Contacts of the helix formed by residues 24 - 35 (chain N) 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 ALA 24 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7090 G 3.5 20.0 + - - +
7100 G 2.9 32.1 + - - +
18N ALA* 5.0 0.9 - - - -
22N GLY 4.6 2.7 - - - +
23N GLY* 1.3 73.3 - - - +
25N VAL* 1.3 67.4 + - - +
26N TRP 3.4 1.3 - - - -
27N GLY* 3.4 4.5 + - - +
28N ASP* 3.1 22.3 + - - +
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Residues in contact with VAL 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7090 G 2.7 36.3 + - - +
7100 G 3.8 0.9 + - - -
24N ALA* 1.3 79.1 - - - +
26N TRP* 1.3 85.4 + - + +
28N ASP* 2.8 10.8 + - - +
29N VAL* 2.6 43.1 + - + +
59N VAL* 5.7 0.2 - - + -
108N GLY* 3.8 26.7 - - - +
111N VAL* 3.6 28.5 - - + -
113N VAL* 4.4 7.6 - - + -
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Residues in contact with TRP 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LEU* 3.3 45.9 - - + +
17N ALA* 3.8 17.3 - - + -
18N ALA* 3.9 6.3 - - + -
23N GLY* 4.6 4.5 - - - -
24N ALA 3.4 0.8 - - - +
25N VAL* 1.3 86.0 - - + +
27N GLY* 1.3 56.9 + - - +
29N VAL* 3.3 6.2 + - + +
30N ALA* 2.8 29.6 + - - +
57N THR* 6.2 0.7 - - + -
59N VAL* 4.2 35.4 - - + -
98N LEU* 4.6 8.7 - - + -
101N ALA* 3.8 23.1 - - + -
102N ILE* 4.1 18.0 - - + +
105N ASN* 3.1 33.3 + - - -
106N PRO* 3.4 22.8 + - - +
108N GLY* 3.7 17.8 - - - +
111N VAL* 5.4 2.2 - - + -
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Residues in contact with GLY 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LEU 4.7 1.1 - - - -
15N LYS* 5.4 3.1 - - - -
18N ALA* 3.3 21.9 - - - +
24N ALA 3.4 4.7 + - - -
25N VAL 3.2 0.2 - - - -
26N TRP* 1.3 79.3 - - - +
28N ASP* 1.3 57.0 + - - +
30N ALA* 3.3 7.4 + - - +
31N GLU* 3.0 40.5 + - - +
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Residues in contact with ASP 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7080 A 2.8 35.6 + - - +
7090 G 3.8 17.3 + - - +
24N ALA 3.1 12.8 + - - +
25N VAL* 2.8 15.4 + - - +
27N GLY* 1.3 74.5 - - - +
29N VAL* 1.3 63.4 + - + +
31N GLU* 3.4 11.5 + - - +
32N ARG* 3.2 21.5 + - - +
113N VAL* 5.5 5.9 - - - +
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Residues in contact with VAL 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LEU* 3.8 11.2 - - + -
25N VAL* 2.6 28.2 + - + +
26N TRP* 3.7 10.1 - - + +
28N ASP* 1.3 73.7 - - + +
30N ALA* 1.3 62.3 + - - +
32N ARG* 3.3 6.2 + - - +
33N LEU* 3.0 29.8 + - + +
59N VAL* 3.8 26.5 - - + -
61N PRO* 4.2 20.4 - - + -
98N LEU* 3.7 29.4 - - + -
113N VAL* 5.3 7.0 - - + -
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Residues in contact with ALA 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ILE* 4.1 9.7 - - + +
14N LEU* 3.9 23.3 - - + +
15N LYS* 4.1 24.2 - - + -
26N TRP 2.8 17.5 + - - +
27N GLY* 3.5 8.1 - - - +
29N VAL* 1.3 78.6 - - - +
31N GLU* 1.3 62.4 + - + +
33N LEU* 3.4 4.2 + - - +
34N GLU* 3.1 29.5 + - - +
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Residues in contact with GLU 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N LYS* 6.4 0.9 - - - -
27N GLY* 3.0 24.4 + - - +
28N ASP* 3.8 10.5 + - - +
29N VAL 3.3 0.2 - - - -
30N ALA* 1.3 77.0 - - + +
32N ARG* 1.3 62.5 + - - +
34N GLU* 3.4 19.1 + - - +
35N LYS* 3.3 28.5 + - - +
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Residues in contact with ARG 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9360 C 3.2 25.2 + - - -
9370 C 5.4 4.2 + - - -
28N ASP 3.2 16.3 + - - +
29N VAL 3.8 4.0 - - - +
30N ALA 3.3 0.2 - - - -
31N GLU* 1.3 73.5 - - - +
33N LEU* 1.3 64.6 + - - +
35N LYS* 3.3 31.6 + - - +
39N THR* 3.7 27.3 + - - +
40N HIS* 3.1 14.7 + - + +
61N PRO* 4.0 34.1 - - + +
115N ARG* 3.8 28.0 - - - +
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Residues in contact with LEU 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2N LYS* 3.1 12.8 + - - -
7N LEU* 4.2 11.8 - - + +
10N LEU* 4.1 11.9 - - + -
11N ILE* 3.8 20.7 - - + +
14N LEU* 3.8 27.4 - - + -
29N VAL* 3.0 22.0 + - + +
30N ALA 3.9 1.3 - - - +
31N GLU 3.3 0.2 - - - -
32N ARG* 1.3 75.7 - - - +
34N GLU* 1.3 60.7 + - - +
40N HIS* 3.0 36.7 + - + +
61N PRO* 3.7 21.8 - - + +
79N VAL* 3.7 33.0 - - + -
98N LEU* 4.6 0.2 - - + -
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Residues in contact with GLU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6550 U 4.7 1.0 + - - -
12790 U 5.4 3.6 - - - +
2N LYS* 3.6 16.0 - - + +
11N ILE* 4.0 18.0 - - + +
15N LYS* 3.0 34.7 + - - -
30N ALA 3.1 20.7 + - - +
31N GLU* 3.5 19.9 - - - +
32N ARG 3.2 0.4 - - - -
33N LEU* 1.3 76.2 - - - +
35N LYS* 1.3 63.9 + - + +
36N PRO* 4.5 0.5 - - - +
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Residues in contact with LYS 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9350 G 4.6 7.9 - - - +
9360 C 3.0 40.5 + - - +
9370 C 5.5 3.0 + - - -
2N LYS* 3.1 8.1 + - - -
31N GLU* 3.3 15.7 + - - +
32N ARG* 3.3 34.1 + - - +
33N LEU 3.2 1.0 - - - -
34N GLU* 1.3 80.7 - - + +
36N PRO* 1.3 69.3 - - + +
39N THR* 3.6 8.7 - - - +
40N HIS* 2.7 28.1 + - - -
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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