Contacts of the helix formed by residues 23 - 32 (chain E) in PDB entry 4I6U
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 THR 23 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 4.2 16.4 - - - +
17C ARG* 4.6 7.4 - - - +
18C LEU* 4.0 23.1 - - + -
17E ARG* 3.7 9.5 - - - +
21E GLY 4.0 0.2 + - - -
22E MET* 1.3 77.0 - - - +
24E GLN* 1.3 63.8 + - - +
25E GLU* 3.4 23.0 + - - +
26E ASP* 2.9 39.6 + - - +
27E LEU 3.0 18.9 + - - -
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Residues in contact with GLN 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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14E LYS* 5.6 1.0 - - - +
17E ARG* 3.6 29.8 - - - +
23E THR* 1.3 73.1 - - - +
25E GLU* 1.3 65.4 + - - +
27E LEU* 3.3 3.1 + - - +
28E ALA* 2.9 28.4 + - - +
35E ARG* 4.1 19.1 + - + +
38E ILE* 4.1 15.6 - - + +
39E SER* 3.5 38.7 + - - +
42E GLU* 2.9 24.7 + - - +
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Residues in contact with GLU 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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23E THR* 3.5 17.9 + - - +
24E GLN* 1.3 89.5 + - - +
26E ASP* 1.4 64.6 + - - +
28E ALA* 3.1 5.1 + - - +
29E TYR* 2.9 50.8 + - + +
35E ARG* 3.2 34.3 - - + -
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Residues in contact with ASP 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 4.5 5.9 + - - -
21E GLY 4.4 2.6 - - - +
22E MET* 3.6 21.6 - - + +
23E THR* 2.9 50.4 + - - +
25E GLU* 1.4 71.4 - - - +
27E LEU* 1.3 63.6 + - - +
29E TYR* 3.4 17.8 + - - +
30E LYS* 3.2 29.2 + - + +
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Residues in contact with LEU 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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13E ILE* 4.1 22.4 - - + -
17E ARG* 4.0 21.3 - - + -
22E MET* 3.7 10.9 - - + +
23E THR 3.0 12.0 + - - +
24E GLN 3.8 6.1 - - - +
25E GLU 3.2 0.2 - - - -
26E ASP* 1.3 76.5 - - - +
28E ALA* 1.3 58.7 + - - +
30E LYS* 3.3 1.1 + - - -
31E SER* 2.8 56.5 + - - +
38E ILE* 4.1 25.4 - - + -
56E ILE* 4.0 6.1 - - + +
59E GLY 3.9 4.5 - - - -
60E LEU* 3.8 39.3 - - + +
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Residues in contact with ALA 28 (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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24E GLN 2.9 17.2 + - - +
25E GLU* 3.4 7.9 - - - +
27E LEU* 1.3 73.9 - - - +
29E TYR* 1.3 66.0 + - + +
31E SER* 4.7 0.4 - - - -
32E ASN* 2.9 20.1 + - - -
33E LEU 3.0 29.6 + - - +
34E ASP 4.0 1.6 - - - -
35E ARG* 3.8 23.6 - - + +
38E ILE* 4.0 10.5 - - + +
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Residues in contact with TYR 29 (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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25E GLU* 2.9 44.1 + - + +
26E ASP* 3.7 18.4 - - - +
28E ALA* 1.3 81.6 - - + +
30E LYS* 1.3 64.6 + - + +
31E SER 3.4 0.2 + - - -
32E ASN* 3.4 19.3 + - - +
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Residues in contact with LYS 30 (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 MET* 4.5 10.1 - - + -
26E ASP* 3.2 18.2 + - - +
27E LEU* 4.0 1.8 - - - +
29E TYR* 1.3 79.5 - - + +
31E SER* 1.3 59.4 + - - +
32E ASN* 3.4 6.1 + - - -
55E LEU 4.6 0.2 - - - +
58E LYS* 4.9 2.3 - - - +
59E GLY* 3.7 36.7 + - - +
61E GLU* 2.8 28.7 + - + +
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Residues in contact with SER 31 (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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27E LEU* 2.8 39.3 + - - +
28E ALA* 4.1 2.2 - - - -
30E LYS* 1.3 76.0 - - - +
32E ASN* 1.3 70.9 + - - +
33E LEU* 3.4 20.0 + - - +
38E ILE* 5.0 0.7 - - - -
55E LEU* 3.4 50.5 + - - +
56E ILE* 3.4 6.4 - - - +
59E GLY* 3.7 1.6 - - - -
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Residues in contact with ASN 32 (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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28E ALA 2.9 7.0 + - - -
29E TYR* 3.4 13.6 + - - +
30E LYS 4.6 4.9 + - - -
31E SER* 1.3 82.5 - - - +
33E LEU* 1.3 64.4 + - - +
55E LEU* 5.3 9.5 - - + +
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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