Contacts of the helix formed by residues 11 - 22 (chain R) in PDB entry 1JJ2
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 11 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14440 G 3.5 38.8 + - - +
14450 G 2.8 17.7 + - - +
9R HIS* 3.4 26.9 - - + +
10R VAL* 1.3 82.1 - - - +
12R GLU* 1.3 71.4 + - - +
13R LYS 3.7 1.6 + - - -
14R ALA* 2.9 25.8 + - - +
15R MET* 3.0 17.1 + - - +
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Residues in contact with GLU 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14430 G 5.6 1.8 + - - -
14440 G 3.4 34.3 + - - +
15010 A 2.8 35.6 + - - +
11R THR* 1.3 71.6 - - - +
13R LYS* 1.3 63.0 + - - +
15R MET* 3.0 20.2 + - - +
16R ASN* 3.2 21.0 + - - +
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Residues in contact with LYS 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14450 G 3.3 41.5 + - - +
14460 U 2.9 24.8 + - - +
14470 U 3.1 16.9 + - - -
15000 U 6.0 0.2 + - - -
15020 A 4.1 25.4 + - - +
15030 U 3.0 26.8 + - - +
11R THR* 3.2 1.2 + - - -
12R GLU* 1.3 80.7 + - - +
14R ALA* 1.3 62.2 + - - +
16R ASN* 3.3 13.4 + - + +
17R ASP* 3.2 31.1 + - - +
25R GLN* 4.7 9.4 - - - +
63R LYS* 5.7 2.0 - - - +
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Residues in contact with ALA 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R HIS 3.2 26.7 - - - +
10R VAL* 4.3 1.6 - - - -
11R THR* 2.9 19.6 + - - +
13R LYS* 1.3 78.6 - - - +
15R MET* 1.3 58.8 + - + +
17R ASP* 3.4 2.9 + - - +
18R MET* 3.0 27.8 + - - +
23R LYS 4.6 1.6 - - - +
25R GLN* 3.5 34.4 + - + +
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Residues in contact with MET 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R VAL* 4.4 20.2 - - + -
11R THR 3.0 21.4 + - - +
12R GLU* 3.0 11.4 + - - +
14R ALA* 1.3 77.4 - - - +
16R ASN* 1.3 56.4 + - - +
18R MET* 3.0 33.4 + - + +
19R ASP* 2.7 47.1 + - - +
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Residues in contact with ASN 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R GLU* 3.2 18.4 + - - +
13R LYS* 3.3 13.3 + - + +
15R MET* 1.3 78.0 - - - +
17R ASP* 1.3 61.5 + - - +
19R ASP* 4.5 4.1 - - - +
20R PHE* 2.8 59.6 + - + +
21R GLN* 4.7 0.6 - - - +
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Residues in contact with ASP 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14470 U 4.8 10.2 + - - +
15070 C 5.5 0.2 + - - -
13R LYS* 3.2 22.7 + - - +
14R ALA 3.7 8.1 - - - +
16R ASN* 1.3 80.3 - - - +
18R MET* 1.3 59.7 + - - +
21R GLN* 2.9 42.6 + - - +
22R ASN 3.1 7.4 + - - -
23R LYS* 3.2 32.5 + - + +
25R GLN* 3.5 22.2 + - + +
65R VAL* 3.8 6.9 - - - +
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Residues in contact with MET 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ALA 3.0 14.0 + - - +
15R MET* 3.0 43.4 + - + +
17R ASP* 1.3 80.2 - - - +
19R ASP* 1.3 88.5 + - - +
22R ASN* 3.4 15.9 + - - +
23R LYS 3.1 16.1 + - - +
24R LEU* 4.6 4.3 - - + -
74R ALA* 3.8 11.1 - - + +
75R GLN* 3.7 33.4 + - + +
78R ALA* 3.8 26.7 - - - -
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Residues in contact with ASP 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15R MET* 2.7 34.2 + - - +
16R ASN* 4.3 2.2 - - - +
18R MET* 1.3 95.4 - - - +
20R PHE* 1.3 80.6 + - + +
22R ASN 4.9 0.4 + - - -
75R GLN* 3.0 35.0 + - - +
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Residues in contact with PHE 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R ASN* 2.8 44.0 + - + +
19R ASP* 1.3 95.0 - - + +
21R GLN* 1.3 66.8 + - + +
22R ASN 3.8 0.4 - - - -
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Residues in contact with GLN 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15070 C 3.0 10.3 + - - +
15080 C 3.3 38.1 + - - -
16R ASN 4.7 0.2 - - - +
17R ASP* 2.9 27.6 + - - +
20R PHE* 1.3 89.0 - - + +
22R ASN* 1.3 73.6 + - - +
23R LYS* 2.7 45.2 + - + +
67R ARG* 3.8 11.6 - - - +
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Residues in contact with ASN 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R ASP 3.1 2.4 + - - -
18R MET 3.4 13.1 + - - +
19R ASP 4.9 0.2 - - - -
20R PHE 3.8 1.2 - - - -
21R GLN* 1.3 81.3 - - - +
23R LYS* 1.3 57.6 + - - +
68R LEU* 3.0 57.4 + - - +
69R SER 3.1 8.1 + - - -
70R GLU* 4.4 3.2 - - - +
72R ASP 3.0 23.4 + - - +
73R ASP* 3.4 5.0 - - - +
74R ALA* 2.8 33.6 + - - +
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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