Contacts of the helix formed by residues 24 - 35 (chain E) in PDB entry 1R8Y
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 24 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E TYR* 3.2 13.2 + - - -
22E ALA 3.7 0.2 - - - -
23E ASP* 1.3 81.7 + - - +
25E GLU* 1.3 68.1 + - - +
26E ALA 3.4 2.5 - - - -
27E ALA 3.4 3.4 + - - -
28E ARG* 3.1 20.4 + - - +
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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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24E GLY* 1.3 66.1 - - - -
26E ALA* 1.3 68.2 + - - +
28E ARG* 3.0 18.8 + - - +
29E VAL* 3.0 15.0 + - - +
235E PHE 3.6 7.1 - - - +
236E SER* 2.6 36.1 + - - +
237E LYS* 3.4 27.0 + - - +
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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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24E GLY 3.4 0.4 - - - -
25E GLU* 1.3 80.9 - - - +
27E ALA* 1.3 59.4 + - - +
29E VAL* 3.1 4.2 + - - +
30E TRP* 2.8 29.5 + - - +
237E LYS 3.8 22.4 - - - +
238E PHE* 3.9 4.7 - - + +
9F SER* 3.9 27.6 - - - -
10F LEU 4.3 8.1 - - - +
12F VAL* 5.0 0.2 - - - -
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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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21E TYR 3.8 15.7 - - - +
22E ALA* 3.8 22.0 - - - +
24E GLY 3.4 5.2 + - - +
25E GLU 3.2 0.4 - - - -
26E ALA* 1.3 78.9 - - - +
28E ARG* 1.3 63.5 + - - +
30E TRP* 3.2 10.0 + - + +
31E GLN* 2.9 28.0 + - + +
89E LYS* 4.7 2.9 - - - +
10F LEU 4.5 2.5 + - - +
11F GLY* 3.7 28.3 - - - +
12F VAL* 4.9 0.4 - - - -
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Residues in contact with ARG 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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22E ALA 5.0 1.0 + - - -
23E ASP* 3.0 43.5 + - - +
24E GLY 3.1 10.6 + - - +
25E GLU* 3.0 11.3 + - - +
27E ALA* 1.3 76.1 - - - +
29E VAL* 1.3 62.4 + - + +
31E GLN* 3.2 31.3 + - - +
32E LEU* 3.5 13.7 + - + +
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Residues in contact with VAL 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 3.0 20.2 + - - +
26E ALA* 3.4 9.2 - - - +
28E ARG* 1.3 74.7 - - - +
30E TRP* 1.3 63.1 + - - +
32E LEU* 2.9 27.6 + - + +
33E TYR* 3.0 10.9 + - - +
222E VAL* 3.6 37.9 - - + +
224E VAL* 4.7 4.5 - - + -
236E SER* 3.2 41.7 - - - +
237E LYS 4.4 2.2 - - - +
238E PHE* 4.1 10.0 - - + -
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Residues in contact with TRP 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 ALA 2.8 16.3 + - - +
27E ALA 3.2 8.7 + - - +
29E VAL* 1.3 77.8 - - - +
31E GLN* 1.3 75.1 + - - +
33E TYR* 3.1 9.6 + + - +
34E ILE* 3.0 64.2 + - + +
89E LYS* 3.1 41.1 - - + -
90E MET* 4.2 13.0 - - + +
93E TYR* 5.7 0.4 - + - -
238E PHE* 4.0 29.3 - + + -
240E LEU* 4.5 6.9 - - + +
11F GLY 4.3 2.7 - - - -
12F VAL* 3.5 27.8 - - + +
13F ALA* 3.5 42.9 + - + -
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Residues in contact with GLN 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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22E ALA 5.0 9.9 + - - +
27E ALA* 2.9 21.1 + - - +
28E ARG* 3.2 23.6 - - + +
30E TRP* 1.3 86.4 - - + +
32E LEU* 1.3 67.3 + - + +
34E ILE* 3.2 14.9 - - + +
35E GLY* 2.9 22.3 + - - -
89E LYS* 4.9 5.2 + - - +
93E TYR* 3.6 26.2 + - + +
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Residues in contact with LEU 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 ARG* 3.5 8.0 + - + +
29E VAL* 2.9 24.5 + - + +
31E GLN* 1.3 79.9 - - + +
33E TYR* 1.3 62.9 + - - +
35E GLY* 3.3 7.9 + - - -
36E ASP* 3.5 5.9 + - - -
198E LEU* 3.3 32.8 - - + +
222E VAL* 5.0 4.9 - - + -
224E VAL* 3.0 37.7 - - + -
225E PRO* 4.5 10.5 - - + -
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Residues in contact with TYR 33 (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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29E VAL 3.0 7.9 + - - +
30E TRP* 3.3 12.3 - + - +
31E GLN 3.0 0.4 - - - -
32E LEU* 1.3 76.6 - - - +
34E ILE* 1.3 78.2 + - + +
36E ASP* 3.1 21.8 + - + +
37E THR* 5.3 0.5 - - - +
198E LEU* 3.8 10.7 - - + +
200E LYS* 4.1 28.0 - - + -
220E TYR* 3.6 34.8 + + - -
222E VAL* 5.5 2.2 - - + -
238E PHE* 3.6 30.1 - + + -
240E LEU* 4.0 16.3 - - + +
242E TYR* 4.1 5.7 + - - -
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Residues in contact with ILE 34 (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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30E TRP* 3.0 67.9 + - + +
31E GLN* 3.2 16.6 - - + +
33E TYR* 1.3 85.5 - - + +
35E GLY* 1.3 61.9 + - - +
36E ASP 3.2 2.0 + - - -
37E THR* 3.5 15.6 - - - +
67E THR* 4.2 16.5 + - + +
90E MET* 3.7 24.5 - - + -
93E TYR* 4.2 27.1 - - + -
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Residues in contact with GLY 35 (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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31E GLN 2.9 15.4 + - - -
32E LEU* 3.8 4.7 - - - -
33E TYR 3.1 0.6 - - - -
34E ILE* 1.3 78.3 - - - +
36E ASP* 1.3 54.4 + - - +
37E THR* 2.9 17.1 + - - -
38E ARG* 3.9 11.2 + - - +
67E THR* 6.0 0.4 - - - -
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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