Contacts of the helix formed by residues 23 - 31 (chain A) in PDB entry 4ZC3
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 ASN 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TYR* 4.3 1.0 + - - -
20A ASN* 3.1 19.1 + - - +
21A ASP 3.2 2.2 - - - +
22A MET* 1.3 75.6 - - - +
24A ALA* 1.4 56.0 + - - +
25A THR* 3.2 12.6 + - - -
26A LYS* 3.0 46.2 + - + +
27A ALA* 3.0 27.8 + - - +
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Residues in contact with ALA 24 (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 PHE* 3.5 11.9 - - + -
17A TYR* 4.2 20.0 - - + -
22A MET 3.4 4.6 + - - +
23A ASN* 1.4 70.6 + - - +
25A THR* 1.3 60.5 + - - +
27A ALA* 4.2 2.5 - - - -
28A ALA* 2.9 29.5 + - - +
42A GLY* 3.8 28.0 - - - +
43A ALA* 4.7 0.7 - - - +
46A LEU* 4.3 11.2 - - + -
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Residues in contact with THR 25 (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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23A ASN* 3.2 8.8 + - - -
24A ALA* 1.3 76.7 - - - +
26A LYS* 1.3 66.9 + - + +
28A ALA* 3.2 2.9 + - - +
29A ILE* 3.0 38.0 + - + +
35A LYS 5.9 0.4 - - - +
38A ALA* 4.0 8.9 - - + +
39A SER* 3.4 43.0 + - - +
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Residues in contact with LYS 26 (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 ASN* 3.0 39.3 + - - +
21A ASP* 5.4 3.6 + - - -
23A ASN* 3.0 36.6 + - - +
25A THR* 1.3 77.1 - - + +
27A ALA* 1.3 58.7 + - - +
29A ILE* 3.4 12.7 + - + +
30A ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 27 (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 PHE* 3.8 15.0 - - + +
16A GLU* 3.5 18.2 - - + +
17A TYR* 3.4 33.9 - - + +
20A ASN* 4.2 1.1 - - - +
23A ASN 3.0 17.6 + - - +
24A ALA* 3.6 5.8 - - - +
25A THR 3.2 0.2 - - - -
26A LYS* 1.3 78.7 - - - +
28A ALA* 1.3 57.5 + - - +
30A ALA 3.3 0.3 + - - -
31A ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 28 (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 PHE* 3.8 6.2 - - + -
24A ALA 2.9 18.0 + - - +
25A THR 3.2 2.2 + - - +
27A ALA* 1.3 77.4 - - - +
29A ILE* 1.3 61.7 + - - +
31A ALA 3.4 0.5 + - - -
32A GLY 3.2 5.0 + - - -
33A TYR* 3.0 46.8 + - + -
38A ALA* 3.5 28.5 - - + +
41A ILE* 4.7 0.2 - - + -
42A GLY* 4.1 10.8 - - - +
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Residues in contact with ILE 29 (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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25A THR* 3.0 36.0 + - + +
26A LYS* 3.7 11.7 - - + +
28A ALA* 1.3 75.4 - - - +
30A ALA* 1.3 64.0 + - - +
32A GLY* 3.0 15.2 + - - -
33A TYR 4.0 9.1 + - - +
35A LYS* 4.4 22.4 - - + +
38A ALA* 3.5 16.4 - - + -
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Residues in contact with ALA 30 (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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12A ARG* 3.5 21.3 + - - +
16A GLU* 3.4 35.0 - - + +
20A ASN* 4.3 4.5 - - - +
26A LYS 2.9 18.3 + - - +
27A ALA 3.8 0.2 - - - +
29A ILE* 1.3 79.9 - - - +
31A ALA* 1.3 58.2 + - - +
32A GLY 3.5 0.7 + - - -
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Residues in contact with ALA 31 (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 LYS* 3.4 27.4 - - - +
12A ARG* 3.7 18.5 - - + +
13A PHE* 3.6 32.5 - - + +
16A GLU* 4.2 0.4 - - - +
27A ALA 2.9 17.8 + - - +
28A ALA 3.8 4.7 - - - +
29A ILE 3.2 0.4 - - - -
30A ALA* 1.3 75.1 - - - +
32A GLY* 1.3 56.8 + - - +
33A TYR* 3.7 8.1 - - + -
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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