Contacts of the helix formed by residues 42 - 51 (chain A) in PDB entry 1ZK2
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 VAL 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A THR* 4.0 31.6 - - - +
16A LEU* 4.4 13.9 - - + -
37A ASP* 4.1 22.2 - - + +
39A HIS* 4.4 10.1 - - + -
41A ASP* 1.3 88.4 - - - +
43A GLY* 1.3 63.2 + - - +
44A GLU 3.5 1.1 - - - -
45A LYS* 3.3 11.9 + - + +
46A ALA* 3.0 26.0 + - + +
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Residues in contact with GLY 43 (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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15A THR* 3.7 9.9 - - - -
35A ILE* 4.2 1.2 - - - +
40A SER 3.4 5.1 + - - -
42A VAL* 1.3 82.8 - - - +
44A GLU* 1.3 56.2 + - - +
46A ALA* 3.4 1.4 + - - +
47A ALA* 3.0 30.0 + - - +
58A PHE* 3.4 40.2 - - - +
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Residues in contact with GLU 44 (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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40A SER* 3.9 13.0 + - - +
41A ASP 5.1 0.6 - - - +
42A VAL 3.5 0.4 - - - -
43A GLY* 1.3 76.6 - - - +
45A LYS* 1.3 63.0 + - + +
47A ALA* 3.5 5.2 + - - +
48A LYS* 3.1 24.8 + - - +
58A PHE* 3.7 31.3 + - + +
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Residues in contact with LYS 45 (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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41A ASP 3.6 21.9 + - - +
42A VAL* 3.3 12.0 + - + +
44A GLU* 1.3 79.4 - - + +
46A ALA* 1.3 56.9 + - - +
48A LYS* 3.3 5.9 + - - +
49A SER* 3.0 29.7 + - - -
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Residues in contact with ALA 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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15A THR* 3.7 38.1 - - - +
20A LEU* 4.3 6.1 - - + -
35A ILE* 4.1 6.5 - - + -
42A VAL* 3.0 18.5 + - + +
43A GLY 3.7 4.3 - - - +
44A GLU 3.3 0.2 - - - -
45A LYS* 1.3 77.4 - - - +
47A ALA* 1.3 62.9 + - - +
49A SER* 2.6 25.3 + - - -
50A VAL* 3.4 10.8 + - - +
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Residues in contact with ALA 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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35A ILE* 3.9 12.2 - - + +
43A GLY 3.0 17.2 + - - +
44A GLU* 3.8 6.7 - - - +
46A ALA* 1.3 76.7 - - - +
48A LYS* 1.3 62.1 + - - +
50A VAL* 3.0 12.0 + - - +
51A GLY 3.1 14.3 + - - +
56A ILE* 3.5 29.7 - - + +
57A GLN* 4.2 19.3 - - - -
58A PHE* 4.3 2.9 - - + +
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Residues in contact with LYS 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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44A GLU 3.1 18.1 + - - +
45A LYS* 3.9 4.9 - - - +
47A ALA* 1.3 76.2 - - - +
49A SER* 1.3 62.2 + - - +
50A VAL 3.3 0.9 + - - -
51A GLY* 3.5 19.3 + - - +
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Residues in contact with SER 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 LEU* 4.5 7.3 - - - +
45A LYS 3.0 15.4 + - - -
46A ALA* 2.6 23.1 + - - -
48A LYS* 1.3 78.7 - - - +
50A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 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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20A LEU* 3.8 17.3 - - + -
23A ALA* 5.0 0.4 - - + -
24A THR* 3.6 46.1 - - + +
27A VAL* 3.9 29.7 - - + +
46A ALA 3.5 13.5 - - - +
47A ALA 3.0 7.2 + - - +
48A LYS 4.2 0.2 - - - -
49A SER* 1.3 82.0 - - - +
51A GLY* 1.3 57.2 + - - +
55A GLN* 4.6 1.4 - - - +
56A ILE* 3.9 17.0 - - + -
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Residues in contact with GLY 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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27A VAL* 5.3 0.2 - - - -
47A ALA 3.1 15.2 + - - +
48A LYS* 3.5 18.5 + - - +
50A VAL* 1.3 80.7 - - - +
52A THR* 1.3 66.9 + - - -
53A PRO* 4.8 0.7 - - - +
55A GLN* 3.3 13.7 - - - -
56A ILE* 3.7 8.7 - - - +
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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