Contacts of the helix formed by residues 45 - 55 (chain A) in PDB entry 1ZU1
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASP 5.4 1.8 - - - -
43A LEU 3.0 7.2 + - - +
44A ILE* 1.3 80.8 - - - +
46A GLU* 1.3 66.2 + - - +
47A SER* 3.3 11.3 + - - -
48A GLN* 3.1 23.2 + - - +
49A LYS* 3.0 19.4 + - - +
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Residues in contact with GLU 46 (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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17A LYS* 2.8 41.1 + - - +
21A ASN* 4.9 0.2 + - - -
33A ASP* 4.6 1.4 + - - +
45A SER* 1.3 75.2 + - - +
47A SER* 1.3 56.1 + - - +
49A LYS* 2.8 41.8 + - + +
50A LEU* 2.8 44.4 + - + +
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Residues in contact with SER 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 SER* 4.0 9.4 + - - -
46A GLU* 1.3 75.1 - - - +
48A GLN* 1.3 77.9 + - - +
50A LEU* 3.6 9.1 + - - +
51A ALA* 3.1 28.6 + - - +
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Residues in contact with GLN 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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42A VAL 5.5 0.4 - - - +
43A LEU* 4.2 13.7 - - + -
44A ILE* 3.6 30.9 - - + +
45A SER* 3.1 30.1 + - - +
47A SER* 1.3 89.6 + - - +
49A LYS* 1.3 59.1 + - - +
51A ALA* 3.4 6.0 + - - +
52A HIS* 2.9 32.9 + - - +
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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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20A VAL* 4.4 5.6 - - + -
21A ASN* 2.9 27.6 + - - -
24A ILE* 3.9 15.4 - - + +
33A ASP* 2.7 42.5 + - - +
43A LEU* 4.0 29.5 - - + +
45A SER 3.0 11.9 + - - +
46A GLU* 2.8 44.3 + - + +
48A GLN* 1.3 75.9 - - - +
50A LEU* 1.3 63.5 + - - +
52A HIS* 3.4 0.3 + - - +
53A TYR* 3.0 45.0 + - + -
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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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16A GLY 4.8 0.9 - - - -
17A LYS* 3.6 45.1 - - + +
20A VAL* 3.9 24.0 - - + +
46A GLU* 2.8 44.7 + - + +
47A SER* 3.9 7.4 - - - +
49A LYS* 1.3 78.4 - - + +
51A ALA* 1.3 61.5 + - - +
53A TYR 4.4 0.2 - - - -
54A GLN* 2.9 39.5 + - - +
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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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47A SER 3.1 18.1 + - - +
48A GLN* 3.8 5.4 - - - +
50A LEU* 1.3 75.3 - - - +
52A HIS* 1.3 59.6 + - - +
54A GLN* 3.4 4.7 + - - +
55A SER* 3.0 29.6 + - - -
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Residues in contact with HIS 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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36A CYS* 3.6 12.6 - - + -
39A CYS* 3.5 18.3 - - + -
41A ALA* 4.2 16.4 - - + +
43A LEU* 3.5 22.2 - - + +
48A GLN 2.9 21.3 + - - +
49A LYS 3.8 2.5 - - - +
51A ALA* 1.3 71.4 - - - +
53A TYR* 1.3 65.1 + + - +
55A SER* 3.1 12.2 + - - -
58A HIS* 3.1 31.3 + + + +
129A ZN 2.1 36.9 - - - -
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Residues in contact with TYR 53 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 5.3 1.2 - - - +
14A PRO* 3.2 20.0 - - - +
20A VAL* 3.6 32.1 - - + -
23A LEU* 4.6 10.0 - - + +
24A ILE* 3.5 24.7 - - + -
31A PHE* 3.6 32.1 - + + +
32A SER 2.9 25.4 + - - -
35A GLN 3.1 17.7 + - - -
36A CYS* 4.1 5.6 - - + -
43A LEU* 3.5 23.1 - - + +
49A LYS* 3.0 28.8 + - + +
52A HIS* 1.3 74.3 - + - +
54A GLN* 1.3 59.6 + - - +
55A SER 3.5 0.8 - - - +
58A HIS* 3.6 38.1 + + - -
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Residues in contact with GLN 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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13A LEU* 3.5 6.8 - - - +
14A PRO* 3.7 18.6 - - + +
15A VAL* 3.6 6.4 - - - +
16A GLY* 2.9 32.8 + - - +
20A VAL* 3.7 18.0 - - + +
50A LEU* 2.9 37.8 + - - +
51A ALA* 3.4 5.3 + - - +
52A HIS 3.2 0.8 - - - -
53A TYR* 1.3 75.1 - - - +
55A SER* 1.3 61.3 + - - +
56A ARG* 3.1 25.1 + - - -
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Residues in contact with SER 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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13A LEU* 3.8 1.7 - - - +
51A ALA 3.0 13.0 + - - -
52A HIS* 3.1 19.5 + - - -
54A GLN* 1.3 79.1 - - - +
56A ARG* 1.3 65.2 + - - +
57A LYS* 3.2 22.8 + - - +
58A HIS* 3.4 8.0 + - - +
59A ALA* 3.2 21.7 + - - +
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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