Contacts of the helix formed by residues 20 - 30 (chain A) in PDB entry 1JR9
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 ASP 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A GLU* 4.1 17.0 + - - +
18A THR 3.9 3.0 + - - -
19A ILE* 1.3 72.6 - - - +
21A LYS* 1.3 56.5 + - - +
22A GLU* 2.6 32.5 + - + +
23A THR* 2.7 51.7 + - - -
24A MET* 3.2 7.8 + - - +
170A TYR* 5.9 1.0 - - - -
172A LEU* 3.7 9.6 - - - +
173A LYS* 3.5 31.6 + - + +
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Residues in contact with LYS 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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12A TYR* 2.8 33.4 - - + +
13A ASP* 3.3 28.0 - - + +
16A GLU* 3.7 28.1 + - + +
19A ILE 3.4 4.9 + - - -
20A ASP* 1.3 69.5 - - + +
22A GLU* 1.3 66.5 + - - +
24A MET* 3.2 5.2 - - - +
25A ASN* 2.9 30.0 + - - +
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Residues in contact with GLU 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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20A ASP* 2.6 19.8 + - + +
21A LYS* 1.3 87.1 + - + +
23A THR* 1.3 64.3 + - - +
25A ASN* 3.3 8.7 + - - +
26A ILE* 3.2 29.2 + - + +
172A LEU* 3.6 26.5 - - + +
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Residues in contact with THR 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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19A ILE* 4.7 8.1 - - + -
20A ASP* 2.7 32.0 + - - -
22A GLU* 1.3 72.8 - - - +
24A MET* 1.3 61.3 + - - +
26A ILE* 3.1 6.6 + - + -
27A HIS* 2.6 48.7 + - + +
168A HIS 3.7 24.0 - - - +
169A ALA* 4.4 15.7 - - - +
170A TYR* 5.5 1.2 + - - -
172A LEU* 3.3 24.8 + - + +
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Residues in contact with MET 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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8A LEU* 4.0 17.1 - - + +
10A TYR* 3.6 37.9 - - + +
11A ALA 5.2 0.2 - - - +
12A TYR* 3.5 28.4 - - + +
15A LEU* 3.9 10.1 - - + -
19A ILE* 3.9 28.3 - - + +
20A ASP 3.2 8.9 + - - +
21A LYS* 3.2 10.3 - - - +
23A THR* 1.3 80.7 - - - +
25A ASN* 1.3 57.2 + - - +
27A HIS* 4.2 4.3 - - - +
28A HIS* 3.0 31.2 + - - +
85A PHE* 6.3 0.2 - - - -
86A TRP* 4.8 15.1 - - + -
89A MET* 4.1 15.3 - - + -
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Residues in contact with ASN 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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12A TYR* 3.1 32.0 - - + -
21A LYS 2.9 11.9 + - - +
22A GLU* 3.3 13.0 - - - +
23A THR 3.1 0.2 - - - -
24A MET* 1.3 75.2 - - - +
26A ILE* 1.3 59.4 + - - +
29A THR* 2.6 56.6 + - - +
30A LYS* 5.0 4.0 + - - -
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Residues in contact with ILE 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 GLU* 3.2 17.7 + - + +
23A THR* 3.1 8.2 + - + +
25A ASN* 1.3 83.3 - - - +
27A HIS* 1.3 56.8 + - - +
28A HIS 2.7 10.4 + - - -
29A THR* 4.2 0.4 - - - -
30A LYS* 2.7 55.5 + - + +
31A HIS* 3.9 20.6 - - + +
172A LEU* 4.9 15.9 - - + -
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Residues in contact with HIS 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 THR* 2.6 35.8 + - + +
24A MET* 4.3 4.1 - - - +
26A ILE* 1.3 74.0 - - - +
28A HIS* 1.3 55.2 + - - +
31A HIS* 3.5 14.8 - + + -
32A HIS* 3.4 19.6 + - - +
82A HIS* 2.8 16.4 + + - -
85A PHE* 4.1 10.3 - + - -
86A TRP* 3.0 32.8 - + + -
164A ASP* 3.0 15.7 - - + -
168A HIS* 2.8 22.3 + + - +
169A ALA* 4.3 6.0 - - + +
204A MN 2.0 36.6 + - - -
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Residues in contact with HIS 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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5A LEU* 3.2 38.7 - - + +
6A PRO 3.0 21.9 + - - -
7A GLU* 5.1 1.1 - - - -
8A LEU* 3.3 28.7 + - + +
12A TYR* 2.8 28.0 + + + -
24A MET 3.0 19.4 + - - +
25A ASN 3.8 1.3 - - - +
26A ILE 2.7 1.8 + - - -
27A HIS* 1.3 79.8 - - - +
29A THR* 1.3 63.7 + - + +
30A LYS 3.2 4.7 + - - -
32A HIS* 3.3 20.5 - - - +
33A ASN 3.4 0.7 + - - -
86A TRP* 3.2 35.9 - - + -
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Residues in contact with THR 29 (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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5A LEU* 4.6 6.3 - - - -
12A TYR* 3.1 31.9 - - + +
25A ASN* 2.6 41.0 + - - +
28A HIS* 1.3 75.6 - - + +
30A LYS* 1.3 84.4 + - - +
33A ASN* 3.7 15.0 - - - +
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Residues in contact with LYS 30 (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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25A ASN* 5.0 4.8 + - - -
26A ILE* 2.7 44.7 + - + +
28A HIS 3.2 0.6 - - - -
29A THR* 1.3 95.5 + - - +
31A HIS* 1.3 72.1 + - + +
32A HIS 3.5 0.4 - - - -
33A ASN* 3.3 3.3 + - - +
34A THR* 2.8 28.8 + - - -
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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