Contacts of the helix formed by residues 17 - 27 (chain E) in PDB entry 3KZ1
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 17 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E ALA 3.3 0.6 - - - -
16E CYS* 1.3 79.5 - - - +
18E LYS* 1.3 65.7 + - - +
20E CYS* 4.1 1.5 - - - +
21E LEU* 3.3 21.7 + - - +
117E ASN* 3.6 12.4 + - - -
161E ALA* 5.5 1.4 - - - +
538E GSP 3.0 42.1 + - - -
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Residues in contact with LYS 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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10E ILE* 4.0 23.6 - - + +
11E VAL* 3.4 33.7 - - - +
12E GLY 2.8 27.8 + - - +
13E ASP 3.1 8.3 + - - -
16E CYS* 3.9 12.1 - - - -
17E GLY* 1.3 74.1 - - - +
19E THR* 1.3 68.0 + - - +
20E CYS 3.1 1.3 - - - -
21E LEU* 2.9 14.4 + - - +
22E LEU* 3.0 16.7 + - - +
59E ASP* 4.1 8.1 - - - +
60E THR* 3.6 21.3 - - - -
61E ALA 4.5 0.2 - - - -
62E GLY* 3.7 2.9 - - - +
83E CYS* 4.3 4.7 - - + -
117E ASN* 4.8 0.9 - - - +
538E GSP 2.8 49.1 + - - +
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Residues in contact with THR 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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18E LYS* 1.3 75.3 - - - +
20E CYS* 1.3 64.9 + - - +
22E LEU* 3.2 5.0 + - - +
23E ILE* 3.0 36.1 + - + +
31E PRO* 6.2 1.1 - - + -
35E VAL 4.7 4.4 + - - +
37E THR* 2.5 8.1 + - + +
40E GLU* 5.6 0.7 - - + -
42E TYR* 3.7 19.7 - - + +
59E ASP* 2.9 20.4 + - - +
538E GSP 2.8 14.3 + - - -
550E MG 2.0 35.0 - - - -
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Residues in contact with CYS 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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17E GLY 4.1 2.5 - - - +
19E THR* 1.3 75.6 - - - +
21E LEU* 1.3 63.3 + - - +
23E ILE* 3.3 1.0 + - - +
24E VAL* 3.1 30.0 + - - +
30E PHE* 3.8 21.5 - - + -
31E PRO* 3.9 26.0 - - - -
33E VAL 5.8 1.6 - - - -
34E TYR* 6.5 0.2 - - - -
161E ALA* 4.5 3.1 - - + -
538E GSP 2.9 67.0 + - + +
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Residues in contact with LEU 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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10E ILE* 3.9 21.5 - - + -
17E GLY 3.3 12.9 + - - +
18E LYS* 2.9 9.7 + - - +
20E CYS* 1.3 82.2 - - - +
22E LEU* 1.3 62.5 + - - +
24E VAL* 3.6 2.0 + - - +
25E PHE* 3.3 21.0 + - - +
81E LEU* 4.7 2.2 - - + -
83E CYS* 4.2 6.5 - - - -
115E VAL* 4.6 2.2 - - + -
117E ASN* 4.1 13.9 - - - +
159E CYS* 3.7 25.1 - - - -
161E ALA* 4.5 13.4 - - + +
167E VAL* 4.0 21.2 - - + +
170E VAL* 4.2 21.3 - - + -
171E PHE* 4.0 14.8 - - + -
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Residues in contact with LEU 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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8E LEU* 5.1 2.0 - - + -
10E ILE* 3.5 50.7 - - + -
18E LYS 3.0 6.6 + - - +
19E THR* 3.5 8.1 - - - +
21E LEU* 1.3 77.9 - - - +
23E ILE* 1.3 60.5 + - - +
25E PHE* 3.6 2.3 + - - +
26E SER* 2.9 29.0 + - - -
42E TYR* 4.2 17.9 - - + -
57E LEU* 4.1 25.0 - - + +
58E TRP 4.4 0.4 - - - -
59E ASP* 3.7 31.9 - - + +
81E LEU* 4.9 1.6 - - + -
171E PHE* 4.2 22.2 - - + -
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Residues in contact with ILE 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 THR* 3.0 27.4 + - + +
20E CYS 3.3 2.9 + - - +
22E LEU* 1.3 75.3 - - - +
24E VAL* 1.3 59.2 + - - +
26E SER* 3.8 3.4 - - - +
27E LYS* 2.7 56.0 + - + +
28E ASP 3.1 3.8 + - - -
29E GLN* 3.4 22.7 - - + +
31E PRO* 4.1 22.2 - - + -
42E TYR* 3.5 45.8 - - + +
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Residues in contact with VAL 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 CYS 3.1 17.6 + - - +
21E LEU 4.3 2.0 - - - +
23E ILE* 1.3 76.5 - - - +
25E PHE* 1.3 59.1 + - - +
28E ASP* 3.1 29.5 - - - +
29E GLN 3.8 2.7 - - - +
30E PHE* 3.6 38.6 - - + +
31E PRO* 4.4 0.9 - - + -
161E ALA* 3.8 25.6 - - + +
164E LYS* 3.9 33.0 - - + +
167E VAL* 4.5 11.9 - - + -
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Residues in contact with PHE 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 LEU 3.3 8.7 + - - +
22E LEU 3.9 2.0 - - - +
23E ILE 3.2 0.2 - - - -
24E VAL* 1.3 82.1 - - - +
26E SER* 1.3 63.6 + - - +
28E ASP* 4.2 5.4 + - - +
44E ALA* 3.6 26.9 - - + +
45E ASP 5.0 3.1 - - - -
46E ILE* 3.8 31.6 - - + -
55E LEU* 3.8 8.7 - - + -
57E LEU* 4.5 4.5 - - + -
167E VAL* 4.4 9.1 - - + +
168E ARG* 4.8 19.5 - - + -
171E PHE* 3.5 67.3 - + + -
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Residues in contact with SER 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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22E LEU 2.9 20.0 + - - -
23E ILE* 3.6 5.2 + - - +
25E PHE* 1.3 78.8 - - - +
27E LYS* 1.3 72.9 + - - +
28E ASP* 5.3 0.3 - - - +
42E TYR* 4.5 10.6 - - - +
43E VAL 3.7 23.6 - - - +
44E ALA* 4.0 15.8 - - - +
57E LEU* 4.0 8.4 - - - +
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Residues in contact with LYS 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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23E ILE* 2.7 42.3 + - + +
26E SER* 1.3 81.2 + - - +
28E ASP* 1.3 68.3 + - - +
29E GLN* 3.3 26.5 + - + +
42E TYR* 4.3 26.0 - - - -
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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