Contacts of the helix formed by residues 21 - 30 (chain E) in PDB entry 4OA5
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 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E VAL* 3.8 6.3 - - + +
20E ASP* 1.3 87.5 - - - +
22E GLU* 1.3 66.2 + - - +
23E GLY 4.5 2.5 - - - -
24E ALA* 3.5 19.2 + - - +
25E LEU* 3.2 19.8 + - - +
49E GLN* 6.2 1.3 - - - +
76E HIS* 3.8 28.6 + - + +
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Residues in contact with GLU 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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20E ASP 3.7 2.9 + - - -
21E THR* 1.3 71.5 - - - +
23E GLY* 1.3 57.9 + - - +
25E LEU* 3.3 8.9 + - - +
26E LYS* 2.9 50.7 + - - +
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Residues in contact with GLY 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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21E THR* 3.3 2.8 + - - -
22E GLU* 1.3 78.4 - - - +
24E ALA* 1.3 57.2 + - - +
26E LYS* 3.5 7.1 + - - +
27E ALA* 3.0 28.4 + - - +
76E HIS* 5.9 1.3 - - - -
100E ASN* 5.7 0.2 - - - +
103E ASN* 6.0 1.3 - - - -
104E CYS* 3.5 29.8 - - - -
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Residues in contact with ALA 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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19E VAL* 3.8 21.3 - - + -
21E THR* 3.4 21.2 + - - +
23E GLY* 1.3 74.4 - - - +
25E LEU* 1.3 63.0 + - - +
27E ALA* 3.2 4.3 + - - +
28E HIS 3.0 19.4 + - - -
69E PHE* 3.3 24.0 - - + -
72E ILE* 3.9 24.0 - - + +
73E CYS* 4.3 4.3 - - - +
76E HIS* 5.2 1.3 - - + +
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Residues in contact with LEU 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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19E VAL* 4.0 8.7 - - + +
20E ASP* 3.9 22.9 - - + +
21E THR 3.2 16.4 + - - +
22E GLU* 3.7 9.4 - - - +
24E ALA* 1.3 75.5 - - + +
26E LYS* 1.3 62.0 + - + +
28E HIS* 3.4 14.7 + - + +
29E LYS* 3.4 29.1 + - - +
36E ARG* 5.2 0.2 + - - -
42E THR* 3.6 31.0 - - + -
69E PHE* 5.0 0.2 - - - -
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Residues in contact with LYS 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 GLU* 2.9 33.8 + - - +
23E GLY* 3.8 6.3 - - - +
25E LEU* 1.3 73.1 - - + +
27E ALA* 1.3 66.5 + - - +
29E LYS* 3.1 19.8 + - - +
30E THR* 3.4 16.7 + - + +
100E ASN* 5.3 0.4 - - - -
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Residues in contact with ALA 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 GLY 3.0 18.5 + - - +
24E ALA* 3.2 5.6 + - - +
26E LYS* 1.3 75.3 - - - +
28E HIS* 1.3 63.9 + - - +
30E THR* 2.7 22.3 + - - -
39E GLN* 4.7 0.2 - - - -
67E VAL* 3.4 13.1 - - - +
69E PHE* 4.6 8.1 - - - -
72E ILE* 3.8 23.3 - - + -
100E ASN* 3.7 27.8 - - + +
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Residues in contact with HIS 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 ALA 3.0 12.5 + - - +
25E LEU* 3.5 12.8 - - + +
26E LYS 3.2 0.2 - - - -
27E ALA* 1.3 77.1 - - - +
29E LYS* 1.3 61.2 + - - +
30E THR 3.4 0.9 + - - -
31E ALA* 3.5 6.2 + - - +
36E ARG* 3.3 41.6 + - - +
39E GLN* 3.1 47.0 + - - +
40E LEU 3.0 28.0 + - - -
41E GLY* 4.4 6.2 - - - -
42E THR* 5.5 3.4 - - + -
69E PHE* 3.6 29.6 - + + -
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Residues in contact with LYS 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 LEU* 3.7 22.9 + - - +
26E LYS* 3.1 13.7 + - - +
28E HIS* 1.3 76.9 - - - +
30E THR* 1.3 60.2 + - + +
31E ALA 3.3 5.5 + - - +
36E ARG* 3.5 30.8 + - - +
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Residues in contact with THR 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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26E LYS* 3.4 15.7 - - + +
27E ALA 2.7 17.3 + - - +
29E LYS* 1.3 75.1 - - + +
31E ALA* 1.3 65.6 + - - +
32E PRO* 3.6 3.3 - - - +
67E VAL* 3.4 9.2 - - - +
96E THR* 3.5 16.7 - - + +
100E ASN* 2.9 31.8 + - - +
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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