Contacts of the helix formed by residues 9 - 19 (chain A) in PDB entry 2DLL
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 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS* 1.3 76.8 - - + +
10A ARG* 1.3 70.8 + - - +
11A GLN 3.2 1.8 - - - -
12A TRP* 3.6 20.6 - - + -
13A LEU* 2.7 43.8 + - + +
59A TRP* 3.4 23.8 - - + -
63A LYS* 4.4 1.0 - - - +
82A LEU* 3.2 33.2 - - + -
85A ALA* 4.0 32.1 - - + +
86A LEU* 4.2 8.1 - - + +
89A SER* 4.8 10.5 - - - -
92A PHE* 4.9 6.1 - - + -
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Residues in contact with ARG 10 (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 LYS* 3.8 13.9 - - + +
9A LEU* 1.3 80.2 - - - +
11A GLN* 1.3 77.0 + - - +
13A LEU* 4.3 1.4 - - - +
14A ILE* 2.8 46.6 + - + +
89A SER* 5.6 1.4 + - - +
91A ASP* 3.7 24.5 - - + +
92A PHE* 4.5 18.8 - - + -
112A ILE* 4.5 11.5 - - + +
114A PRO* 6.0 3.8 - - - +
115A GLU* 5.3 6.7 + - - -
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Residues in contact with GLN 11 (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 LYS* 4.5 8.5 + - + +
9A LEU 3.2 0.4 - - - -
10A ARG* 1.3 94.1 + - + +
12A TRP* 1.3 70.8 + - - +
14A ILE* 2.8 24.7 + - - +
15A ASP* 2.8 36.9 + - + +
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Residues in contact with TRP 12 (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 LYS 2.7 26.1 + - - +
9A LEU* 3.2 17.7 + - + +
11A GLN* 1.3 80.5 - - - +
13A LEU* 1.3 106.0 + - + +
15A ASP* 3.0 12.3 + - - +
16A GLN* 3.0 35.4 + - + +
55A LEU* 3.5 29.4 - - + -
58A ALA* 3.8 8.4 + - + +
59A TRP* 3.0 55.2 - + + -
62A PHE* 3.2 50.0 - + + +
82A LEU* 4.1 3.6 - - + -
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Residues in contact with LEU 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 LEU* 2.7 29.4 + - + +
10A ARG 4.3 2.0 - - - +
12A TRP* 1.3 103.1 - - + +
14A ILE* 1.3 54.7 + - + +
16A GLN* 2.7 29.2 + - + +
17A ILE* 3.1 21.3 + - + +
25A LEU* 5.0 4.9 - - + -
35A PHE* 3.7 27.8 - - + -
37A ILE* 6.2 3.4 - - + -
55A LEU* 4.6 18.6 - - + -
82A LEU* 5.2 5.4 - - + -
86A LEU* 4.0 15.0 - - + -
92A PHE* 3.9 20.4 - - + -
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Residues in contact with ILE 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 ARG* 2.8 53.1 + - + +
11A GLN* 2.8 24.6 + - - +
13A LEU* 1.3 76.1 - - + +
15A ASP* 1.3 57.9 + - - +
17A ILE* 3.2 10.2 + - + -
18A ASP* 2.9 33.5 + - + +
27A TRP* 3.5 16.8 - - + -
32A LYS* 4.9 4.0 - - + +
35A PHE* 5.6 0.2 - - + -
92A PHE* 5.6 0.9 - - + -
112A ILE* 3.5 33.4 - - + -
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Residues in contact with ASP 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 GLN* 2.8 24.4 + - + +
12A TRP* 3.2 15.5 - - - +
14A ILE* 1.3 76.5 - - - +
16A GLN* 1.3 58.4 + - - +
18A ASP* 4.0 5.6 - - - +
19A SER* 2.6 42.5 + - - -
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Residues in contact with GLN 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 TRP* 3.0 49.4 + - + +
13A LEU* 2.7 19.5 + - + +
15A ASP* 1.3 86.4 + - - +
17A ILE* 1.3 57.2 + - - +
19A SER* 2.6 17.0 + - - -
20A GLY* 3.2 8.3 + - - -
21A LYS* 3.9 16.5 + - - -
22A TYR* 2.9 40.2 + - + -
25A LEU* 3.7 11.0 - - + +
55A LEU* 3.6 22.4 - - + -
58A ALA* 5.2 0.8 - - - +
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Residues in contact with ILE 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 LEU* 3.1 19.0 + - + +
14A ILE* 3.7 4.7 - - - +
16A GLN* 1.3 74.1 - - - +
18A ASP* 1.3 65.7 + - - +
20A GLY* 2.9 15.4 + - - -
25A LEU* 3.2 38.2 - - + +
26A VAL* 3.9 3.9 - - - -
27A TRP* 3.0 66.5 + - + +
35A PHE* 3.5 45.3 - - + -
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Residues in contact with ASP 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 ILE* 2.9 21.6 + - + +
15A ASP* 4.0 5.8 - - - +
17A ILE* 1.3 75.2 - - - +
19A SER* 1.3 63.3 + - - +
20A GLY* 3.3 0.7 + - - -
27A TRP* 3.0 13.6 - - + +
32A LYS* 3.0 35.6 - - - +
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Residues in contact with SER 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 ASP* 2.6 30.0 + - - -
16A GLN* 2.6 21.0 + - - -
18A ASP* 1.3 76.0 - - - +
20A GLY* 1.3 61.8 + - - +
21A LYS* 3.3 30.3 + - - +
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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