - + + +
90A PHE* 3.8 14.1 - + - -
93A ALA* 3.6 34.1 - - + -
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Residues in contact with ARG 48 (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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46A SER* 3.1 16.6 + - - +
47A TYR* 1.3 78.5 - - - +
49A GLU* 1.3 67.6 + - - +
52A ILE* 3.3 35.1 + - + +
96A LYS* 6.5 0.9 - - - +
100A ALA* 6.1 3.6 - - - +
102A ASP* 2.7 37.5 + - + +
103A PHE* 3.9 14.5 - - + -
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Residues in contact with GLU 49 (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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46A SER* 3.1 28.0 + - - +
48A ARG* 1.3 86.4 - - - +
50A LEU* 1.3 68.6 - - + +
52A ILE* 4.1 3.8 - - - +
53A GLU* 2.9 33.2 + - - +
77A TYR* 5.7 3.1 - - + +
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Residues in contact with LEU 50 (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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45A LYS* 3.9 15.9 - - + -
46A SER 3.3 16.4 - - - +
47A TYR* 3.1 13.9 + - + +
49A GLU* 1.3 83.5 - - + +
51A ILE* 1.3 62.6 + - - +
53A GLU* 3.5 5.9 + - - +
54A GLY* 3.2 16.6 + - - -
72A PHE* 4.2 4.7 - - - -
73A ILE* 3.6 34.6 - - + +
77A TYR* 3.5 40.2 - - + -
80A VAL* 3.4 39.0 - - + -
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Residues in contact with ILE 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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47A TYR* 2.7 26.4 + - + +
50A LEU* 1.3 72.6 - - - +
52A ILE* 1.3 53.0 + - - +
54A GLY 3.1 1.9 + - - -
55A LEU* 2.5 43.5 + - + +
69A LEU* 3.4 30.1 - - + +
73A ILE* 4.2 3.8 - - + -
90A PHE* 3.4 23.6 - - + -
93A ALA* 4.0 20.4 - - + -
94A ILE* 3.6 25.8 - - + -
103A PHE* 3.7 35.9 - - + -
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Residues in contact with ILE 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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48A ARG* 3.3 20.5 + - + +
49A GLU* 4.1 4.3 - - - +
51A ILE* 1.3 77.9 - - - +
53A GLU* 1.3 66.1 + - - +
56A THR* 2.9 31.4 + - + -
102A ASP* 3.4 35.2 - - - +
103A PHE* 3.2 19.1 - - + -
115A LEU* 3.6 31.0 - - + -
117A LYS* 6.2 0.2 - - - -
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Residues in contact with GLU 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 GLU 2.9 20.8 + - - +
50A LEU* 3.5 6.5 - - - +
51A ILE 3.3 0.2 - - - -
52A ILE* 1.3 78.8 - - - +
54A GLY* 1.3 61.7 + - - +
56A THR* 3.4 17.5 - - - +
57A ALA* 3.7 8.5 - - - +
72A PHE* 3.9 18.7 - - + -
77A TYR* 3.8 27.3 + - + +
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Residues in contact with GLY 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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50A LEU 3.2 4.0 + - - -
51A ILE 3.1 4.9 + - - -
53A GLU* 1.3 77.5 - - - +
55A LEU* 1.3 54.8 + - - +
56A THR 3.0 2.7 - - - -
57A ALA 2.6 23.0 + - - -
58A LEU* 2.6 28.1 + - - +
69A LEU* 4.2 0.9 - - - -
72A PHE* 3.3 32.0 - - - -
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Residues in contact with LEU 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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51A ILE* 2.5 25.2 + - + +
54A GLY* 1.3 71.6 - - - +
56A THR* 1.3 60.3 + - - +
58A LEU* 3.6 8.3 - - + -
59A LYS* 3.3 22.8 + - - +
62A LYS 4.9 0.2 - - - +
63A GLY* 4.7 0.4 - - - -
64A SER 4.2 9.0 - - - +
69A LEU* 3.4 21.4 - - + +
103A PHE* 3.8 12.1 - - + -
113A VAL* 3.1 52.7 - - + +
114A LYS* 3.5 2.8 + - - +
115A LEU* 3.3 43.0 + - + +
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Residues in contact with THR 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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52A ILE* 2.9 25.7 + - + +
53A GLU* 3.4 13.5 - - - +
55A LEU* 1.3 78.7 - - - +
57A ALA* 1.3 64.8 + - + +
59A LYS* 3.3 22.8 + - - +
114A LYS* 6.2 0.7 - - - +
115A LEU* 4.0 17.8 - - - +
117A LYS* 5.3 5.9 + - - -
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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