Contacts of the helix formed by residues 54 - 63 (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 ALA 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.2 25.2 + - + -
23A PRO* 6.1 3.4 - - + -
50A GLU 2.6 16.0 + - - +
51A GLU* 2.7 25.9 + - + +
52A ASP 3.3 0.2 - - - -
53A ALA* 1.3 75.8 - - - +
55A LEU* 1.3 60.4 + - - +
57A LYS* 4.3 2.8 - - - +
58A ALA* 4.0 9.7 + - - +
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Residues in contact with LEU 55 (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* 3.5 28.4 - - + -
13A LEU* 4.6 11.7 - - + -
16A GLN* 3.6 11.9 - - + -
22A TYR* 3.2 44.4 - - + +
25A LEU* 4.6 16.4 - - + -
37A ILE* 4.9 16.8 - - + -
38A PRO* 6.5 0.2 - - + -
51A GLU 4.5 0.6 + - - -
52A ASP 4.9 0.4 + - - -
54A ALA* 1.3 79.7 - - - +
56A PHE* 1.3 76.6 + - + +
58A ALA* 3.1 6.8 + - - +
59A TRP 3.1 16.5 + - - -
82A LEU* 4.6 11.9 - - + -
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Residues in contact with PHE 56 (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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37A ILE* 5.2 12.8 - - + -
38A PRO 6.0 2.9 - - - -
39A TRP* 5.7 8.5 - + - -
52A ASP* 3.3 31.6 - - - -
53A ALA* 3.4 10.0 + - + +
55A LEU* 1.3 85.6 - - + +
57A LYS* 1.3 63.8 + - - +
59A TRP* 3.0 24.2 + - - +
60A ALA* 3.3 6.8 + - - +
78A TRP* 3.9 20.8 - - + +
79A LYS* 3.6 48.7 - - + -
82A LEU* 3.6 30.5 - - + -
83A ARG* 4.9 3.4 - - + -
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Residues in contact with LYS 57 (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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50A GLU* 3.4 27.5 + - - +
53A ALA* 2.7 31.7 + - + +
54A ALA* 4.3 3.8 - - - +
56A PHE* 1.3 74.8 - - - +
58A ALA* 1.3 63.9 + - - +
60A ALA* 3.3 3.3 + - - +
61A LEU* 3.1 47.5 + - + +
66A PHE* 4.1 15.0 - - + -
68A GLU* 4.8 12.8 - - - -
73A PRO* 5.6 0.6 - - - +
78A TRP* 3.5 49.9 - - + +
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Residues in contact with ALA 58 (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* 3.8 11.2 - - + +
16A GLN* 5.2 0.7 - - - +
22A TYR* 3.6 20.9 - - - +
54A ALA 4.0 5.7 + - - +
55A LEU 3.1 10.8 + - - +
57A LYS* 1.3 80.3 - - - +
59A TRP* 1.3 66.2 + - - +
61A LEU* 3.8 7.5 - - - +
62A PHE* 2.7 28.2 + - + +
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Residues in contact with TRP 59 (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 3.9 4.5 - - - -
9A LEU* 3.4 41.5 - - + -
12A TRP* 3.0 52.1 - + + -
55A LEU 3.1 2.1 + - - +
56A PHE* 3.0 14.5 + - - +
58A ALA* 1.3 74.5 - - - +
60A ALA* 1.3 61.5 + - + +
62A PHE* 3.4 2.8 - + - +
63A LYS* 2.9 81.5 + - + +
78A TRP 4.5 2.9 - - - -
81A ARG* 4.0 14.9 - - + +
82A LEU* 3.4 51.8 - - + +
85A ALA* 4.4 11.7 - - + -
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Residues in contact with ALA 60 (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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56A PHE 3.3 2.7 + - - +
57A LYS 3.7 4.3 - - - +
58A ALA 3.2 0.6 - - - -
59A TRP* 1.3 79.6 - - + +
61A LEU* 1.3 70.4 + - - +
62A PHE 2.7 2.5 + - - -
63A LYS* 2.7 6.9 + - - -
64A GLY* 2.7 28.4 + - - +
66A PHE* 5.3 5.6 - - + -
78A TRP* 3.5 37.0 - - + +
81A ARG* 6.0 4.5 - - + -
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Residues in contact with LEU 61 (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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57A LYS* 3.1 45.6 + - + +
58A ALA* 3.8 5.8 - - - +
60A ALA* 1.3 76.9 - - + +
62A PHE* 1.3 57.0 + - - +
64A GLY 2.6 22.7 - - - +
65A LYS* 4.6 4.4 - - - +
66A PHE* 3.3 48.4 - - + +
67A ARG* 6.1 0.2 - - - +
68A GLU* 4.6 13.0 - - + +
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Residues in contact with PHE 62 (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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4A GLY* 5.3 13.0 - - - -
6A SER 5.1 0.4 - - - -
7A GLY* 3.8 20.0 - - - -
8A LYS 3.4 34.3 - - - -
12A TRP* 3.2 35.4 - + + +
58A ALA* 2.7 21.7 + - + +
59A TRP 3.4 2.2 - - - +
60A ALA 2.7 3.8 + - - -
61A LEU* 1.3 71.8 - - - +
63A LYS* 1.3 93.0 + - + +
64A GLY 3.9 1.0 - - - +
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Residues in contact with LYS 63 (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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7A GLY* 3.6 23.6 + - - -
8A LYS* 3.7 16.4 - - - +
9A LEU 4.4 0.8 - - - +
59A TRP* 2.9 65.5 + - + +
60A ALA* 2.7 9.5 + - - +
62A PHE* 1.3 88.5 - - + +
64A GLY* 1.3 60.0 + - - +
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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