Contacts of the helix formed by residues 12 - 22 (chain A) in PDB entry 5J3V
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 LEU 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ASP* 3.6 27.8 - - - +
9A GLU* 4.1 14.2 - - - +
10A GLN 3.7 0.6 - - - +
11A GLY* 1.3 76.8 - - - +
13A GLN* 1.3 90.8 + - - +
14A GLN 3.1 1.6 - - - -
15A ILE* 3.2 6.3 + - - +
16A LEU* 3.1 47.1 + - + +
49A TYR* 4.0 20.7 - - + -
52A PHE* 3.6 32.5 - - + -
53A VAL* 5.7 3.4 - - + -
57A LEU* 5.2 7.2 - - + -
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Residues in contact with GLN 13 (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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9A GLU* 3.2 23.2 - - - +
10A GLN 5.1 2.2 - - - +
11A GLY* 4.5 0.6 - - - +
12A LEU* 1.3 95.6 - - - +
14A GLN* 1.3 62.3 + - - +
15A ILE 3.1 1.1 - - - -
16A LEU* 3.9 18.1 - - + +
17A GLN* 3.3 37.9 + - + +
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Residues in contact with GLN 14 (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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10A GLN 4.6 5.5 + - - +
11A GLY* 3.4 25.2 - - - +
12A LEU 3.1 0.6 - - - -
13A GLN* 1.3 79.6 - - - +
15A ILE* 1.3 58.8 + - + +
17A GLN* 4.4 8.1 - - - +
18A LEU* 3.3 27.8 + - + +
40A LEU* 5.9 8.7 - - + +
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Residues in contact with ILE 15 (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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11A GLY 3.5 16.4 - - - +
12A LEU* 3.2 6.2 + - + +
13A GLN 3.1 0.2 - - - -
14A GLN* 1.3 80.1 - - + +
16A LEU* 1.3 62.5 + - + +
17A GLN 3.2 1.8 - - - -
18A LEU* 2.9 24.1 + - + +
19A LEU* 3.0 26.7 + - + +
37A LEU* 5.3 4.0 - - + -
40A LEU* 5.1 7.9 - - + -
46A PHE* 3.8 32.5 - - + -
49A TYR* 3.6 45.5 - - + -
50A LEU* 4.7 11.2 - - + -
53A VAL* 5.8 3.6 - - + -
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Residues in contact with LEU 16 (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 LEU* 3.1 37.7 + - + +
13A GLN* 3.7 20.2 + - + +
15A ILE* 1.3 77.1 - - + +
17A GLN* 1.3 62.0 + - + +
19A LEU* 3.2 15.6 + - + +
20A LYS* 3.2 30.2 + - + +
53A VAL* 3.8 29.4 - - + -
57A LEU* 4.0 9.6 - - + -
60A GLU* 3.2 37.9 - - - +
64A THR* 5.3 0.4 - - + +
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Residues in contact with GLN 17 (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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13A GLN* 3.3 24.6 + - + +
14A GLN* 4.6 7.7 - - - +
15A ILE 3.2 0.6 - - - -
16A LEU* 1.3 78.0 - - + +
18A LEU* 1.3 59.8 + - + +
19A LEU 3.3 0.2 - - - -
20A LYS* 3.6 7.3 + - - +
21A GLU* 3.1 29.9 + - - +
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Residues in contact with LEU 18 (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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14A GLN* 3.3 20.9 - - + +
15A ILE* 2.9 12.4 + - + +
17A GLN* 1.3 76.4 - - + +
19A LEU* 1.3 61.6 + - - +
21A GLU* 3.7 20.2 - - - +
22A SER* 3.0 29.3 + - - -
33A VAL* 3.5 15.0 - - + +
36A LYS* 4.0 32.3 - - + +
37A LEU* 4.0 18.8 - - + +
40A LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 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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15A ILE* 3.0 27.6 + - + +
16A LEU* 3.2 27.3 + - + +
18A LEU* 1.3 77.3 - - + +
20A LYS* 1.3 63.7 + - - +
22A SER* 2.7 19.4 + - - +
23A GLN* 3.4 17.4 - - - +
37A LEU* 4.9 15.3 - - + -
50A LEU* 5.1 5.2 - - + -
53A VAL* 4.3 7.4 - - + -
64A THR* 3.9 26.0 - - + +
67A LEU* 3.8 15.1 - - + +
68A SER* 3.9 35.7 - - - +
71A ILE* 5.0 3.1 - - + -
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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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16A LEU* 3.2 17.6 + - - +
17A GLN* 4.0 7.4 - - - +
19A LEU* 1.3 76.3 - - - +
21A GLU* 1.3 61.2 + - - +
23A GLN* 3.4 23.2 + - - +
24A SER* 3.8 5.7 + - - -
60A GLU* 4.3 15.6 + - - +
61A ASP* 2.7 36.0 + - - -
64A THR* 2.9 23.2 + - + +
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Residues in contact with GLU 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 GLN 3.1 17.7 + - - +
18A LEU* 3.7 20.7 - - - +
19A LEU 3.3 0.2 - - - -
20A LYS* 1.3 75.2 - - - +
22A SER* 1.3 56.6 + - - +
23A GLN 3.1 2.2 - - - -
24A SER* 2.6 31.3 + - - +
29A ILE* 3.6 24.7 - - + +
32A THR* 5.6 0.3 + - - -
33A VAL* 3.5 24.8 - - + +
36A LYS* 4.4 7.9 + - - -
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Residues in contact with SER 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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18A LEU 3.0 16.1 + - - -
19A LEU* 2.7 25.5 + - - +
21A GLU* 1.3 76.6 - - - +
23A GLN* 1.3 57.9 + - - +
24A SER 3.3 2.1 + - - -
30A GLN* 3.9 24.9 + - - +
33A VAL* 4.2 15.7 - - - +
34A GLN* 5.5 11.8 + - - -
37A LEU* 5.3 7.5 - - - +
67A LEU* 3.3 18.2 - - - +
71A ILE* 6.5 1.1 - - - -
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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