Contacts of the helix formed by residues 43 - 56 (chain A) in PDB entry 2HZD
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 ARG 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 5.2 14.3 + - - +
25A PRO 4.2 17.8 + - - -
26A PRO* 5.7 4.0 + - - +
29A ARG 5.1 8.8 + - - -
30A ARG* 3.4 27.4 - - - +
32A ILE* 6.3 2.9 - - + -
41A TYR 3.4 3.7 + - - +
42A GLY* 1.3 70.4 - - - -
44A ASN* 1.3 50.3 + - - +
45A GLU 3.0 0.2 - - - -
46A LEU* 2.7 45.2 + - + +
47A ILE* 2.7 28.5 - - + +
68A ILE* 5.9 7.6 - - - +
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Residues in contact with ASN 44 (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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42A GLY* 3.0 3.9 - - - +
43A ARG* 1.3 78.1 - - - +
45A GLU* 1.3 61.7 + - + +
47A ILE* 3.3 16.3 - - - +
48A ALA* 3.2 23.6 + - - +
61A ARG* 3.0 46.6 + - + +
62A LYS* 4.3 3.4 - - - +
65A SER* 3.4 27.3 + - - -
68A ILE* 5.0 1.7 - - - +
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Residues in contact with GLU 45 (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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41A TYR* 3.1 46.6 - - - +
42A GLY* 2.9 14.7 + - - +
44A ASN* 1.3 78.5 - - + +
46A LEU* 1.3 59.0 + - - +
48A ALA* 3.9 5.9 - - - +
49A ARG* 3.0 54.4 + - + +
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Residues in contact with LEU 46 (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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24A TYR* 3.1 46.9 + - + +
42A GLY 4.1 0.6 + - - +
43A ARG* 2.7 40.5 + - + +
45A GLU* 1.3 71.5 - - - +
47A ILE* 1.3 64.6 + - + +
49A ARG* 3.6 23.0 + - + +
50A TYR* 3.5 14.2 + - - +
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Residues in contact with ILE 47 (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 ALA* 3.5 21.4 - - + +
21A LEU* 4.7 0.7 - - + -
24A TYR* 3.5 32.3 - - + -
43A ARG* 2.7 40.8 - - + +
44A ASN* 3.3 25.1 - - - +
46A LEU* 1.3 76.0 - - + +
48A ALA* 1.3 60.6 + - - +
50A TYR* 3.4 9.2 + - - +
51A ILE* 2.9 22.7 + - - +
64A VAL* 3.2 34.5 - - + -
68A ILE* 4.5 16.8 - - + -
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Residues in contact with ALA 48 (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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44A ASN 3.2 17.0 + - - +
45A GLU* 4.1 6.1 - - - +
47A ILE* 1.3 75.0 - - - +
49A ARG* 1.3 61.1 + - - +
50A TYR 3.2 0.7 - - - -
51A ILE* 3.3 13.0 - - + +
52A LYS* 3.0 28.8 + - - +
59A ARG* 3.7 27.0 - - + +
60A THR 4.4 5.8 + - - +
61A ARG* 4.8 7.0 - - + -
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Residues in contact with ARG 49 (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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41A TYR* 5.4 8.1 + - - +
42A GLY 5.3 1.4 + - - -
45A GLU* 3.0 49.3 + - + +
46A LEU* 3.8 25.4 - - + +
47A ILE 3.3 0.2 - - - -
48A ALA* 1.3 75.9 - - - +
50A TYR* 1.3 62.3 + - - +
52A LYS* 3.6 8.1 - - + +
53A LEU* 3.1 32.7 + - + +
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Residues in contact with TYR 50 (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 SER 4.5 3.1 - - - -
19A GLU* 2.5 51.1 + - + -
20A ALA* 4.1 14.6 - - + -
23A ILE* 4.0 24.6 - - + +
24A TYR* 4.1 22.0 - + + -
46A LEU 3.5 8.7 + - - +
47A ILE 3.4 10.7 + - - +
48A ALA 3.2 0.6 - - - -
49A ARG* 1.3 76.6 - - - +
51A ILE* 1.3 61.8 + - - +
52A LYS 3.0 1.1 - - - -
53A LEU* 2.9 21.8 + - + +
54A ARG* 3.0 43.7 + - - -
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Residues in contact with ILE 51 (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 ILE* 4.6 3.6 - - + +
16A SER* 3.1 44.6 - - - +
17A PHE* 4.1 13.9 - - + +
20A ALA* 5.1 0.9 - - + -
47A ILE 2.9 17.7 - - - +
48A ALA* 3.3 15.7 - - - +
50A TYR* 1.3 75.6 - - - +
52A LYS* 1.3 58.7 + - - +
54A ARG* 3.3 19.3 + - - +
55A THR 4.1 2.9 + - - -
57A LYS* 4.3 6.2 + - - +
58A THR* 3.9 16.3 - - + +
59A ARG* 3.3 26.2 - - - -
60A THR 3.4 22.0 - - - +
64A VAL* 3.9 10.3 - - + -
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Residues in contact with LYS 52 (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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48A ALA 3.0 18.9 + - - +
49A ARG* 3.6 9.6 - - - +
51A ILE* 1.3 77.5 - - - +
53A LEU* 1.3 57.7 + - + +
56A GLY* 3.2 27.0 + - - +
57A LYS 4.4 9.0 - - - +
58A THR 4.5 0.2 + - - -
59A ARG* 3.4 48.2 - - + +
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Residues in contact with LEU 53 (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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49A ARG* 3.1 21.9 + - + +
50A TYR* 2.9 12.2 + - - +
52A LYS* 1.3 77.7 - - - +
54A ARG* 1.3 70.8 + - - +
55A THR* 3.4 1.1 + - - -
56A GLY 4.6 0.2 - - - -
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Residues in contact with ARG 54 (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 ASP* 4.9 6.7 - - - +
15A GLN 5.1 0.7 - - - -
16A SER* 2.8 45.3 - - - +
19A GLU* 4.0 14.7 + - - +
50A TYR* 3.0 51.1 + - - -
51A ILE 3.3 15.3 - - - +
52A LYS 3.3 0.6 - - - -
53A LEU* 1.3 84.8 - - - +
55A THR* 1.3 71.4 + - + +
57A LYS* 6.0 0.7 - - + -
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Residues in contact with THR 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 ASP* 4.9 15.9 - - + +
16A SER* 5.6 0.7 - - - +
51A ILE 4.1 0.8 + - - -
53A LEU 3.4 1.1 - - - -
54A ARG* 1.3 88.7 - - + +
56A GLY* 1.3 65.5 + - - +
57A LYS* 3.0 42.4 + - + +
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Residues in contact with GLY 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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52A LYS* 3.2 26.8 + - - +
53A LEU 4.6 0.6 - - - -
55A THR* 1.3 75.3 - - - +
57A LYS* 1.3 71.7 + - - +
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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