Contacts of the helix formed by residues 38 - 52 (chain D) in PDB entry 1H47
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 ASP 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D ILE* 3.3 20.2 - - - +
20D ILE* 3.4 2.8 - - - -
21D GLY 2.9 19.8 + - - -
22D GLY* 2.8 30.5 + - - -
36D ASP* 3.2 12.3 + - - +
37D GLY* 1.3 71.2 - - - +
39D VAL* 1.3 57.9 + - - +
40D ALA 3.3 3.8 + - - -
41D LEU* 3.1 24.8 + - - +
42D HIS* 2.9 33.8 + - - -
73D SER* 3.5 20.6 + - - +
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Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASP* 3.5 15.1 - - + +
9D VAL* 3.9 4.3 - - - -
10D HIS* 3.2 45.5 - - + +
20D ILE* 3.8 17.4 - - + +
31D LEU* 5.0 0.9 - - + -
37D GLY 2.7 11.7 + - - +
38D ASP* 1.3 71.9 + - - +
40D ALA* 1.3 65.5 + - - +
43D ALA* 3.0 25.8 + - - +
98D ILE* 5.2 1.3 - - + -
146D ILE* 3.6 37.0 - - + +
147D ALA 4.5 0.7 - - - +
148D CYS* 3.6 17.1 - - + +
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Residues in contact with ALA 40 (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 ILE* 3.9 13.2 - - + -
21D GLY* 3.7 17.9 - - - +
38D ASP* 3.2 9.0 + - - +
39D VAL* 1.3 81.3 - - - +
41D LEU* 1.3 61.2 + - + +
43D ALA* 3.9 2.4 - - - +
44D LEU* 3.0 27.9 + - - +
96D VAL* 4.2 12.1 - - + +
98D ILE* 4.4 5.2 - - + -
112D MET* 5.5 1.1 - - - -
116D ILE* 6.2 1.3 - - + -
129D VAL* 6.0 0.4 - - + -
148D CYS* 3.5 22.9 - - - -
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Residues in contact with LEU 41 (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 GLY* 3.7 17.3 - - - -
22D GLY* 3.8 6.1 - - - +
38D ASP* 3.1 30.6 + - - +
40D ALA* 1.3 82.2 - - + +
42D HIS* 1.3 54.7 + - - +
44D LEU* 3.8 6.2 - - + +
45D THR* 2.6 39.2 + - - +
73D SER* 3.9 14.6 - - - +
74D ARG* 3.4 43.1 - - + +
77D LEU* 4.5 15.1 - - + +
115D PHE* 6.3 0.9 - - + -
116D ILE* 3.7 29.4 - - + -
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Residues in contact with HIS 42 (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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8D ASP* 3.1 19.0 + - - +
10D HIS* 3.5 4.4 + + - -
35D SER* 2.9 30.5 + - - -
38D ASP 2.9 30.2 + - - +
39D VAL 3.9 0.2 - - - +
41D LEU* 1.3 74.0 - - - +
43D ALA* 1.3 64.6 + - - +
45D THR* 3.3 6.4 + - - -
46D ASP* 3.0 27.7 + - - +
57D ILE* 4.0 21.4 - - + +
73D SER* 2.7 31.5 + - - -
76D LEU* 5.2 9.3 - - + +
1158D ZN 2.3 32.7 - - - -
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Residues in contact with ALA 43 (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 GLY* 3.5 21.1 - - - +
7D PHE 4.0 9.2 - - - +
8D ASP* 4.0 6.4 - - - +
39D VAL 3.0 18.5 + - - +
40D ALA 3.9 3.4 - - - +
42D HIS* 1.3 76.0 - - - +
44D LEU* 1.3 63.0 + - - +
46D ASP* 3.3 2.8 + - - -
47D ALA* 2.9 20.1 + - - +
148D CYS* 3.6 30.5 - - + +
150D ALA* 3.7 8.7 - - + -
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Residues in contact with LEU 44 (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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40D ALA 3.0 17.9 + - - +
41D LEU* 3.8 6.5 - - + +
43D ALA* 1.3 78.5 - - - +
45D THR* 1.3 61.8 + - - +
47D ALA* 3.2 3.6 + - + +
48D LEU* 3.0 33.6 + - + +
77D LEU* 4.2 17.3 - - + -
94D VAL* 3.8 35.0 - - + -
96D VAL* 4.3 14.1 - - + -
116D ILE* 3.8 43.1 - - + -
120D LEU* 4.6 1.1 - - + -
150D ALA* 3.7 14.1 - - + +
151D VAL 5.0 2.0 - - - +
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Residues in contact with THR 45 (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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41D LEU 2.6 23.8 + - - -
42D HIS* 3.6 6.2 - - - -
44D LEU* 1.3 75.6 - - - +
46D ASP* 1.3 57.2 + - - +
48D LEU* 3.3 4.5 + - - +
49D LEU* 2.9 32.9 + - + +
57D ILE* 3.4 25.4 - - + -
61D PHE* 5.1 1.1 - - + -
73D SER 4.9 1.2 + - - -
76D LEU* 4.4 9.4 - - + +
77D LEU* 3.5 28.9 + - + +
80D ALA* 3.8 26.0 - - + -
