Contacts of the helix formed by residues 13 - 24 (chain A) in PDB entry 1ZIO
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 LYS 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.5 30.2 - - + +
6A MET* 4.3 2.0 - - - -
7A GLY* 3.1 46.3 + - - +
8A LEU 3.5 9.3 + - - -
11A ALA* 4.9 0.9 - - + -
12A GLY* 1.3 78.9 - - - +
14A GLY* 1.3 59.0 + - - +
16A GLN 3.5 0.2 + - - -
17A ALA* 2.8 31.4 + - - +
84A ASP* 3.3 25.8 - - - +
85A GLY* 4.2 11.7 - - - +
88A ARG* 4.5 1.1 - - - +
113A ILE* 4.4 13.2 - - + -
218A AP5 2.9 57.3 + - - +
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Residues in contact with GLY 14 (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* 1.3 73.0 - - - +
15A THR* 1.3 60.1 + - - +
17A ALA* 3.7 3.3 - - - +
18A GLU* 3.0 37.6 + - - +
28A HIS* 4.6 4.9 - - - -
84A ASP* 3.9 11.8 + - - -
218A AP5 3.0 20.1 + - - -
220A MG 4.4 3.1 - - - -
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Residues in contact with THR 15 (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 GLY 3.7 5.4 - - - -
13A LYS 3.4 0.2 - - - -
14A GLY* 1.3 75.5 - - - +
16A GLN* 1.3 74.0 + - - +
18A GLU* 3.6 5.6 + - - +
19A LYS* 3.4 24.2 + - - +
201A MET* 3.4 42.4 - - + -
218A AP5 2.7 47.3 + - - +
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Residues in contact with GLN 16 (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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5A LEU* 4.5 7.2 - - + -
12A GLY* 3.1 17.7 + - - +
13A LYS 3.9 1.8 - - - +
15A THR* 1.3 90.9 - - - +
17A ALA* 1.3 64.8 + - - +
19A LYS* 3.0 8.9 + - - +
20A ILE* 2.9 26.7 + - - +
113A ILE* 4.3 7.9 - - + -
201A MET* 3.2 25.1 + - - +
204A VAL* 3.6 29.7 - - + +
205A PHE* 3.3 33.5 - - - +
208A ILE* 3.9 18.3 - - + +
218A AP5 5.4 3.0 + - - -
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Residues in contact with ALA 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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5A LEU* 3.8 16.8 - - + +
13A LYS 2.8 22.4 + - - +
14A GLY 3.3 1.8 + - - +
16A GLN* 1.3 72.7 - - - +
18A GLU* 1.3 63.3 + - - +
20A ILE* 3.1 6.4 + - - +
21A VAL* 3.0 31.1 + - - +
28A HIS* 3.3 39.3 - - + +
82A LEU* 4.1 5.6 - - + -
84A ASP* 4.2 0.4 - - - +
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Residues in contact with GLU 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 GLY 3.0 19.7 + - - +
15A THR* 3.8 7.2 - - - +
16A GLN 3.2 0.2 - - - -
17A ALA* 1.3 75.8 - - - +
19A LYS* 1.3 62.6 + - + +
21A VAL* 3.6 14.8 - - - +
22A ALA* 3.3 24.4 + - - +
28A HIS* 3.0 32.3 + - + +
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Residues in contact with LYS 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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15A THR 3.4 13.0 + - - +
16A GLN* 3.0 16.5 + - - +
18A GLU* 1.3 77.6 - - + +
20A ILE* 1.3 63.7 + - - +
22A ALA* 3.5 6.0 + - - +
23A ALA* 3.4 15.9 + - - +
201A MET* 3.7 34.3 - - - +
202A GLU* 2.8 36.5 + - - -
205A PHE* 3.7 51.3 - - + -
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Residues in contact with ILE 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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1A MET* 5.0 0.2 - - + -
3A LEU* 4.6 6.1 - - + -
5A LEU* 4.2 23.6 - - + -
16A GLN 2.9 22.8 + - - +
17A ALA* 3.6 7.0 - - - +
19A LYS* 1.3 77.2 - - - +
21A VAL* 1.3 63.4 + - + +
23A ALA* 3.1 3.9 + - - +
24A TYR* 3.1 41.6 + - + +
26A ILE* 4.8 8.5 - - + -
82A LEU* 4.5 18.4 - - + -
111A ILE* 5.1 2.7 - - + -
205A PHE* 4.0 19.5 - - + -
208A ILE* 3.9 30.3 - - + -
212A LEU* 4.6 11.9 - - + -
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Residues in contact with VAL 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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17A ALA 3.0 19.6 + - - +
18A GLU* 3.6 22.7 - - - +
20A ILE* 1.3 74.6 - - + +
22A ALA* 1.3 61.6 + - + +
25A GLY* 2.7 32.7 + - - +
26A ILE* 3.3 35.9 - - + +
27A PRO 4.3 0.2 - - - -
28A HIS* 3.8 28.9 - - + +
82A LEU* 4.4 10.8 - - + -
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Residues in contact with ALA 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 GLU 3.3 19.9 + - - +
19A LYS* 3.8 7.0 - - - +
20A ILE 3.2 0.4 - - - -
21A VAL* 1.3 79.1 - - - +
23A ALA* 1.3 59.9 + - - +
25A GLY* 4.5 1.1 + - - -
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Residues in contact with ALA 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 LYS 3.4 10.2 + - - +
20A ILE 3.1 9.5 + - - +
22A ALA* 1.3 81.7 - - - +
24A TYR* 1.3 68.0 + - + +
205A PHE* 4.5 5.4 - - + -
209A ARG* 3.1 36.9 + - - +
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Residues in contact with TYR 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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1A MET* 3.7 34.8 - - + -
20A ILE* 3.1 25.1 + - + +
23A ALA* 1.3 85.2 - - + +
25A GLY* 1.3 63.0 + - - +
26A ILE* 3.6 18.1 + - + +
205A PHE* 5.9 0.9 - + - -
209A ARG* 3.4 33.2 + - + -
212A LEU* 3.5 40.8 + - + +
213A GLY* 5.5 0.5 - - - -
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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