Contacts of the helix formed by residues 15 - 27 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E VAL* 5.0 0.6 - - - +
13E GLN* 2.8 31.7 + - - +
14E GLN* 1.3 69.4 - - - +
16E LEU* 1.3 59.2 + - - +
17E ASP* 2.8 13.2 + - - +
18E ILE* 2.9 43.9 + - - +
19E GLN* 3.6 7.1 + - - +
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 4.0 24.0 - - + +
8E ARG* 4.1 11.0 - - - +
9E VAL* 3.9 29.7 - - + +
14E GLN* 2.7 16.6 + - + +
15E SER* 1.3 71.9 - - - +
17E ASP* 1.3 61.0 + - - +
19E GLN* 3.4 9.7 + - - +
20E VAL* 3.0 37.4 + - + +
35E THR* 3.5 33.4 - - + +
36E ASP 4.7 0.7 - - - +
37E LYS* 5.5 8.5 - - + -
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Residues in contact with ASP 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLN 5.2 2.7 - - - +
15E SER* 2.8 4.6 + - - +
16E LEU* 1.3 77.8 - - - +
18E ILE* 1.3 57.4 + - + +
20E VAL* 3.0 7.6 + - - +
21E ARG* 2.6 61.1 + - + +
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Residues in contact with ILE 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E SER* 2.9 33.8 + - - +
17E ASP* 1.3 73.6 - - + +
19E GLN* 1.3 59.0 + - + +
21E ARG* 3.4 18.1 - - - +
22E ALA* 2.9 28.2 + - - +
64E LYS* 4.2 22.2 - - - +
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Residues in contact with GLN 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E TYR 4.0 4.2 - - - +
7E ALA* 3.2 31.6 - - + +
8E ARG 2.5 38.5 + - - +
9E VAL* 5.1 0.4 - - - +
15E SER 3.6 6.1 + - - +
16E LEU* 3.4 12.5 + - - +
17E ASP 3.1 0.6 - - - -
18E ILE* 1.3 77.7 - - + +
20E VAL* 1.3 59.5 + - - +
22E ALA* 3.1 4.9 + - - +
23E LEU* 2.9 34.0 + - + +
64E LYS* 4.1 30.5 + - + +
68E ARG* 3.7 25.8 - - - +
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Residues in contact with VAL 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA* 4.5 9.6 - - + -
16E LEU* 3.0 24.6 + - + +
17E ASP* 3.8 6.1 - - - +
19E GLN* 1.3 74.8 - - - +
21E ARG* 1.3 59.6 + - - +
23E LEU* 3.6 8.7 + - - +
24E LYS* 3.1 48.5 + - - +
30E ALA* 6.2 0.2 - - + -
33E ILE* 4.3 18.4 - - + -
35E THR* 4.4 16.6 - - - +
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Residues in contact with ARG 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ASP* 2.6 42.5 + - + +
18E ILE* 3.4 16.0 - - - +
20E VAL* 1.3 70.4 - - - +
22E ALA* 1.3 57.0 + - - +
24E LYS* 3.0 7.4 + - + +
25E ASP* 2.8 45.7 + - - +
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ILE* 2.9 15.1 + - + +
19E GLN 3.3 9.2 - - - +
21E ARG* 1.3 74.3 - - - +
23E LEU* 1.3 56.9 + - - +
25E ASP* 3.4 8.4 - - - +
26E ALA* 2.9 30.2 + - - +
64E LYS* 4.0 32.1 - - + +
93E ILE* 5.6 10.0 - - + +
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Residues in contact with LEU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E GLY* 3.6 13.0 - - - -
6E TYR 3.4 31.6 - - - +
7E ALA* 4.5 2.7 - - + +
19E GLN* 2.9 20.8 + - + +
20E VAL* 3.8 8.7 - - - +
21E ARG 3.2 0.2 - - - -
22E ALA* 1.3 73.2 - - + +
24E LYS* 1.3 65.8 + - - +
26E ALA* 3.2 6.4 + - - +
27E GLY 3.1 15.6 + - - -
28E VAL* 3.2 18.3 - - + +
33E ILE* 3.9 24.9 - - + -
62E LEU* 3.5 42.0 - - + +
63E VAL* 4.3 5.4 - - - +
64E LYS* 5.1 4.7 - - + +
93E ILE* 5.5 4.5 - - + -
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Residues in contact with LYS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E VAL* 3.1 38.5 + - - +
21E ARG* 3.0 7.1 + - - +
23E LEU* 1.3 73.1 - - - +
25E ASP* 1.3 58.7 + - - +
27E GLY* 2.7 25.6 + - - -
28E VAL 3.6 21.6 + - - +
30E ALA* 3.8 29.3 - - - +
33E ILE* 3.8 7.2 - - + -
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Residues in contact with ASP 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ARG* 2.8 27.3 + - - +
22E ALA* 3.4 8.4 - - - +
24E LYS* 1.3 80.0 - - - +
26E ALA* 1.3 59.7 + - - +
27E GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.9 5.9 - - - +
22E ALA 2.9 17.7 + - - +
23E LEU* 3.4 7.9 - - - +
24E LYS 3.2 0.2 - - - -
25E ASP* 1.3 75.2 - - - +
27E GLY* 1.3 58.3 + - - +
28E VAL* 5.1 0.4 - - - -
62E LEU* 4.0 24.3 - - + +
91E ARG* 5.5 3.2 + - - +
93E ILE* 4.2 16.2 - - + -
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Residues in contact with GLY 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 3.6 18.2 - - - +
23E LEU 3.1 0.4 + - - -
24E LYS 2.7 13.5 + - - -
25E ASP 3.1 1.5 - - - -
26E ALA* 1.3 81.1 - - - +
28E VAL* 1.3 63.5 + - - +
29E LYS* 4.2 4.2 + - - +
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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