Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 1ZR4
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 15 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLN* 2.8 32.1 + - - +
14D GLN* 1.3 69.0 - - - +
16D LEU* 1.3 55.6 + - - +
17D ASP* 2.9 15.2 + - - +
18D ILE* 3.0 43.7 + - - +
19D GLN* 3.5 9.4 + - - +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 4.1 20.0 - - + -
8D ARG 4.1 10.1 - - - +
9D VAL* 3.9 30.4 - - + +
14D GLN* 2.7 14.1 + - + +
15D SER* 1.3 75.3 - - - +
17D ASP* 1.3 59.1 + - - +
19D GLN* 3.6 11.6 - - - +
20D VAL* 3.1 33.9 + - + +
35D THR* 3.8 32.3 - - + +
36D ASP 4.3 1.1 - - - +
37D LYS* 5.6 8.1 - - + -
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Residues in contact with ASP 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLN 5.0 4.0 - - - +
15D SER* 2.9 4.9 - - - -
16D LEU* 1.3 75.4 - - - +
18D ILE* 1.3 56.9 + - + +
19D GLN 3.0 1.6 - - - -
20D VAL* 2.7 9.4 + - - +
21D ARG* 2.6 53.8 + - + +
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D SER* 3.0 29.9 + - - +
17D ASP* 1.3 77.1 - - + +
19D GLN* 1.3 58.0 + - + +
21D ARG* 3.3 20.0 + - - +
22D ALA* 2.9 29.5 + - + +
64D LYS* 4.5 20.9 - - - +
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D TYR 4.1 3.1 - - - +
7D ALA* 3.3 30.4 - - + +
8D ARG 2.5 37.1 + - - +
9D VAL* 5.1 0.6 - - - +
15D SER 3.5 8.6 + - - +
16D LEU* 3.6 12.8 - - - +
17D ASP 3.0 0.6 - - - -
18D ILE* 1.3 77.3 - - + +
20D VAL* 1.3 56.5 + - - +
22D ALA* 3.2 8.8 + - - +
23D LEU* 2.9 32.8 + - + +
64D LYS* 4.0 34.2 - - + +
68D ARG* 3.9 19.5 - - - +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ALA* 4.3 12.3 - - + -
16D LEU* 3.1 21.7 + - + +
17D ASP* 2.7 12.4 + - - +
19D GLN* 1.3 71.3 - - - +
21D ARG* 1.3 59.9 + - - +
23D LEU* 3.9 5.8 - - - -
24D LYS* 3.0 44.4 + - - +
33D ILE* 3.8 36.1 - - + -
35D THR* 4.6 8.5 - - - +
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASP* 2.6 36.5 + - + +
18D ILE* 3.5 18.4 - - - +
20D VAL* 1.3 72.9 - - - +
22D ALA* 1.3 51.5 + - - +
24D LYS* 3.2 10.2 + - - +
25D ASP* 2.7 50.6 + - - +
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Residues in contact with ALA 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 2.9 15.2 + - + +
19D GLN* 3.2 12.8 + - - +
21D ARG* 1.3 76.6 - - - +
23D LEU* 1.3 56.5 + - + +
25D ASP* 3.4 10.1 + - - +
26D ALA* 2.9 29.5 + - - +
64D LYS* 5.0 18.8 - - + +
93D ILE* 4.5 11.3 - - + +
94D ASP* 6.1 0.2 - - - +
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLY* 3.7 16.4 - - - -
6D TYR 3.4 33.0 - - - +
7D ALA* 4.3 7.4 - - + +
19D GLN* 2.9 19.7 + - + +
20D VAL* 3.9 3.4 - - - +
21D ARG 3.3 0.4 - - - -
22D ALA* 1.3 74.1 - - + +
24D LYS* 1.3 58.8 + - - +
26D ALA* 4.0 3.1 - - - +
27D GLY 3.7 2.1 + - - -
28D VAL* 3.0 35.0 + - + +
33D ILE* 3.7 34.3 - - + -
62D LEU* 3.8 28.7 - - + +
63D VAL* 4.5 4.7 - - - +
64D LYS* 5.2 3.8 - - + +
93D ILE* 4.6 10.1 - - + -
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D VAL* 3.0 37.6 + - - +
21D ARG* 3.7 8.9 - - - +
23D LEU* 1.3 73.4 - - - +
25D ASP* 1.3 65.2 + - - +
26D ALA 3.1 4.9 - - - -
27D GLY* 3.1 13.7 + - - -
28D VAL 3.9 12.4 + - - +
30D ALA* 4.3 22.9 - - + +
33D ILE* 3.7 13.0 - - + -
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Residues in contact with ASP 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 2.7 35.8 + - - +
22D ALA* 3.4 9.7 + - - +
24D LYS* 1.3 74.1 - - - +
26D ALA* 1.3 58.8 + - - +
27D GLY 3.3 0.4 - - - -
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 4.6 8.8 - - - +
22D ALA 2.9 16.8 + - - +
23D LEU* 4.0 6.1 - - - +
24D LYS 3.1 0.6 - - - -
25D ASP* 1.3 78.0 - - - +
27D GLY* 1.3 58.4 + - - +
28D VAL* 3.8 0.9 - - - -
62D LEU* 3.7 26.5 - - + +
91D ARG* 5.9 0.5 + - - -
93D ILE* 4.3 10.8 - - + -
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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