Contacts of the helix formed by residues 15 - 25 (chain E) in PDB entry 3ZWG
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 GLY 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E GLY 3.3 6.0 + - - -
14E LEU* 1.3 75.2 - - - +
16E PHE* 1.3 67.5 + - - -
17E ASP* 3.1 4.7 + - - -
18E VAL* 3.4 12.4 + - - +
19E LEU* 3.4 17.4 + - - +
173E GLU* 4.2 13.2 - - - -
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Residues in contact with PHE 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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15E GLY* 1.3 74.1 - - - -
17E ASP* 1.3 85.0 + - + +
19E LEU* 3.8 4.3 - - - +
20E LYS* 2.7 39.4 + - + +
171E ILE* 4.6 4.7 - - + +
173E GLU* 4.1 3.6 + - - -
2F ALA* 5.5 1.1 - - + -
4F VAL* 3.1 33.2 - - + -
5F ALA* 3.9 6.5 - - + -
6F GLY* 2.9 55.9 - - - -
7F ALA* 3.4 8.1 - - + -
59F ILE* 4.4 13.0 - - + -
60F VAL* 3.8 37.0 - - + +
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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
----------------------------------------------------------
15E GLY* 3.1 1.6 - - - -
16E PHE* 1.3 98.8 - - + +
18E VAL* 1.3 68.0 + - + +
20E LYS* 3.7 7.5 - - - +
21E THR* 3.1 36.6 + - - +
2F ALA* 4.3 9.5 - - + +
4F VAL* 3.7 32.0 - - - +
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Residues in contact with VAL 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ASP* 3.6 20.0 - - + +
9E ILE* 4.7 6.1 - - + -
13E GLY 3.3 27.1 - - - +
14E LEU* 5.1 1.3 - - + -
15E GLY* 3.4 10.5 + - - +
16E PHE 3.4 0.4 - - - -
17E ASP* 1.3 79.0 - - + +
19E LEU* 1.3 59.4 + - + +
21E THR* 3.1 8.3 + - - -
22E VAL* 3.1 25.3 + - - +
72E LEU* 3.4 38.1 - - + -
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Residues in contact with LEU 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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14E LEU* 3.9 18.6 - - + -
15E GLY 3.4 15.7 + - - +
16E PHE* 3.4 6.5 + - - +
17E ASP 3.2 0.2 - - - -
18E VAL* 1.3 79.5 - - - +
20E LYS* 1.3 66.6 + - - +
21E THR 3.2 0.2 - - - -
22E VAL* 3.2 7.4 + - + +
23E LEU* 3.0 24.4 + - - +
34E ALA* 3.6 13.0 - - + +
35E VAL 3.8 9.9 - - - +
36E GLY* 3.7 21.8 - - - +
72E LEU* 4.7 9.4 - - + -
171E ILE* 3.7 32.8 - - + -
172E LEU 3.9 7.2 - - - +
173E GLU* 3.8 27.1 - - + +
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Residues in contact with LYS 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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16E PHE* 2.7 29.3 + - + +
17E ASP* 3.7 13.9 - - - +
19E LEU* 1.3 75.9 - - - +
21E THR* 1.3 64.8 + - + +
23E LEU* 3.2 11.4 + - + +
24E GLU* 3.2 48.5 + - + +
171E ILE* 4.1 17.5 - - + +
58F ASP* 5.2 14.1 - - + +
59F ILE* 4.8 15.8 - - - +
74F ASN* 6.0 1.0 - - - +
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Residues in contact with THR 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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3E ASP* 4.3 12.6 + - - +
17E ASP* 3.1 23.7 + - - +
18E VAL* 3.1 11.3 + - - -
19E LEU 3.2 0.4 - - - -
20E LYS* 1.3 77.7 - - + +
22E VAL* 1.3 68.6 + - - +
23E LEU 3.0 2.0 - - - -
24E GLU* 3.2 13.1 + - - +
25E ALA* 3.0 25.9 + - - +
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Residues in contact with VAL 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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3E ASP 3.9 16.6 - - - +
4E VAL* 4.3 16.2 - - - +
5E ALA* 4.3 7.4 - - + +
18E VAL 3.1 20.9 + - - +
19E LEU* 3.4 12.3 - - + +
21E THR* 1.3 83.0 + - - +
23E LEU* 1.3 59.4 + - - +
25E ALA* 3.7 14.9 + - - +
26E LEU* 4.0 11.1 + - - +
34E ALA* 3.5 19.3 - - + -
35E VAL 5.2 0.2 - - - +
72E LEU* 4.4 14.8 - - + -
73E TYR 3.9 15.7 - - - +
74E ASN* 4.0 16.4 + - + +
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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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19E LEU 3.0 11.8 + - - +
20E LYS* 3.3 16.4 - - + +
21E THR 3.0 0.2 - - - -
22E VAL* 1.3 77.2 - - - +
24E GLU* 1.3 64.2 + - + +
25E ALA 3.3 0.2 - - - -
26E LEU* 3.4 13.7 - - + +
32E LYS* 2.8 53.7 + - + +
33E ILE 3.9 2.7 - - - -
34E ALA* 3.7 28.9 - - + +
169E HIS* 3.8 31.6 - - + +
170E ALA 3.7 9.2 - - - +
171E ILE* 4.2 13.7 - - + -
58F ASP* 4.7 5.2 - - - +
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Residues in contact with GLU 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 LYS* 3.2 44.7 + - + +
21E THR* 3.2 13.9 + - - +
23E LEU* 1.3 75.4 - - + +
25E ALA* 1.3 62.9 - - - +
26E LEU 3.0 6.6 + - - -
27E GLY* 3.1 14.9 + - - +
32E LYS* 3.9 7.6 - - - +
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Residues in contact with ALA 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 THR 3.0 16.2 + - - +
22E VAL* 3.8 10.3 - - - +
23E LEU 3.3 0.4 - - - -
24E GLU* 1.3 77.2 - - - +
26E LEU* 1.3 56.0 + - - +
27E GLY* 3.0 5.5 + - - -
74E ASN* 6.2 0.7 - - - +
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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