Contacts of the helix formed by residues 14 - 21 (chain A) in PDB entry 2JNU
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER 3.2 2.2 + - - -
11A TRP 2.9 14.4 + - - +
13A LEU* 1.3 88.0 + - - +
15A PHE* 1.3 63.7 + - - +
16A GLU* 4.3 10.8 - - - -
17A ARG* 3.2 21.5 + - - +
18A LEU 3.2 13.2 + - - -
118A TYR* 3.9 1.6 - - - -
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Residues in contact with PHE 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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14A SER* 1.3 68.7 - - - +
16A GLU* 1.3 55.5 + - - +
18A LEU* 3.0 17.4 + - + +
19A LEU* 2.7 62.3 + - + +
28A PHE* 4.1 11.4 - + - -
110A PHE* 3.5 44.0 - + + -
113A MET* 3.5 32.5 - - + -
114A LYS* 3.8 24.0 - - + -
118A TYR* 3.4 56.5 + + + -
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Residues in contact with GLU 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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14A SER* 4.7 10.1 - - - -
15A PHE* 1.3 78.4 - - - +
17A ARG* 1.3 61.0 + - - +
19A LEU* 3.1 5.0 + - - +
20A GLN* 2.7 65.8 + - - +
110A PHE* 4.3 20.7 - - + -
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Residues in contact with ARG 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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5A GLU* 2.7 33.2 + - + +
6A GLN 3.9 2.6 + - - -
7A PRO* 3.8 17.5 + - - +
8A VAL* 4.7 1.8 - - - +
10A SER* 3.3 32.6 - - - +
11A TRP* 2.9 31.8 - - - +
14A SER* 3.2 18.6 + - - +
15A PHE 3.2 0.6 - - - -
16A GLU* 1.3 90.3 + - - +
18A LEU* 1.3 58.0 + - - +
20A GLN* 3.8 2.1 - - + +
21A ASP* 2.8 54.1 + - - +
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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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11A TRP* 3.5 37.2 - - + +
14A SER 3.2 7.5 + - - +
15A PHE* 3.0 23.2 + - + +
17A ARG* 1.3 78.1 - - - +
19A LEU* 1.3 58.3 + - - +
21A ASP 3.2 9.5 - - - +
24A GLY* 3.5 21.6 - - - +
25A LEU 3.2 26.6 + - - +
28A PHE* 4.3 15.3 - - + -
118A TYR* 3.4 29.2 - - + -
121A PHE* 3.5 38.4 - - + -
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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 PHE* 2.7 32.8 + - + +
16A GLU* 3.4 4.7 - - - +
18A LEU* 1.3 73.9 - - - +
20A GLN* 1.3 61.6 + - - +
25A LEU* 3.3 51.3 - - + +
28A PHE* 5.1 4.0 - - + -
41A VAL* 5.1 2.5 - - + -
44A TRP* 3.6 38.1 - - + -
110A PHE* 3.3 38.1 - - + -
113A MET* 3.7 22.2 - - + -
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Residues in contact with GLN 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 GLU* 2.7 37.6 + - - +
17A ARG* 3.8 4.3 - - - +
19A LEU* 1.3 80.0 - - - +
21A ASP* 1.3 60.2 + - - +
22A PRO* 3.7 7.6 - - - +
25A LEU* 5.8 0.2 - - - -
44A TRP* 4.7 15.5 - - - -
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Residues in contact with ASP 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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11A TRP* 2.9 23.9 + - - +
17A ARG* 2.8 45.9 + - - +
18A LEU 3.2 2.8 - - - +
20A GLN* 1.3 78.0 - - - +
22A PRO* 1.4 77.4 - - - +
23A LEU* 3.4 15.6 + - - +
24A GLY 2.9 13.6 + - - -
25A LEU* 2.9 23.8 + - - +
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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