Contacts of the helix formed by residues 51 - 63 (chain D) in PDB entry 2ZUQ
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 51 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D ALA* 4.1 14.4 - - + +
25D LEU* 4.1 18.4 - - + -
26D GLU* 2.9 39.9 - - + +
47D GLU 3.5 3.6 + - - +
48D ARG* 2.7 10.7 + - - +
50D ALA* 1.3 70.3 - - - +
52D PHE* 1.3 51.3 + - - +
53D GLY 2.6 6.0 + - - +
54D VAL* 2.5 43.6 + - + +
55D LEU* 2.8 9.7 + - - +
146D LEU* 5.0 4.5 - - + -
149D ILE* 5.7 2.2 - - + -
150D PHE* 3.7 33.2 - - + -
153D TYR* 4.3 16.4 - - + -
177D UQ1 4.8 14.1 - - + -
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Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 5.1 9.2 - - + -
26D GLU* 3.1 38.4 + - + -
30D LEU* 4.7 16.4 - - + -
48D ARG* 3.0 47.1 + - + +
49D VAL* 4.0 15.5 - - + +
51D LEU* 1.3 72.2 - - - +
53D GLY* 1.3 55.3 + - - +
54D VAL 3.5 0.2 - - - -
55D LEU* 3.2 37.1 - - + +
56D GLY* 3.7 4.5 + - - -
123D VAL* 4.8 14.4 - - + -
124D PHE* 5.1 13.5 - + + -
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Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D VAL 3.8 9.8 + - - -
51D LEU* 2.6 5.4 - - - +
52D PHE* 1.3 79.1 - - - +
54D VAL* 1.3 54.9 + - - -
55D LEU 3.2 4.3 - - - -
56D GLY* 4.1 0.8 + - - -
57D ALA* 3.3 12.3 + - - +
76D ILE* 3.2 16.8 - - - +
80D SER* 3.0 30.5 + - - -
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET 6.4 0.7 - - - -
19D ALA* 4.3 4.2 - - - -
22D ALA* 4.2 15.9 - - + +
50D ALA 3.9 2.9 - - - +
51D LEU* 2.5 39.0 + - + +
53D GLY* 1.3 71.6 - - - -
55D LEU* 1.3 63.8 + - - +
57D ALA* 3.8 5.2 - - + -
58D ALA* 3.9 10.6 + - - +
77D TRP* 3.6 39.0 - - + +
80D SER* 3.7 19.1 - - - -
81D ALA* 4.4 10.8 - - + +
150D PHE* 5.0 0.7 - - + -
153D TYR* 4.6 21.5 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 3.6 23.2 - - - +
22D ALA* 5.6 1.1 - - + -
23D LEU* 3.7 34.1 - - + +
26D GLU* 5.1 1.8 - - - +
51D LEU 2.8 5.8 + - - +
52D PHE* 3.2 37.2 - - + +
53D GLY 3.2 0.2 - - - -
54D VAL* 1.3 78.2 - - - +
56D GLY* 1.3 71.9 + - - +
57D ALA 3.1 0.5 + - - -
59D LEU* 2.8 46.4 + - + +
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Residues in contact with GLY 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D PHE 3.7 6.8 + - - -
53D GLY 4.1 1.3 + - - -
55D LEU* 1.3 77.2 - - - +
57D ALA* 1.3 55.5 + - - +
59D LEU* 4.3 5.2 - - - -
60D ILE* 2.4 54.4 + - - +
76D ILE* 5.6 0.9 - - - -
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY 3.3 14.1 + - - +
54D VAL* 3.8 9.6 - - - -
55D LEU 3.1 0.6 + - - -
56D GLY* 1.3 74.8 - - - +
58D ALA* 1.3 57.8 + - - +
60D ILE* 3.7 0.5 - - - +
61D GLY 3.0 16.8 + - - -
73D ALA* 3.2 23.5 - - - +
76D ILE* 3.0 36.7 - - - +
77D TRP* 3.3 24.7 - - + -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP* 3.5 17.3 - - + +
18D MET* 3.6 5.2 - - + -
19D ALA* 3.5 27.6 - - - +
54D VAL 3.9 4.2 + - - +
55D LEU 3.3 2.0 + - - -
57D ALA* 1.3 75.5 - - - +
59D LEU* 1.3 55.7 + - - +
60D ILE 3.1 2.0 - - - -
61D GLY 3.0 2.4 + - - -
62D ALA* 2.5 36.0 + - - +
77D TRP* 3.0 28.9 - - + -
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 6.4 1.8 - - + -
19D ALA* 3.6 19.6 - - + +
23D LEU* 5.6 3.1 - - + -
55D LEU* 2.8 50.6 + - + +
56D GLY* 3.2 4.0 - - - +
58D ALA* 1.3 75.8 - - - +
60D ILE* 1.3 58.7 + - + +
62D ALA* 3.7 5.4 - - + -
63D ILE* 3.0 43.8 + - + +
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLY* 2.4 41.7 + - - +
57D ALA 3.7 2.7 - - - +
59D LEU* 1.3 67.8 - - + +
61D GLY* 1.3 62.2 + - - +
62D ALA 3.0 5.9 + - - -
63D ILE* 3.3 12.4 - - + +
69D LEU* 3.1 47.1 - - + +
72D VAL* 3.9 22.7 - - + -
73D ALA* 4.0 9.6 - - + -
76D ILE* 4.6 14.6 - - + -
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TRP* 3.1 34.8 + - - -
57D ALA 3.0 9.3 + - - -
58D ALA 3.0 8.4 + - - -
60D ILE* 1.3 75.6 - - - +
62D ALA* 1.3 60.1 + - - +
65D PRO* 3.5 16.4 - - - +
69D LEU 4.4 4.0 - - - -
73D ALA* 3.1 23.9 - - - +
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Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ARG* 4.2 11.4 - - - +
15D TRP* 3.6 14.1 - - + -
16D LEU* 3.9 29.8 - - + +
19D ALA* 5.2 0.4 - - + -
58D ALA 2.5 18.1 + - - +
59D LEU* 3.8 11.0 - - + +
61D GLY* 1.3 72.4 - - - +
63D ILE* 1.3 60.8 + - + +
64D ALA 2.7 19.1 + - - -
65D PRO* 3.0 19.8 - - - +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 5.4 9.0 - - + -
59D LEU* 3.0 38.8 + - + +
60D ILE* 3.3 3.6 + - + +
62D ALA* 1.3 84.0 - - + +
64D ALA* 1.3 66.1 + - + +
69D LEU* 3.2 21.3 - - - +
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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