Contacts of the helix formed by residues 46 - 60 (chain A) in PDB entry 1U0O
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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43A LYS* 2.7 51.1 + - - +
44A ILE 3.7 0.8 + - - -
45A TYR* 1.3 74.4 - - - +
47A LYS* 1.3 64.6 + - - +
48A GLU* 2.9 22.2 - - - +
49A LYS* 3.0 24.6 + - - +
50A ASP* 4.4 1.3 - - - +
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Residues in contact with LYS 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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9A TYR* 3.1 33.3 + - + +
46A SER* 1.3 72.8 - - - +
48A GLU* 1.3 60.4 + - - +
49A LYS 3.1 0.4 - - - -
50A ASP* 3.1 42.4 + - - +
51A PHE* 3.2 16.8 + - - +
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Residues in contact with GLU 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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9A TYR* 3.4 27.3 + - + -
14A TYR* 2.5 31.1 + - - +
41A SER 2.8 25.0 - - - +
42A ILE* 4.2 3.8 - - + -
43A LYS* 3.2 34.6 + - + +
46A SER* 2.9 11.1 - - - +
47A LYS* 1.3 76.1 - - - +
49A LYS* 1.3 64.6 + - - +
51A PHE* 3.2 2.3 + - - +
52A VAL* 3.0 32.4 + - + +
129A LYS* 3.0 10.6 + - - -
283B MET* 5.3 0.5 - - - +
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Residues in contact with LYS 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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42A ILE* 3.8 25.9 - - + +
44A ILE 4.1 16.8 - - - +
45A TYR* 4.6 11.0 - - + +
46A SER* 3.0 17.9 + - - +
48A GLU* 1.3 79.7 - - - +
50A ASP* 1.3 69.8 + - - +
52A VAL* 3.6 2.0 - - - +
53A GLY* 2.5 36.2 + - - -
113A VAL* 3.2 35.8 + - + +
114A LEU* 6.1 1.0 - - - +
115A TRP* 6.0 1.3 - - - +
635C VAL* 5.8 0.8 - - - +
639C GLN* 2.4 33.5 + - - +
642C LYS* 4.9 4.5 - - - +
667C LYS 5.7 0.2 + - - -
668C GLN* 3.3 19.4 + - - +
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Residues in contact with ASP 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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46A SER 4.4 0.7 - - - +
47A LYS* 3.1 42.6 + - - +
49A LYS* 1.3 102.2 - - - +
51A PHE* 1.3 57.7 + - - +
53A GLY* 4.6 1.3 - - - -
54A ASP* 2.8 36.8 + - - +
113A VAL* 5.0 2.8 - - - +
639C GLN* 5.0 3.3 + - - -
642C LYS* 4.2 18.7 + - - -
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Residues in contact with PHE 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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7A SER* 3.7 20.2 - - - -
8A SER 3.3 26.7 - - - -
9A TYR* 3.4 37.0 - + + -
14A TYR* 3.4 29.8 - + + -
47A LYS* 3.2 14.0 + - - +
48A GLU 3.3 8.5 - - - +
50A ASP* 1.3 74.8 - - - +
52A VAL* 1.3 60.4 + - + +
54A ASP* 3.7 2.6 - - - +
55A LEU* 2.5 58.3 + - + +
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Residues in contact with VAL 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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14A TYR* 4.2 16.2 - - + -
40A VAL* 3.8 28.3 - - + -
42A ILE* 5.0 8.1 - - + -
48A GLU* 3.0 20.5 + - + +
49A LYS* 4.1 3.4 - - - +
51A PHE* 1.3 76.9 - - + +
53A GLY* 1.3 69.8 + - - +
55A LEU* 3.3 7.9 - - + -
56A VAL* 2.9 20.3 + - - +
106A LEU* 3.9 21.1 - - + -
112A PHE 4.5 0.4 - - - +
127A VAL* 4.1 27.8 - - + -
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Residues in contact with GLY 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 2.5 24.1 + - - -
