Contacts of the helix formed by residues 18 - 28 (chain A) in PDB entry 1R8E
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 SER 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 3.9 2.5 - - - -
17A VAL* 1.3 81.8 - - - +
19A ILE* 1.3 64.4 + - - +
20A LYS* 3.5 10.3 + - - +
21A ALA* 2.9 28.0 + - - +
22A LEU* 3.1 17.2 + - - +
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Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.8 19.7 - - + +
9A GLY* 4.3 8.7 - - - -
12A SER* 3.8 20.4 + - - +
17A VAL 3.6 0.4 + - - -
18A SER* 1.3 69.9 - - - +
20A LYS* 1.3 69.6 + - + +
22A LEU* 2.9 21.3 + - - +
23A ARG* 2.9 45.5 + - - +
-9B C 3.8 22.7 - - + +
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A SER* 3.3 8.2 - - - +
19A ILE* 1.3 78.5 - - + +
21A ALA* 1.3 57.0 + - - +
23A ARG* 3.4 29.5 + - - +
24A TYR* 2.9 29.9 + - - +
-7B T 5.2 2.0 + - - +
-6B C 4.1 20.4 - - - +
-5B C 4.7 7.5 - - - +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 3.7 16.4 - - + -
18A SER* 2.9 26.2 + - - +
20A LYS* 1.3 74.7 - - - +
22A LEU* 1.3 60.7 + - - +
24A TYR* 3.2 5.7 + - - +
25A TYR* 2.8 54.9 + - + +
60A LYS* 5.8 4.0 - - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.6 44.0 - - + +
11A VAL* 3.8 22.0 - - + -
12A SER* 3.8 12.6 - - - +
17A VAL* 4.1 15.7 - - + +
18A SER 3.1 16.8 + - - +
19A ILE* 2.9 8.1 + - - +
21A ALA* 1.3 76.1 - - - +
23A ARG* 1.3 63.2 + - - +
25A TYR* 3.2 7.2 + - + +
26A ASP* 2.9 24.2 + - - +
31A PHE* 4.1 33.0 - - + +
45A TYR* 4.0 8.8 + - - +
53A LEU* 4.4 8.1 - - + -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.7 10.7 - - + +
19A ILE* 2.9 33.9 + - - +
20A LYS* 3.7 36.4 - - - +
22A LEU* 1.3 74.5 - - - +
24A TYR* 1.3 57.9 + - - +
26A ASP* 3.2 9.6 + - - +
27A LYS* 2.9 28.3 + - - +
43A ARG* 3.8 30.0 + - - +
-9B C 3.8 15.0 - - - +
-8B C 2.9 38.2 + - - -
-7B T 3.5 32.8 + - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS 2.9 18.5 + - - +
21A ALA* 3.5 7.9 - - - +
23A ARG* 1.3 72.8 - - - +
25A TYR* 1.3 66.5 + + - +
26A ASP 3.0 2.0 + - - -
27A LYS* 3.1 15.5 + - + +
28A ILE* 2.8 66.2 + - + +
66A LEU* 3.5 29.2 - - + -
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL* 4.3 13.5 - - + +
21A ALA* 2.8 46.6 + - + +
22A LEU* 3.8 7.6 - - + +
24A TYR* 1.3 83.3 - + - +
26A ASP* 1.3 59.7 + - - +
28A ILE* 3.9 5.4 - - + -
29A ASP 3.1 1.7 + - - -
30A LEU* 2.9 43.9 + - + -
31A PHE* 3.1 24.3 + - + +
53A LEU* 4.8 12.8 - - + -
56A ILE* 4.0 23.6 - - + +
60A LYS* 4.1 26.2 + - - +
66A LEU* 3.8 33.1 - - + +
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Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU 2.9 13.7 + - - +
23A ARG* 3.2 12.8 - - - +
24A TYR 3.0 0.2 - - - -
25A TYR* 1.3 74.6 - - - +
27A LYS* 1.3 66.4 + - - +
29A ASP* 2.9 9.5 + - - -
31A PHE 3.4 12.5 + - - +
32A LYS* 2.7 53.2 + - - +
33A PRO* 3.5 25.7 - - + +
43A ARG* 2.9 31.0 + - - +
45A TYR* 5.1 0.7 - - - +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG 2.9 13.1 + - - +
24A TYR* 3.6 18.2 - - + +
26A ASP* 1.3 77.6 - - - +
28A ILE* 1.3 68.1 + - + +
29A ASP* 3.3 10.0 + - - +
32A LYS* 4.9 1.3 - - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 2.8 63.8 + - + +
25A TYR* 4.0 7.6 - - - +
27A LYS* 1.3 84.0 - - + +
29A ASP* 1.3 62.4 + - - +
30A LEU* 4.3 8.7 - - + -
66A LEU* 5.1 13.5 - - + -
67A GLU* 4.0 19.7 - - + +
70A LYS* 2.8 30.2 + - + +
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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