Contacts of the helix formed by residues 16 - 27 (chain A) in PDB entry 1BZG
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 GLN 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LYS* 4.9 16.1 - - + +
12A GLY* 4.0 31.0 - - - +
13A LYS 4.2 2.9 - - - +
15A ILE* 1.3 78.4 - - + +
17A ASP* 1.3 59.2 + - - +
19A ARG* 2.8 59.6 + - - +
20A ARG* 3.5 3.8 + - - +
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Residues in contact with ASP 17 (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 LYS 4.1 0.8 + - - +
14A SER* 3.7 22.0 - - - +
15A ILE 2.9 1.2 - - - +
16A GLN* 1.3 79.0 - - - +
18A LEU* 1.3 56.8 + - - +
19A ARG 2.7 4.5 - - - -
20A ARG* 2.5 72.5 + - - +
21A ARG* 2.8 21.6 + - - +
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Residues in contact with LEU 18 (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 SER* 2.7 34.6 + - - +
15A ILE* 3.6 12.6 - - + +
17A ASP* 1.3 75.5 - - - +
19A ARG* 1.3 58.7 + - - +
21A ARG* 3.0 47.5 - - + +
22A PHE* 2.8 49.5 - - + -
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Residues in contact with ARG 19 (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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11A LYS* 5.9 1.8 - - - +
15A ILE 2.9 9.3 + - - +
16A GLN* 2.8 59.6 + - - +
17A ASP 2.6 0.4 + - - -
18A LEU* 1.3 75.1 - - - +
20A ARG* 1.3 50.2 + - - +
21A ARG 2.9 4.0 - - - -
22A PHE* 2.7 14.9 + - - +
23A PHE* 2.4 57.4 + - + -
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Residues in contact with ARG 20 (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 GLN 4.4 2.5 - - - +
17A ASP* 2.5 54.6 + - - +
19A ARG* 1.3 76.6 - - - +
21A ARG* 1.3 73.6 + - - +
22A PHE 3.1 0.2 - - - -
23A PHE* 3.1 46.5 - - + +
24A LEU 4.6 0.3 + - - -
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Residues in contact with ARG 21 (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 SER* 4.2 10.1 - - - -
17A ASP* 2.8 28.7 + - - -
18A LEU* 3.0 50.0 - - + +
19A ARG 2.9 0.2 - - - -
20A ARG* 1.3 96.0 - - - +
22A PHE* 1.3 67.3 + - + +
24A LEU 5.0 0.5 + - - -
25A HIS* 3.9 9.9 + - - +
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Residues in contact with PHE 22 (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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18A LEU* 2.8 51.4 - - + -
19A ARG* 2.7 9.5 + - - +
21A ARG* 1.3 84.9 - - + +
23A PHE* 1.3 53.2 + - - +
24A LEU 3.2 1.8 - - - -
25A HIS* 2.4 31.2 + + + -
26A HIS* 2.4 49.7 + - + +
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Residues in contact with PHE 23 (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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19A ARG* 2.4 46.7 + - + -
20A ARG* 3.1 42.2 - - + +
21A ARG 3.4 0.2 - - - -
22A PHE* 1.3 71.3 - - - +
24A LEU* 1.3 75.4 + - + +
26A HIS* 3.3 4.4 + - - +
27A LEU* 3.2 31.4 + - + +
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Residues in contact with LEU 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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20A ARG 4.6 0.6 + - - -
21A ARG 5.0 0.6 + - - -
22A PHE 2.9 0.6 + - - -
23A PHE* 1.3 91.9 - - + +
25A HIS* 1.3 57.9 + - - +
26A HIS 3.0 2.7 - - - -
27A LEU* 4.4 11.7 - - + +
28A ILE* 2.6 51.0 + - + +
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Residues in contact with HIS 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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21A ARG 3.9 7.4 + - - +
22A PHE* 2.4 46.8 + + + +
24A LEU* 1.3 73.4 - - - +
26A HIS* 1.3 50.4 + - - -
28A ILE 4.2 0.7 - - - -
29A ALA* 2.5 70.3 + - + +
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Residues in contact with HIS 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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22A PHE* 2.4 40.6 + - + +
23A PHE* 3.6 5.8 - - - +
25A HIS* 1.3 67.2 + - - +
27A LEU* 1.3 70.4 + - + +
28A ILE 3.0 5.1 + - - -
29A ALA 4.9 2.4 + - - -
30A GLU* 2.7 52.0 + - + +
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Residues in contact with LEU 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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23A PHE* 3.2 24.2 + - + +
24A LEU* 4.3 10.3 - - + +
26A HIS* 1.3 83.0 - - + +
28A ILE* 1.3 77.5 + - + +
29A ALA 3.9 0.4 - - - -
30A GLU* 5.4 0.2 - - - -
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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