Contacts of the helix formed by residues 15 - 26 (chain D) in PDB entry 4EDZ
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 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.4 7.6 - - + -
8D TYR* 3.3 38.9 - - + -
12D ARG 3.2 1.4 + - - -
14D ARG* 1.3 76.6 - - - +
16D GLU* 1.3 65.9 + - - +
17D ILE 3.3 2.5 - - - -
18D ILE* 2.9 21.1 + - - +
19D ARG* 3.1 30.5 + - - +
52D PRO* 4.2 11.2 - - + -
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Residues in contact with GLU 16 (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* 3.1 41.6 + - + +
13D GLY 3.9 4.7 - - - +
14D ARG 3.5 1.4 - - - -
15D ALA* 1.3 76.9 - - - +
17D ILE* 1.3 56.5 - - - +
19D ARG* 3.0 32.4 + - - +
20D TYR* 2.8 49.3 + - + -
33D ARG* 4.7 1.4 + - - -
155D ILE* 3.9 16.2 - - + -
190D TRP* 3.0 23.7 + - - -
194D ARG* 2.7 30.4 + - - +
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Residues in contact with ILE 17 (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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13D GLY 5.0 0.6 + - - -
14D ARG 4.0 17.0 + - - +
16D GLU* 1.3 77.6 - - - +
18D ILE* 1.3 73.1 + - + +
20D TYR* 3.4 0.9 + - - +
21D ILE* 3.1 28.4 + - + +
64D SER* 4.4 5.2 - - - +
65D LEU* 4.4 7.2 - - + -
68D ALA* 4.2 11.2 - - + -
148D TRP* 3.8 36.1 - - + +
151D PHE* 3.6 33.9 - - + -
152D TYR* 3.8 32.0 - - + +
155D ILE* 3.5 14.2 - - + +
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Residues in contact with ILE 18 (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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6D LEU* 3.8 30.5 - - + -
15D ALA 2.9 11.2 + - - +
17D ILE* 1.3 78.8 - - + +
19D ARG* 1.3 64.2 + - - +
21D ILE* 3.1 11.3 + - - +
22D PHE* 3.0 48.5 + - + -
52D PRO* 4.1 21.5 - - + -
54D LEU* 5.0 0.4 - - + -
64D SER* 3.9 22.4 - - - +
67D ILE* 3.8 25.8 - - + -
68D ALA* 4.5 4.5 - - + +
71D LEU* 3.8 12.1 - - + -
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Residues in contact with ARG 19 (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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6D LEU* 3.8 10.1 - - + +
8D TYR* 3.9 6.1 - - - +
9D PHE 3.8 11.3 + - - -
11D MET 3.0 26.9 + - - -
12D ARG* 3.3 10.9 + - - +
15D ALA* 3.1 29.9 + - - +
16D GLU* 3.0 28.9 + - - +
18D ILE* 1.3 76.5 - - - +
20D TYR* 1.3 62.0 + - - +
22D PHE* 3.5 2.4 + - - +
23D ALA* 3.2 22.9 + - - +
29D TYR* 3.4 23.2 + - - +
31D ASP* 2.8 27.0 + - - -
32D HIS 5.3 0.4 + - - -
33D ARG* 3.2 23.3 - - - +
190D TRP* 3.5 35.9 - - + +
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Residues in contact with TYR 20 (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 GLU* 2.8 54.4 + - + +
17D ILE 3.6 9.0 - - - +
19D ARG* 1.3 73.7 - - - +
21D ILE* 1.3 57.3 + - - +
23D ALA* 3.4 6.8 + - - +
24D TYR* 3.0 29.5 + - - +
151D PHE* 3.7 31.9 - + + -
154D GLU* 2.5 36.0 + - - -
155D ILE* 3.6 19.4 - - + +
158D THR* 6.1 0.2 - - - -
181D VAL* 4.6 3.4 - - + -
187D VAL* 3.7 32.3 - - + +
190D TRP* 3.9 13.5 - + - -
191D ILE* 4.0 8.1 - - + +
194D ARG* 3.4 17.1 + - - -
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Residues in contact with ILE 21 (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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17D ILE* 3.1 20.0 + - + +
18D ILE* 3.1 8.5 + - - +
20D TYR* 1.3 73.2 - - - +
22D PHE* 1.3 67.4 + - + +
24D TYR* 3.4 1.0 + - - +
25D LEU* 2.9 48.1 + - + +
68D ALA* 3.4 46.7 - - + +
71D LEU* 3.7 20.6 - - + -
72D THR* 3.6 19.5 - - + -
77D LEU* 4.3 8.5 - - + -
148D TRP* 4.5 8.5 - - + -
151D PHE* 4.5 7.9 - - + -
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Residues in contact with PHE 22 (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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4D TYR* 3.7 32.3 - + + -
6D LEU* 4.7 0.7 - - + -
18D ILE* 3.0 42.4 + - + +
19D ARG 3.9 1.8 - - - +
21D ILE* 1.3 74.9 - - + +
23D ALA* 1.3 57.9 + - - +
25D LEU* 3.6 1.5 - - + -
26D ASP* 2.8 24.3 + - - -
27D ILE* 2.9 39.9 + - + +
29D TYR* 3.5 51.1 - + + -
54D LEU* 3.7 27.8 - - + -
71D LEU* 3.7 27.1 - - + -
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Residues in contact with ALA 23 (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 ARG 3.2 11.7 + - - +
20D TYR* 3.5 9.9 - - - +
21D ILE 3.2 0.2 - - - -
22D PHE* 1.3 77.0 - - - +
24D TYR* 1.3 64.6 + - - +
26D ASP* 3.0 15.7 + - - +
29D TYR* 5.3 1.2 - - - -
186D ALA* 3.4 31.6 - - - +
187D VAL* 5.1 1.6 - - - +
190D TRP* 4.0 20.9 - - + -
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Residues in contact with TYR 24 (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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20D TYR 3.0 16.9 + - - +
21D ILE 3.9 2.7 - - - +
23D ALA* 1.3 76.5 - - - +
25D LEU* 1.3 69.8 + - + +
26D ASP* 3.2 2.8 + - - +
76D ASP* 3.0 39.6 + - - -
77D LEU* 3.7 26.7 - - + -
146D VAL* 4.2 17.3 - - + +
151D PHE* 3.7 27.1 - + + -
184D ILE* 4.0 27.4 - - + -
186D ALA* 3.7 14.9 - - + +
187D VAL* 4.7 2.9 - - + +
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Residues in contact with LEU 25 (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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21D ILE* 2.9 35.2 + - + +
22D PHE* 4.2 1.1 - - + +
24D TYR* 1.3 91.9 - - + +
26D ASP* 1.3 71.7 + - - +
27D ILE* 3.5 30.8 + - + +
71D LEU* 3.3 28.0 - - + +
72D THR* 5.0 0.4 - - - -
75D THR* 3.8 30.7 - - + +
76D ASP* 5.0 0.7 - - - +
77D LEU* 4.7 2.7 - - + -
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Residues in contact with ASP 26 (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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22D PHE 2.8 7.0 + - - -
23D ALA* 3.0 12.6 + - - +
24D TYR 4.6 2.5 - - - +
25D LEU* 1.3 81.3 - - - +
27D ILE* 1.3 61.6 + - - +
28D GLN* 4.1 16.3 + - - +
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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