Contacts of the helix formed by residues 13 - 24 (chain A) in PDB entry 2EZT
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 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ILE 3.5 2.2 + - - -
12A LEU* 1.3 71.1 - - - +
14A GLY* 1.3 55.7 + - - +
16A ALA* 3.2 3.1 + - - +
17A VAL* 2.8 33.7 + - - +
143A ALA* 3.7 27.4 - - + +
146A LEU* 4.6 7.0 - - + -
147A PRO* 4.4 0.9 - - - +
172A LEU 3.3 24.5 - - - +
173A PRO* 3.9 2.4 + - + -
175A GLN 2.9 13.3 + - - +
177A ILE* 3.9 15.7 - - + +
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Residues in contact with GLY 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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13A ALA* 1.3 72.3 - - - +
15A ALA* 1.3 64.8 + - - +
17A VAL* 3.3 7.9 + - - +
18A ILE* 3.1 28.8 + - - +
39A SER 4.8 0.2 - - - -
40A ILE* 4.4 4.0 - - - -
43A ALA* 3.3 15.0 - - - +
173A PRO* 3.1 34.3 + - - +
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Residues in contact with ALA 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 ILE* 3.6 21.5 - - + -
12A LEU* 2.9 23.4 + - + +
14A GLY* 1.3 75.3 - - - +
16A ALA* 1.3 63.0 + - - +
18A ILE* 3.2 6.1 + - - +
19A LYS* 3.0 27.3 + - + +
43A ALA* 3.8 11.0 - - + +
47A GLU* 5.6 3.9 - - + +
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Residues in contact with ALA 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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11A ILE* 4.0 10.2 - - + +
12A LEU 3.0 11.3 + - - +
13A ALA 3.5 7.9 - - - +
15A ALA* 1.3 74.7 - - - +
17A VAL* 1.3 57.1 + - - +
19A LYS* 3.2 8.2 + - - +
20A VAL* 2.9 32.5 + - - +
147A PRO* 3.6 20.4 - - + -
177A ILE* 4.1 7.0 - - + -
182A TRP* 3.9 27.7 - - + +
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Residues in contact with VAL 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 ALA 2.8 21.1 + - - +
14A GLY* 3.6 11.0 - - - +
15A ALA 3.3 0.2 - - - -
16A ALA* 1.3 71.7 - - - +
18A ILE* 1.3 67.5 + - + +
20A VAL* 3.2 11.8 + - - +
21A LEU* 3.2 24.7 + - + +
40A ILE* 4.2 17.9 - - + -
107A LEU* 5.0 7.6 - - + -
146A LEU* 3.6 34.5 - - + -
147A PRO* 4.2 8.7 - - + -
150A ILE* 4.0 29.3 - - + +
168A ILE* 5.6 0.7 - - + -
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Residues in contact with ILE 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 GLY 3.1 18.3 + - - +
15A ALA 3.8 4.0 - - - +
17A VAL* 1.3 83.3 - - + +
19A LYS* 1.3 58.3 + - - +
21A LEU* 3.1 18.7 + - + +
22A GLU* 2.9 36.6 + - - +
29A LEU* 6.0 0.2 - - + -
40A ILE* 4.5 11.9 - - + -
43A ALA* 3.5 23.1 - - + -
44A LEU* 3.7 26.7 - - + -
47A GLU* 3.8 16.2 - - + -
51A ILE* 3.6 33.0 - - + -
107A LEU* 6.1 0.7 - - + -
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Residues in contact with LYS 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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11A ILE* 4.8 7.0 - - + -
15A ALA* 3.0 19.7 + - + +
16A ALA* 3.4 5.2 - - - +
18A ILE* 1.3 76.5 - - - +
20A VAL* 1.3 55.6 + - - +
22A GLU* 3.1 23.4 + - - +
23A ALA* 2.8 29.8 + - - +
47A GLU* 3.1 35.3 + - - +
50A ARG* 3.8 15.4 - - - +
182A TRP* 3.4 34.7 - - + -
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Residues in contact with VAL 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 ALA 2.9 18.8 + - - +
17A VAL* 3.2 8.9 + - - +
19A LYS* 1.3 73.5 - - - +
21A LEU* 1.3 63.2 + - - +
23A ALA* 3.2 2.1 + - - +
24A TRP* 3.0 45.9 + - + -
147A PRO* 3.9 22.9 - - + +
150A ILE* 4.0 11.7 - - + -
151A ASP* 3.9 28.5 - - + +
154A ILE* 4.3 2.0 - - + -
182A TRP* 3.9 21.2 - - + -
183A TYR 4.2 7.6 - - - +
184A ALA* 4.3 8.7 - - + -
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Residues in contact with LEU 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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17A VAL* 3.2 19.1 + - + +
18A ILE* 3.1 28.5 + - + +
20A VAL* 1.3 75.2 - - - +
22A GLU* 1.3 61.9 + - - +
24A TRP* 3.2 8.0 + - - -
25A GLY 3.3 0.2 + - - -
26A VAL* 3.0 38.8 + - + +
29A LEU* 4.5 16.8 - - + -
51A ILE* 3.8 24.7 - - + -
78A VAL* 4.6 10.8 - - + -
105A LEU* 3.8 29.2 - - + -
107A LEU* 5.2 6.3 - - + -
150A ILE* 4.2 7.4 - - + -
154A ILE* 3.8 13.2 - - + -
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Residues in contact with GLU 22 (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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18A ILE* 2.9 20.2 + - - +
19A LYS* 3.1 36.8 + - - +
21A LEU* 1.3 73.6 - - - +
23A ALA* 1.3 60.0 + - - +
25A GLY* 2.9 20.7 + - - +
26A VAL 4.7 6.3 - - - +
47A GLU* 2.5 36.1 - - - +
50A ARG* 3.6 33.7 + - + +
51A ILE* 3.8 19.6 - - + +
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Residues in contact with ALA 23 (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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19A LYS 2.8 20.6 + - - +
20A VAL 3.6 4.5 - - - +
22A GLU* 1.3 72.3 - - - +
24A TRP* 1.3 60.8 + - - +
25A GLY* 3.3 1.4 + - - -
182A TRP* 5.9 2.2 - - + -
184A ALA* 3.6 23.8 - - + -
186A ALA* 3.2 18.0 - - + +
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Residues in contact with TRP 24 (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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20A VAL* 3.0 36.4 + - + +
21A LEU 3.8 4.5 - - - +
22A GLU 3.1 0.8 - - - -
23A ALA* 1.3 76.4 - - - +
25A GLY* 1.3 60.9 + - - +
26A VAL* 3.3 7.4 + - + +
75A LYS* 3.8 16.5 - - - +
76A ILE* 5.3 1.3 - - + +
151A ASP* 2.7 25.4 + - - +
154A ILE* 3.5 36.0 - - + +
155A ARG* 4.2 27.6 - - + -
158A TYR* 3.7 20.9 + + - -
184A ALA* 4.2 2.2 - - + -
185A SER* 3.5 17.3 - - - -
186A ALA* 3.4 37.5 - - + +
189A TYR* 3.6 42.8 - + + -
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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