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Residues in contact with ASP 46 (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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5D HIS 3.9 1.1 - - - -
6D GLY* 3.9 8.7 - - - -
7D PHE 4.4 11.3 + - - +
42D HIS 3.0 16.1 + - - +
43D ALA* 3.7 7.6 - - - +
45D THR* 1.3 74.1 - - - +
47D ALA* 1.3 60.6 + - - +
49D LEU* 4.0 3.7 - - - +
50D GLY 2.9 22.9 + - - -
56D ASP* 3.4 4.6 - - - +
57D ILE* 2.8 44.9 + - - +
130E LYS* 3.5 37.9 - - + +
131E ALA 5.1 3.6 - - - +
132E THR* 5.2 4.2 - - - -
1157E C5P 5.2 0.7 + - - -
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Residues in contact with ALA 47 (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 GLY* 3.3 14.2 - - - +
5D HIS 3.6 15.9 + - - +
6D GLY 3.6 16.2 - - - +
43D ALA 2.9 11.2 + - - +
44D LEU* 3.2 8.7 + - + +
46D ASP* 1.3 75.9 - - - +
48D LEU* 1.3 58.2 + - - +
51D ALA* 3.1 24.4 + - - +
150D ALA* 3.6 20.2 - - + +
151D VAL 4.2 1.1 - - - -
152D ALA* 4.0 12.1 - - + +
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Residues in contact with LEU 48 (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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44D LEU* 3.0 33.8 + - + +
45D THR* 3.8 4.0 - - - +
47D ALA* 1.3 75.2 - - - +
49D LEU* 1.3 65.0 + - - +
50D GLY 3.3 0.2 + - - -
51D ALA* 3.4 5.7 + - - +
52D ALA* 3.2 22.0 + - - +
77D LEU* 3.8 26.7 - - + -
80D ALA* 6.2 1.6 - - + -
81D TRP* 4.1 9.6 - - + +
84D ILE* 3.6 17.7 - - + +
91D LEU* 3.7 30.1 - - + -
94D VAL* 3.9 3.4 - - + -
120D LEU* 4.0 14.4 - - + -
152D ALA* 3.9 14.1 - - + -
154D LEU* 3.8 17.3 - - + +
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Residues in contact with LEU 49 (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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45D THR* 2.9 30.5 + - + +
46D ASP 4.0 2.9 - - - +
48D LEU* 1.3 76.9 - - - +
50D GLY* 1.3 59.2 + - - +
52D ALA* 3.2 3.3 + - - +
53D ALA 3.2 3.8 + - - -
54D LEU* 2.9 47.5 + - + -
55D GLY 4.2 13.2 - - - +
56D ASP* 3.4 32.8 - - - +
57D ILE* 3.5 9.9 - - - +
60D LEU* 3.8 28.7 - - + -
61D PHE* 5.2 0.4 - - + -
80D ALA* 3.8 19.5 - - + +
84D ILE* 4.0 11.7 - - + -
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Residues in contact with GLY 50 (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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2D ARG* 4.9 0.5 + - - -
3D ILE 4.2 1.4 - - - +
46D ASP 2.9 14.8 + - - -
47D ALA 3.8 0.2 - - - -
48D LEU 3.2 0.2 - - - -
49D LEU* 1.3 73.1 - - - +
51D ALA* 1.3 65.7 + - - +
53D ALA* 3.1 10.4 + - - +
55D GLY 4.3 0.6 + - - -
93E ASN* 4.6 3.1 + - - -
95E ASP* 3.4 26.7 - - - +
128E ASN* 3.4 31.0 - - - +
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Residues in contact with ALA 51 (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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2D ARG* 3.1 41.5 + - - +
3D ILE 3.2 30.5 - - - -
4D GLY* 3.6 2.1 - - - +
47D ALA 3.1 16.4 + - - +
48D LEU* 3.4 2.0 + - - +
50D GLY* 1.3 75.3 - - - +
52D ALA* 1.3 57.1 + - - +
53D ALA 3.3 0.4 - - - -
89D TYR* 4.4 0.2 + - - -
152D ALA* 4.6 4.0 - - + +
154D LEU* 3.6 28.8 - - + +
93E ASN* 4.2 0.7 + - - -
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Residues in contact with ALA 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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2D ARG* 4.0 2.7 - - - -
48D LEU 3.2 14.6 + - - +
49D LEU 3.2 5.7 + - - +
50D GLY 3.1 1.0 - - - -
51D ALA* 1.3 78.2 - - - +
53D ALA* 1.3 54.8 + - - +
54D LEU* 3.2 9.9 + - + +
84D ILE* 4.0 18.8 - - + -
87D LYS* 2.6 34.5 + - - -
89D TYR* 3.8 24.8 + - + -
154D LEU* 3.9 8.5 - - + -
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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
------------------------------------------------------------
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