50A ASP* 3.8 2.2 - - - -
52A VAL* 1.3 76.8 - - - +
54A ASP* 1.3 60.8 + - - +
56A VAL* 3.2 2.9 + - - +
57A THR* 3.1 21.0 + - - -
106A LEU* 5.1 0.4 - - - +
111A GLY 3.5 11.2 - - - +
112A PHE* 2.9 25.8 - - - +
113A VAL* 4.8 2.7 - - - -
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Residues in contact with ASP 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 ASP* 2.8 22.5 + - - +
51A PHE* 3.9 2.5 - - - +
53A GLY* 1.3 69.9 - - - -
55A LEU* 1.3 67.6 + - - +
57A THR* 3.0 13.0 + - - +
58A LYS* 2.9 44.8 + - + +
111A GLY* 5.3 0.9 - - - +
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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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7A SER* 3.6 25.4 - - - +
14A TYR* 4.6 8.5 - - + -
15A LYS* 4.5 6.1 - - - +
16A PHE* 4.0 30.5 - - + +
51A PHE* 2.5 58.2 + - + +
52A VAL* 3.2 15.3 - - + +
53A GLY 3.1 0.2 - - - -
54A ASP* 1.3 74.4 - - - +
56A VAL* 1.3 61.7 + - - +
58A LYS* 3.8 3.8 + - - +
59A ASN* 3.4 26.0 + - - +
127A VAL* 5.0 6.7 - - + -
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Residues in contact with VAL 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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16A PHE* 4.3 14.4 - - + -
52A VAL* 2.9 22.1 + - + +
53A GLY 3.8 3.1 - - - +
55A LEU* 1.3 73.8 - - - +
57A THR* 1.3 62.1 + - - +
58A LYS 2.9 2.5 + - - -
59A ASN 3.0 0.3 + - - -
60A ILE* 2.6 58.9 + - + +
67A ALA* 4.5 7.4 - - + -
106A LEU* 4.5 10.3 - - + -
112A PHE* 3.8 23.6 - - + -
127A VAL* 3.3 33.9 - - + -
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Residues in contact with THR 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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53A GLY 3.1 14.7 + - - -
54A ASP* 3.0 17.5 + - - +
56A VAL* 1.3 76.7 - - - +
58A LYS* 1.3 64.3 + - + +
60A ILE* 3.3 18.3 - - - +
111A GLY* 3.2 30.9 + - - -
112A PHE* 4.1 5.3 - - + -
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Residues in contact with LYS 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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54A ASP* 2.9 33.9 + - + +
55A LEU* 4.1 4.5 - - - +
57A THR* 1.3 81.8 - - + +
59A ASN* 1.3 70.2 + - - +
60A ILE 3.4 2.9 - - - +
61A GLN* 4.7 3.8 - - - +
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Residues in contact with ASN 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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16A PHE* 3.3 37.1 + - + +
18A GLN* 4.4 0.5 - - - +
55A LEU* 3.4 20.1 + - - +
56A VAL 3.0 1.0 + - - -
58A LYS* 1.3 81.6 - - - +
60A ILE* 1.3 70.5 + - - +
61A GLN* 3.2 22.0 + - - +
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Residues in contact with ILE 60 (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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16A PHE* 3.5 29.2 - - + -
18A GLN* 3.8 2.0 - - - +
56A VAL* 2.6 49.3 + - + +
57A THR* 3.3 16.5 - - - +
58A LYS 3.4 2.9 - - - +
59A ASN* 1.3 78.8 - - - +
61A GLN* 1.3 97.5 + - - +
62A SER 5.1 0.9 - - - +
64A ASP* 3.3 41.1 - - + +
108A LYS* 5.9 2.9 - - - -
112A PHE* 3.8 18.8 - - + -
125A PRO* 4.9 2.5 - - + -
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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